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Sample records for region acquires methylation

  1. Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy

    PubMed Central

    Dębski, Konrad J.; Pitkanen, Asla; Puhakka, Noora; Bot, Anna M.; Khurana, Ishant; Harikrishnan, KN; Ziemann, Mark; Kaspi, Antony; El-Osta, Assam; Lukasiuk, Katarzyna; Kobow, Katja

    2016-01-01

    This study tested the hypothesis that acquired epileptogenesis is accompanied by DNA methylation changes independent of etiology. We investigated DNA methylation and gene expression in the hippocampal CA3/dentate gyrus fields at 3 months following epileptogenic injury in three experimental models of epilepsy: focal amygdala stimulation, systemic pilocarpine injection, or lateral fluid-percussion induced traumatic brain injury (TBI) in rats. In the models studies, DNA methylation and gene expression profiles distinguished controls from injured animals. We observed consistent increased methylation in gene bodies and hypomethylation at non-genic regions. We did not find a common methylation signature in all three different models and few regions common to any two models. Our data provide evidence that genome-wide alteration of DNA methylation signatures is a general pathomechanism associated with epileptogenesis and epilepsy in experimental animal models, but the broad pathophysiological differences between models (i.e. pilocarpine, amygdala stimulation, and post-TBI) are reflected in distinct etiology-dependent DNA methylation patterns. PMID:27157830

  2. DNA Methylation within Transcribed Regions

    PubMed Central

    To, Taiko K.; Saze, Hidetoshi; Kakutani, Tetsuji

    2015-01-01

    DNA methylation within transcribed genes is commonly found in diverse animals and plants. Here, we provide an overview of recent advances and the remaining mystery regarding intragenic DNA methylation. PMID:26143255

  3. Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia

    PubMed Central

    Wan, Zi Yi; Xia, Jun Hong; Lin, Grace; Wang, Le; Lin, Valerie C. L.; Yue, Gen Hua

    2016-01-01

    Sexual dimorphism is an interesting biological phenomenon. Previous studies showed that DNA methylation might play a role in sexual dimorphism. However, the overall picture of the genome-wide methylation landscape in sexually dimorphic species remains unclear. We analyzed the DNA methylation landscape and transcriptome in hybrid tilapia (Oreochromis spp.) using whole genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq). We found 4,757 sexually dimorphic differentially methylated regions (DMRs), with significant clusters of DMRs located on chromosomal regions associated with sex determination. CpG methylation in promoter regions was negatively correlated with the gene expression level. MAPK/ERK pathway was upregulated in male tilapia. We also inferred active cis-regulatory regions (ACRs) in skeletal muscle tissues from WGBS datasets, revealing sexually dimorphic cis-regulatory regions. These results suggest that DNA methylation contribute to sex-specific phenotypes and serve as resources for further investigation to analyze the functions of these regions and their contributions towards sexual dimorphisms. PMID:27782217

  4. DHPLC-based method for DNA methylation analysis of differential methylated regions from imprinted genes.

    PubMed

    Couvert, P; Poirier, K; Carrié, A; Chalas, C; Jouannet, P; Beldjord, C; Bienvenu, T; Chelly, J; Kerjean, A

    2003-02-01

    The bisulfite genomic sequencing method is one of the most widely used techniques for methylation analysis in heterogeneous unbiased PCR, amplifying for both methylated and unmethylated alleles simultaneously. However, it requires labor-intensive and time-consuming cloning and sequencing steps. In the current study, we used a denaturing high-performance liquid chromatography (DHPLC) procedure in a complementary way with the bisulfite genomic sequencing to analyze the methylation of differentially methylated regions (DMRs) of imprinted genes. We showed reliable and reproducible results in distinguishing overall methylation profiles of DMRs regions of human SNRPN, H19, MEST/PEG1, LIT1, IGF2, TSSC5, WT1 antisense, and mouse H19, Mest/Peg1, Igf2R imprinted genes. These DHPLC profiles were in accordance with bisulfite genomic sequencing data and may serve as a type of "fingerprint," revealing the overall methylation status of DMRs associated with sample heterogeneity. We conclude that DHPLC analysis could be used to increase the throughput efficiency of methylation pattern analysis of imprinted genes after the bisulfite conversion of genomic DNA and unbiased PCR amplification.

  5. An optimized algorithm for detecting and annotating regional differential methylation

    PubMed Central

    2013-01-01

    Background DNA methylation profiling reveals important differentially methylated regions (DMRs) of the genome that are altered during development or that are perturbed by disease. To date, few programs exist for regional analysis of enriched or whole-genome bisulfate conversion sequencing data, even though such data are increasingly common. Here, we describe an open-source, optimized method for determining empirically based DMRs (eDMR) from high-throughput sequence data that is applicable to enriched whole-genome methylation profiling datasets, as well as other globally enriched epigenetic modification data. Results Here we show that our bimodal distribution model and weighted cost function for optimized regional methylation analysis provides accurate boundaries of regions harboring significant epigenetic modifications. Our algorithm takes the spatial distribution of CpGs into account for the enrichment assay, allowing for optimization of the definition of empirical regions for differential methylation. Combined with the dependent adjustment for regional p-value combination and DMR annotation, we provide a method that may be applied to a variety of datasets for rapid DMR analysis. Our method classifies both the directionality of DMRs and their genome-wide distribution, and we have observed that shows clinical relevance through correct stratification of two Acute Myeloid Leukemia (AML) tumor sub-types. Conclusions Our weighted optimization algorithm eDMR for calling DMRs extends an established DMR R pipeline (methylKit) and provides a needed resource in epigenomics. Our method enables an accurate and scalable way of finding DMRs in high-throughput methylation sequencing experiments. eDMR is available for download at http://code.google.com/p/edmr/. PMID:23735126

  6. An optimized algorithm for detecting and annotating regional differential methylation.

    PubMed

    Li, Sheng; Garrett-Bakelman, Francine E; Akalin, Altuna; Zumbo, Paul; Levine, Ross; To, Bik L; Lewis, Ian D; Brown, Anna L; D'Andrea, Richard J; Melnick, Ari; Mason, Christopher E

    2013-01-01

    DNA methylation profiling reveals important differentially methylated regions (DMRs) of the genome that are altered during development or that are perturbed by disease. To date, few programs exist for regional analysis of enriched or whole-genome bisulfate conversion sequencing data, even though such data are increasingly common. Here, we describe an open-source, optimized method for determining empirically based DMRs (eDMR) from high-throughput sequence data that is applicable to enriched whole-genome methylation profiling datasets, as well as other globally enriched epigenetic modification data. Here we show that our bimodal distribution model and weighted cost function for optimized regional methylation analysis provides accurate boundaries of regions harboring significant epigenetic modifications. Our algorithm takes the spatial distribution of CpGs into account for the enrichment assay, allowing for optimization of the definition of empirical regions for differential methylation. Combined with the dependent adjustment for regional p-value combination and DMR annotation, we provide a method that may be applied to a variety of datasets for rapid DMR analysis. Our method classifies both the directionality of DMRs and their genome-wide distribution, and we have observed that shows clinical relevance through correct stratification of two Acute Myeloid Leukemia (AML) tumor sub-types. Our weighted optimization algorithm eDMR for calling DMRs extends an established DMR R pipeline (methylKit) and provides a needed resource in epigenomics. Our method enables an accurate and scalable way of finding DMRs in high-throughput methylation sequencing experiments. eDMR is available for download at http://code.google.com/p/edmr/.

  7. Diclofop-methyl affects microbial rhizosphere community and induces systemic acquired resistance in rice.

    PubMed

    Chen, Si; Li, Xingxing; Lavoie, Michel; Jin, Yujian; Xu, Jiahui; Fu, Zhengwei; Qian, Haifeng

    2017-01-01

    Diclofop-methyl (DM), a widely used herbicide in food crops, may partly contaminate the soil surface of natural ecosystems in agricultural area and exert toxic effects at low dose to nontarget plants. Even though rhizosphere microorganisms strongly interact with root cells, little is known regarding their potential modulating effect on herbicide toxicity in plants. Here we exposed rice seedlings (Xiushui 63) to 100μg/L DM for 2 to 8days and studied the effects of DM on rice rhizosphere microorganisms, rice systemic acquired resistance (SAR) and rice-microorganisms interactions. The results of metagenomic 16S rDNA Illumina tags show that DM increases bacterial biomass and affects their community structure in the rice rhizosphere. After DM treatment, the relative abundance of the bacterium genera Massilia and Anderseniella increased the most relative to the control. In parallel, malate and oxalate exudation by rice roots increased, potentially acting as a carbon source for several rhizosphere bacteria. Transcriptomic analyses suggest that DM induced SAR in rice seedlings through the salicylic acid (but not the jasmonic acid) signal pathway. This response to DM stress conferred resistance to infection by a pathogenic bacterium, but was not influenced by the presence of bacteria in the rhizosphere since SAR transcripts did not change significantly in xenic and axenic plant roots exposed to DM. The present study provides new insights on the response of rice and its associated microorganisms to DM stress.

  8. Acquired Encephalocele With Hydrocephalus and Pineal Region Epidermoid Cyst.

    PubMed

    Toktaş, Zafer Orkun; Yilmaz, Baran; Ekşi, Murat Şakir; Bayoumi, Ahmed B; Akakin, Akin; Yener, Yasin; Demir, Mustafa Kemal; Kiliç, Türker

    2016-07-01

    A combination of trauma and a missed inflammatory response (nasal operation) concomitant with hydrocephalus and tumor in secondary encephalocele has not been described in the English literature yet. A 38-year-old man was admitted to the clinic with rhinorrhea that started 3 months ago. In his medical history, nothing abnormal was present except a nasal operation performed 1 year ago. Brain magnetic resonance imaging depicted left frontal encephalocele concomitant with obstructive hydrocephalus caused by an epidermoid cyst originated from the pineal region. A 2-staged surgery was planned. In the first stage, a ventriculoperitoneal shunt insertion was conveyed successfully. In the second-stage surgery, the herniated brain tissue was excised, and the frontal sinus was cleansed with serum saline combined with antibiotic. The bony defect and the dura defect were repaired. The patient's presenting complaint recovered fully, and he was discharged to home in a well condition. Acquired encephalocele is a rare entity. In case of rhinorrhea and encephalocele, even in the presence of prior history of nasal surgery, intracranial evaluation should be conveyed to exclude the presence of hydrocephalus and/or tumor. The cranial defect should be repaired to prevent future infections and brain tissue damage.

  9. DNA Methylation in Promoter Region as Biomarkers in Prostate Cancer

    PubMed Central

    Yang, Mihi; Park, Jong Y.

    2013-01-01

    The prostate gland is the most common site of cancer and the second leading cause of cancer death in American men. Recent emerging molecular biological technologies help us to know that epigenetic alterations such as DNA methylation within the regulatory (promoter) regions of genes are associated with transcriptional silencing in cancer. Promoter hypermethylation of critical pathway genes could be potential biomarkers and therapeutic targets for prostate cancer. In this chapter, we updated current information on methylated genes associated with the development and progression of prostate cancer. Over 40 genes have been investigated for methylation in promoter region in prostate cancer. These methylated genes are involved in critical pathways, such as DNA repair, metabolism, and invasion/metastasis. The role of hypermethylated genes in regulation of critical pathways in prostate cancer is discussed. These findings may provide new information of the pathogenesis, the exciting potential to be predictive and to provide personalized treatment of prostate cancer. Indeed, some epigenetic alterations in prostate tumors are being translated into clinical practice for therapeutic use. PMID:22359288

  10. mRNA and methylation profiling of radioresistant esophageal cancer cells: the involvement of Sall2 in acquired aggressive phenotypes

    PubMed Central

    Luo, Judong; Wang, Wenjie; Tang, Yiting; Zhou, Dandan; Gao, Yi; Zhang, Qi; Zhou, Xifa; Zhu, Hui; Xing, Ligang; Yu, Jinming

    2017-01-01

    Esophageal squamous cell carcinoma (ESCC) is one of the deadliest malignancies worldwide. Radiotherapy plays a critical role in the curative management of inoperable ESCC patients. However, radioresistance restricts the efficacy of radiotherapy for ESCC patients. The molecules involved in radioresistance remain largely unknown, and new approaches to sensitize cells to irradiation are in demand. Technical advances in analysis of mRNA and methylation have enabled the exploration of the etiology of diseases and have the potential to broaden our understanding of the molecular pathways of ESCC radioresistance. In this study, we constructed radioresistant TE-1 and Eca-109 cell lines (TE-1/R and Eca-109/R, respectively). The radioresistant cells showed an increased migration ability but reduced apoptosis and cisplatin sensitivity compared with their parent cells. mRNA and methylation profiling by microarray revealed 1192 preferentially expressed mRNAs and 8841 aberrantly methylated regions between TE-1/R and TE-1 cells. By integrating the mRNA and methylation profiles, we related the decreased expression of transcription factor Sall2 with a corresponding increase in its methylation in TE-1/R cells, indicating its involvement in radioresistance. Upregulation of Sall2 decreased the growth and migration advantage of radioresistant ESCC cells. Taken together, our present findings illustrate the mRNA and DNA methylation changes during the radioresistance of ESCC and the important role of Sall2 in esophageal cancer malignancy. PMID:28367244

  11. Preferential binding of the methyl-CpG binding domain protein 2 at methylated transcriptional start site regions.

    PubMed

    Chatagnon, Amandine; Perriaud, Laury; Nazaret, Nicolas; Croze, Séverine; Benhattar, Jean; Lachuer, Joël; Dante, Robert

    2011-11-01

    Methyl-CpG Binding Domain (MBD) proteins are thought to be key molecules in the interpretation of DNA methylation signals leading to gene silencing through recruitment of chromatin remodeling complexes. In cancer, the MBD-family member, MBD2, may be primarily involved in the repression of genes exhibiting methylated CpG at their 5' end. Here we ask whether MBD2 randomly associates methylated sequences, producing chance effects on transcription, or exhibits a more specific recognition of some methylated regions. Using chromatin and DNA immunoprecipitation, we analyzed MBD2 and RNA polymerase II deposition and DNA methylation in HeLa cells on arrays representing 25,500 promoter regions. This first whole-genome mapping revealed the preferential localization of MBD2 near transcription start sites (TSSs), within the region analyzed, 7.5 kb upstream through 2.45 kb downstream of 5' transcription start sites. Probe by probe analysis correlated MBD2 deposition and DNA methylation. Motif analysis did not reveal specific sequence motifs; however, CCG and CGC sequences seem to be overrepresented. Nonrandom association (multiple correspondence analysis, p < 0.0001) between silent genes, DNA methylation and MBD2 binding was observed. The association between MBD2 binding and transcriptional repression weakened as the distance between binding site and TSS increased, suggesting that MBD2 represses transcriptional initiation. This hypothesis may represent a functional explanation for the preferential binding of MBD2 at methyl-CpG in TSS regions.

  12. Methylation of coding region alone inhibits gene expression in plant protoplasts.

    PubMed Central

    Hohn, T; Corsten, S; Rieke, S; Müller, M; Rothnie, H

    1996-01-01

    Derivatives of the cauliflower mosaic virus 35S promoter lacking CG and CNG methylation targets were constructed and used to direct transcription of reporter gene constructs in transiently transformed protoplasts. Such methylation-target-free (MTF) promoters, although weaker than the 35S promoter, retain significant activity despite mutation of the as-1 element. The effect of methylation on gene expression in MTF- and 35S-promoter driven constructs was examined. Even when the promoter region was free of methylation targets, reporter gene expression was markedly reduced when cytosine residues in CG dinucleotides were methylated in vitro prior to transformation. Mosaic methylation experiments, in which only specific parts of the plasmids were methylated, revealed that methylation of the coding region alone has a negative effect on reporter gene expression. Methylation nearer the 5' end of the coding region was more inhibitory, consistent with inhibition of transcription elongation. Images Fig. 5 PMID:8710871

  13. Method to acquire regions of fruit, branch and leaf from image of red apple in orchard

    NASA Astrophysics Data System (ADS)

    Lv, Jidong; Xu, Liming

    2017-07-01

    This work proposed a method to acquire regions of fruit, branch and leaf from red apple image in orchard. To acquire fruit image, R-G image was extracted from the RGB image for corrosive working, hole filling, subregion removal, expansive working and opening operation in order. Finally, fruit image was acquired by threshold segmentation. To acquire leaf image, fruit image was subtracted from RGB image before extracting 2G-R-B image. Then, leaf image was acquired by subregion removal and threshold segmentation. To acquire branch image, dynamic threshold segmentation was conducted in the R-G image. Then, the segmented image was added to fruit image to acquire adding fruit image which was subtracted from RGB image with leaf image. Finally, branch image was acquired by opening operation, subregion removal and threshold segmentation after extracting the R-G image from the subtracting image. Compared with previous methods, more complete image of fruit, leaf and branch can be acquired from red apple image with this method.

  14. Methylation Status of H19/IGF2 Differentially Methylated Region in in vitro Human Blastocysts Donated by Healthy Couples

    PubMed Central

    Derakhshan-Horeh, Marzieh; Abolhassani, Farid; Jafarpour, Farnoosh; Moini, Ashraf; Karbalaie, Khadijeh; Hosseini, Sayyed Morteza; Ostadhosseini, Somayyeh; Nasr-Esfahani, Mohammad Hossein

    2017-01-01

    Background: Imprinted genes are a unique subset of few genes that have been differentially methylated region (DMR) in a parental origin-dependent manner during gametogenesis, and these genes are highly protected during pre-implantation epigenetic reprogramming. Several studies have shown that the particular vulnerability of imprinting genes during suboptimal pre- and peri-conception micro-environments often is occurred by assisted reproduction techniques (ART). This study investigated the methylation status of H19/IGF2 DMR at high-quality expanding/expanded human blastocysts donated by healthy individuals to evaluate the risks linked to ART. Method: Methylation levels of H19/IGF2 DMR were analyzed by bisulfite conversion and sequencing at 18 CpG sites (CpGs) located in this region. Result: The overall percentage of methylated CpGs and the proportion of hyper-methylated clones of H19/IGF2 DMR in analyzed blastocysts were 37.85±4.87% and 43.75±5.1%, respectively. For validation of our technique, the corresponding methylation levels of peripheral human lymphocytes were defined (49.52±1.86% and 50%, respectively). Conclusion: Considering the absence of in vivo- produced human embryos, it is not possible to conclude that the methylation found in H19/IGF2 DMR is actually normal or abnormal. Regarding the possible risks associated with ART, the procedures should be optimized in order to at least reduce some of the epigenetic risks. PMID:27432596

  15. Bivalent Regions of Cytosine Methylation and H3K27 Acetylation Suggest an Active Role for DNA Methylation at Enhancers.

    PubMed

    Charlet, Jessica; Duymich, Christopher E; Lay, Fides D; Mundbjerg, Kamilla; Dalsgaard Sørensen, Karina; Liang, Gangning; Jones, Peter A

    2016-05-05

    The role of cytosine methylation in the structure and function of enhancers is not well understood. In this study, we investigate the role of DNA methylation at enhancers by comparing the epigenomes of the HCT116 cell line and its highly demethylated derivative, DKO1. Unlike promoters, a portion of regular and super- or stretch enhancers show active H3K27ac marks co-existing with extensive DNA methylation, demonstrating the unexpected presence of bivalent chromatin in both cultured and uncultured cells. Furthermore, our findings also show that bivalent regions have fewer nucleosome-depleted regions and transcription factor-binding sites than monovalent regions. Reduction of DNA methylation genetically or pharmacologically leads to a decrease of the H3K27ac mark. Thus, DNA methylation plays an unexpected dual role at enhancer regions, being anti-correlated focally at transcription factor-binding sites but positively correlated globally with the active H3K27ac mark to ensure structural enhancer integrity. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. QDMR: a quantitative method for identification of differentially methylated regions by entropy

    PubMed Central

    Zhang, Yan; Liu, Hongbo; Lv, Jie; Xiao, Xue; Zhu, Jiang; Liu, Xiaojuan; Su, Jianzhong; Li, Xia; Wu, Qiong; Wang, Fang; Cui, Ying

    2011-01-01

    DNA methylation plays critical roles in transcriptional regulation and chromatin remodeling. Differentially methylated regions (DMRs) have important implications for development, aging and diseases. Therefore, genome-wide mapping of DMRs across various temporal and spatial methylomes is important in revealing the impact of epigenetic modifications on heritable phenotypic variation. We present a quantitative approach, quantitative differentially methylated regions (QDMRs), to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy. QDMR was applied to synthetic methylation patterns and methylation profiles detected by methylated DNA immunoprecipitation microarray (MeDIP-chip) in human tissues/cells. This approach can give a reasonable quantitative measure of methylation difference across multiple samples. Then DMR threshold was determined from methylation probability model. Using this threshold, QDMR identified 10 651 tissue DMRs which are related to the genes enriched for cell differentiation, including 4740 DMRs not identified by the method developed by Rakyan et al. QDMR can also measure the sample specificity of each DMR. Finally, the application to methylation profiles detected by reduced representation bisulphite sequencing (RRBS) in mouse showed the platform-free and species-free nature of QDMR. This approach provides an effective tool for the high-throughput identification of potential functional regions involved in epigenetic regulation. PMID:21306990

  17. Methylation Analysis of the BMPR2 Gene Promoter Region in Patients With Pulmonary Arterial Hypertension.

    PubMed

    Pousada, Guillermo; Baloira, Adolfo; Valverde, Diana

    2016-06-01

    Pulmonary arterial hypertension is characterizated by obstruction of the pulmonary arteries. The gene mainly related to pathology is the bone morphogenetic protein receptor type II (BMPR2). The aim of this study was to analyze the methylation pattern of the BMPR2 promoter region in patients and controls. We used Methyl Primer Express(®) v.1.0 and MatInspector softwares to analyze this region. Genomic DNA obtained from the peripheral blood of patients and controls was modified with sodium bisulphite. Methylation was analyzed using methylation-specific PCR. DNA treated with CpG methyltransferase was used as a positive control for methylation and H1299 cell culture DNA was used as positive control for gene expression. We identified a CpG island, which may have been methylated, in the BMPR2 promoter region, in addition to NIT-2 (global-acting regulatory protein), sex-determining region Y) and heat shock factor transcription factor binding sites. We found no evidence of methylation in patients and controls. No methylated CpG sites were identified in H1299 cells expressing the BMPR2 gene. The BMPR2 promoter region is the most suitable for study because of the high number of transcription factor binding sites that could alter gene function. No evidence of methylation was detected in this region in patients and controls. Copyright © 2015 SEPAR. Published by Elsevier Espana. All rights reserved.

  18. Aberrant methylation of H19-DMR acquired after implantation was dissimilar in soma versus placenta of patients with Beckwith-Wiedemann syndrome.

    PubMed

    Higashimoto, Ken; Nakabayashi, Kazuhiko; Yatsuki, Hitomi; Yoshinaga, Hokuto; Jozaki, Kosuke; Okada, Junichiro; Watanabe, Yoriko; Aoki, Aiko; Shiozaki, Arihiro; Saito, Shigeru; Koide, Kayoko; Mukai, Tsunehiro; Hata, Kenichiro; Soejima, Hidenobu

    2012-07-01

    Gain of methylation (GOM) at the H19-differentially methylated region (H19-DMR) is one of several causative alterations in Beckwith-Wiedemann syndrome (BWS), an imprinting-related disorder. In most patients with epigenetic changes at H19-DMR, the timing of and mechanism mediating GOM is unknown. To clarify this, we analyzed methylation at the imprinting control regions of somatic tissues and the placenta from two unrelated, naturally conceived patients with sporadic BWS. Maternal H19-DMR was abnormally and variably hypermethylated in both patients, indicating epigenetic mosaicism. Aberrant methylation levels were consistently lower in placenta than in blood and skin. Mosaic and discordant methylation strongly suggested that aberrant hypermethylation occurred after implantation, when genome-wide de novo methylation normally occurs. We expect aberrant de novo hypermethylation of H19-DMR happens to a greater extent in embryos than in placentas, as this is normally the case for de novo methylation. In addition, of 16 primary imprinted DMRs analyzed, only H19-DMR was aberrantly methylated, except for NNAT DMR in the placental chorangioma of Patient 2. To our knowledge, these are the first data suggesting when GOM of H19-DMR occurs.

  19. Regional variation in travel-related illness acquired in Africa, March 1997-May 2011.

    PubMed

    Mendelson, Marc; Han, Pauline V; Vincent, Peter; von Sonnenburg, Frank; Cramer, Jakob P; Loutan, Louis; Kain, Kevin C; Parola, Philippe; Hagmann, Stefan; Gkrania-Klotsas, Effrossyni; Sotir, Mark; Schlagenhauf, Patricia

    2014-04-01

    To understand geographic variation in travel-related illness acquired in distinct African regions, we used the GeoSentinel Surveillance Network database to analyze records for 16,893 ill travelers returning from Africa over a 14-year period. Travelers to northern Africa most commonly reported gastrointestinal illnesses and dog bites. Febrile illnesses were more common in travelers returning from sub-Saharan countries. Eleven travelers died, 9 of malaria; these deaths occurred mainly among male business travelers to sub-Saharan Africa. The profile of illness varied substantially by region: malaria predominated in travelers returning from Central and Western Africa; schistosomiasis, strongyloidiasis, and dengue from Eastern and Western Africa; and loaisis from Central Africa. There were few reports of vaccine-preventable infections, HIV infection, and tuberculosis. Geographic profiling of illness acquired during travel to Africa guides targeted pretravel advice, expedites diagnosis in ill returning travelers, and may influence destination choices in tourism.

  20. Regional Variation in Travel-related Illness acquired in Africa, March 1997–May 2011

    PubMed Central

    Han, Pauline V.; Vincent, Peter; von Sonnenburg, Frank; Cramer, Jakob P.; Loutan, Louis; Kain, Kevin C.; Parola, Philippe; Hagmann, Stefan; Gkrania-Klotsas, Effrossyni; Sotir, Mark; Schlagenhauf, Patricia

    2014-01-01

    To understand geographic variation in travel-related illness acquired in distinct African regions, we used the GeoSentinel Surveillance Network database to analyze records for 16,893 ill travelers returning from Africa over a 14-year period. Travelers to northern Africa most commonly reported gastrointestinal illnesses and dog bites. Febrile illnesses were more common in travelers returning from sub-Saharan countries. Eleven travelers died, 9 of malaria; these deaths occurred mainly among male business travelers to sub-Saharan Africa. The profile of illness varied substantially by region: malaria predominated in travelers returning from Central and Western Africa; schistosomiasis, strongyloidiasis, and dengue from Eastern and Western Africa; and loaisis from Central Africa. There were few reports of vaccine-preventable infections, HIV infection, and tuberculosis. Geographic profiling of illness acquired during travel to Africa guides targeted pretravel advice, expedites diagnosis in ill returning travelers, and may influence destination choices in tourism. PMID:24655358

  1. The H19 Differentially Methylated Region Marks the Parental Origin of a Heterologous Locus without Gametic DNA Methylation

    PubMed Central

    Park, Kye-Yoon; Sellars, Elizabeth A.; Grinberg, Alexander; Huang, Sing-Ping; Pfeifer, Karl

    2004-01-01

    Igf2 and H19 are coordinately regulated imprinted genes physically linked on the distal end of mouse chromosome 7. Genetic analyses demonstrate that the differentially methylated region (DMR) upstream of the H19 gene is necessary for three distinct functions: transcriptional insulation of the maternal Igf2 allele, transcriptional silencing of paternal H19 allele, and marking of the parental origin of the two chromosomes. To test the sufficiency of the DMR for the third function, we inserted DMR at two heterologous positions in the genome, downstream of H19 and at the alpha-fetoprotein locus on chromosome 5. Our results demonstrate that the DMR alone is sufficient to act as a mark of parental origin. Moreover, this activity is not dependent on germ line differences in DMR methylation. Thus, the DMR can mark its parental origin by a mechanism independent of its own DNA methylation. PMID:15082756

  2. DNA methylation at differentially methylated regions of imprinted genes is resistant to developmental programming by maternal nutrition.

    PubMed

    Ivanova, Elena; Chen, Jian-Hua; Segonds-Pichon, Anne; Ozanne, Susan E; Kelsey, Gavin

    2012-10-01

    The nutritional environment in which the mammalian fetus or infant develop is recognized as influencing the risk of chronic diseases, such as type 2 diabetes and hypertension, in a phenomenon that has become known as developmental programming. The late onset of such diseases in response to earlier transient experiences has led to the suggestion that developmental programming may have an epigenetic component, because epigenetic marks such as DNA methylation or histone tail modifications could provide a persistent memory of earlier nutritional states. One class of genes that has been considered a potential target or mediator of programming events is imprinted genes, because these genes critically depend upon epigenetic modifications for correct expression and because many imprinted genes have roles in controlling fetal growth as well as neonatal and adult metabolism. In this study, we have used an established model of developmental programming-isocaloric protein restriction to female mice during gestation or lactation-to examine whether there are effects on expression and DNA methylation of imprinted genes in the offspring. We find that although expression of some imprinted genes in liver of offspring is robustly and sustainably changed, methylation of the differentially methylated regions (DMRs) that control their monoallelic expression remains largely unaltered. We conclude that deregulation of imprinting through a general effect on DMR methylation is unlikely to be a common factor in developmental programming.

  3. The differentially DNA-methylated region responsible for expression of runt-related transcription factor 2

    PubMed Central

    WAKITANI, Shoichi; YOKOI, Daigo; HIDAKA, Yuichi; NISHINO, Koichiro

    2016-01-01

    Runt-related transcription factor 2 (Runx2) is essential for osteogenesis. This study aimes at identification of the genomic region differentially methylated in DNA for regulation of Runx2 expression. In the proximal promoter of mouse Runx2, DNA methylation was frequent at the region further than 3 kb relative to the transcription start site, in contrast to lower methylation status of the closer locus within 2 kb from the transcription start site. At the intermediate part, we identified a novel differentially methylated region in the Runx2 promoter region (Runx2-DMR): from −2.7 to −2.2 kb relative to the start site of Runx2 transcription in mice. In this region, the DNA methylation rate correlated negatively with Runx2 expression among mouse organs as well as among primary cultures of bone marrow from different dogs. Induction of mouse and dog mesenchymal-like cells into osteoblastic differentiation decreased the methylation rate of Runx2-DMR. Thus, in this study, we identified a novel genomic region in which DNA methylation status is related to Runx2 expression and detected demethylation of Runx2-DMR during osteoblastic differentiation in mouse and dog. PMID:27916785

  4. Detection of regional DNA methylation using DNA-graphene affinity interactions.

    PubMed

    Haque, Md Hakimul; Gopalan, Vinod; Yadav, Sharda; Islam, Md Nazmul; Eftekhari, Ehsan; Li, Qin; Carrascosa, Laura G; Nguyen, Nam-Trung; Lam, Alfred K; Shiddiky, Muhammad J A

    2017-01-15

    We report a new method for the detection of regional DNA methylation using base-dependent affinity interaction (i.e., adsorption) of DNA with graphene. Due to the strongest adsorption affinity of guanine bases towards graphene, bisulfite-treated guanine-enriched methylated DNA leads to a larger amount of the adsorbed DNA on the graphene-modified electrodes in comparison to the adenine-enriched unmethylated DNA. The level of the methylation is quantified by monitoring the differential pulse voltammetric current as a function of the adsorbed DNA. The assay is sensitive to distinguish methylated and unmethylated DNA sequences at single CpG resolution by differentiating changes in DNA methylation as low as 5%. Furthermore, this method has been used to detect methylation levels in a collection of DNA samples taken from oesophageal cancer tissues. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Identification of differentially methylated regions during vernalization revealed a role for RNA methyltransferases in bolting.

    PubMed

    Hébrard, Claire; Trap-Gentil, Marie-Véronique; Lafon-Placette, Clément; Delaunay, Alain; Joseph, Claude; Lefèbvre, Marc; Barnes, Steve; Maury, Stéphane

    2013-01-01

    Sugar beet (Beta vulgaris altissima) is a biennial root crop with an absolute requirement for cold exposure to bolt and flower, a process called vernalization. Global DNA methylation variations have been reported during vernalization in several plants. However, few genes targeted by DNA methylation during vernalization have been described. The objectives of this study were to identify differentially methylated regions and to study their involvement in bolting induction and tolerance. Restriction landmark genome scanning was applied to DNA from shoot apical meristems of sugar beet genotypes, providing a direct quantitative epigenetic assessment of several CG methylated genes without prior knowledge of gene sequence. Several differentially methylated regions exhibiting variations of gene-body DNA methylation and expression during cold exposure and/or between genotypes were identified, including an AROGENATE DEHYDRATASE and two RNA METHYLCYTOSINE TRANSFERASE sequences. One RNA METHYLCYTOSINE TRANSFERASE sequence displayed gene-body hypermethylation and activation of expression, while the other was hypomethylated and inhibited by cold exposure. Global RNA methylation and phenolic compound levels changed during cold exposure in a genotype-dependent way. The use of methyl RNA immunoprecipitation of total RNA and reverse transcription-PCR analysis revealed mRNA methylation in a vernalized bolting-resistant genotype for the FLOWERING LOCUS 1 gene, a repressor of flowering. Finally, Arabidopsis mutants for RNA METHYLCYTOSINE TRANSFERASE and AROGENATE DEHYDRATASE were shown to exhibit, under different environmental conditions, early or late bolting phenotypes, respectively. Overall, the data identified functional targets of DNA methylation during vernalization in sugar beet, and it is proposed that RNA methylation and phenolic compounds play a role in the floral transition.

  6. Region of interest methylation analysis: a comparison of MSP with MS-HRM and direct BSP.

    PubMed

    Akika, Reem; Awada, Zainab; Mogharbil, Nahed; Zgheib, Nathalie K

    2017-07-01

    The aim of this study was to compare and contrast three DNA methylation methods of a specific region of interest (ROI): methylation-specific PCR (MSP), methylation-sensitive high resolution melting (MS-HRM) and direct bisulfite sequencing (BSP). The methylation of a CpG area in the promoter region of Estrogen receptor alpha (ESR1) was evaluated by these three methods with samples and standards of different methylation percentages. MSP data were neither reproducible nor sensitive, and the assay was not specific due to non-specific binding of primers. MS-HRM was highly reproducible and a step forward into categorizing the methylation status of the samples as percent ranges. Direct BSP was the most informative method regarding methylation percentage of each CpG site. Though not perfect, it was reproducible and sensitive. We recommend the use of either method depending on the research question and target amplicon, and provided that the designed primers and expected amplicons are within recommendations. If the research question targets a limited number of CpG sites and simple yes/no results are enough, MSP may be attempted. For short amplicons that are crowded with CpG sites and of single melting domain, MS-HRM may be the method of choice though it only indicates the overall methylation percentage of the entire amplicon. Although the assay is highly reproducible, being semi-quantitative makes it of lesser interest to study ROI methylation of samples with little methylation differences. Direct BSP is a step forward as it gives information about the methylation percentage at each CpG site.

  7. A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes

    PubMed Central

    Choufani, Sanaa; Shapiro, Jonathan S.; Susiarjo, Martha; Butcher, Darci T.; Grafodatskaya, Daria; Lou, Youliang; Ferreira, Jose C.; Pinto, Dalila; Scherer, Stephen W.; Shaffer, Lisa G.; Coullin, Philippe; Caniggia, Isabella; Beyene, Joseph; Slim, Rima; Bartolomei, Marisa S.; Weksberg, Rosanna

    2011-01-01

    Imprinted genes are critical for normal human growth and neurodevelopment. They are characterized by differentially methylated regions (DMRs) of DNA that confer parent of origin-specific transcription. We developed a new strategy to identify imprinted gene-associated DMRs. Using genome-wide methylation profiling of sodium bisulfite modified DNA from normal human tissues of biparental origin, candidate DMRs were identified by selecting CpGs with methylation levels consistent with putative allelic differential methylation. In parallel, the methylation profiles of tissues of uniparental origin, i.e., paternally-derived androgenetic complete hydatidiform moles (AnCHMs), and maternally-derived mature cystic ovarian teratoma (MCT), were examined and then used to identify CpGs with parent of origin-specific DNA methylation. With this approach, we found known DMRs associated with imprinted genomic regions as well as new DMRs for known imprinted genes, NAP1L5 and ZNF597, and novel candidate imprinted genes. The paternally methylated DMR for one candidate, AXL, a receptor tyrosine kinase, was also validated in experiments with mouse embryos that demonstrated Axl was expressed preferentially from the maternal allele in a DNA methylation-dependent manner. PMID:21324877

  8. An evaluation of methods to test predefined genomic regions for differential methylation in bisulfite sequencing data.

    PubMed

    Klein, Hans-Ulrich; Hebestreit, Katja

    2016-09-01

    In the biology of tissue development and diseases, DNA methylation plays an important role. For a deeper understanding, it is crucial to accurately compare DNA methylation patterns between groups of samples representing different conditions. A widely used method to investigate DNA methylation in the CpG context is bisulfite sequencing, which produces data on the single-nucleotide scale. While there are benefits to analyzing CpG sites on a basepair level, there are both biological and statistical reasons to test entire genomic regions for differential methylation. However, the analysis of DNA methylation is hampered by the lack of best practice standards. Here, we compared multiple approaches for testing predefined genomic regions for differential DNA methylation in bisulfite sequencing data. Nine methods were evaluated: BiSeq, COHCAP, Goeman's Global Test, Limma, methylKit/eDMR, RADMeth and three log-linear regression approaches with different distribution assumptions. We applied these methods to simulated data and determined their sensitivity and specificity. This revealed performance differences, which were also seen when applied to real data. Methods that first test single CpG sites and then test regions based on transformed CpG-wise P-values performed better than methods that summarize methylation levels or raw reads. Interestingly, smoothing of methylation levels had a negligible impact. In particular, Global Test, BiSeq and RADMeth/z-test outperformed the other methods we evaluated, providing valuable guidance for more accurate analysis of DNA methylation. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  9. Methylation status of the promoter region of the human frizzled 9 gene in acute myeloid leukemia.

    PubMed

    Zhang, Yingjie; Jiang, Qi; Kong, Xiaolin; Yang, Lili; Hu, Wanzhen; Lv, Chengfang; Li, Yinghua

    2016-08-01

    The FZD9 gene is located at chromosome 7q11.23, and has been indicated to be a tumor suppressor gene. The present study examined the involvement of FZD9 promoter methylation in the downregulation of FZD9 expression in leukemia cells. The expression of the FZD9 gene was absent in various leukemic cell lines, while it was restored following treatment with DNA demethylating agent 5‑aza‑2'‑deoxycytidine. Bisulfite sequencing analysis of the FZD9 promoter region showed that it was partially methylated in cell lines in which FZD9 gene was not expressed. Thus, DNA methylation in the promoter region may lead to inactivation of the FZD9 gene, which may represent and aberration associated with leukemia, since DNA was not methylated in normal peripheral blood mononuclear cells. Methylation‑specific polymerase chain reaction analysis revealed that the promoter region of the FZD9 gene was frequently methylated in primary or relapse acute myeloid leukemia (52.9%; excluding acute promyelocytic leukemia); however, methylation was infrequent in B‑cell acute lymphocytic leukemia (5.6%). In conclusion, the present study indicated that the methylation profile of the FZD9 gene corresponded to that of a candidate tumor‑suppressor gene in acute myeloid leukemia.

  10. No Evidence for a Parent-of-Origin Specific Differentially Methylated Region Linked to RASGRF1.

    PubMed

    Pitamber, Punita Navnitlal; Lombard, Zané; Ramsay, Michèle

    2012-01-01

    Imprinted genes are expressed from one parental allele in a parent-of-origin manner. This monoallelic behavior is regulated by allele-specific DNA methylation that is confined to differentially methylated regions (DMRs). To date there are over 80 known human imprinted genes of which only three are known to have paternally methylated DMRs. In mice there exists an additional paternally methylated DMR associated with Rasgrf1. The Rasgrf1 gene forms part of the MAPK signaling pathway and plays a role in long-term memory formation and growth control. A RASGRF1-associated parent-of-origin specific DMR in humans and its methylation status in sperm DNA have not been explored. The primary aim of this study was to determine whether the human RASGRF1 gene contains a DMR and whether this DMR is paternally methylated and shows roughly 50% methylation in somatic tissue. Computational assessments were done to identify putative CTCF binding sites, CpG islands (CGIs) that could serve as potential RASGRF1 DMRs and tandem repeats within or adjacent to these CGIs. The methylation status of three putative CGIs was assessed using quantitative pyrosequencing technology. None of the putative CTCF binding sites was found to occur in the predicted CGIs. The three putative CGIs linked to RASGRF1 did not display allele-specific methylation. While one of the three CGIs was found to be hypomethylated in both blood DNA and sperm DNA, the other two were found to be hypermethylated. The CGIs evaluated in this study did not fit the criteria of being a allele-specific DMR. Unlike the mouse Rasgrf1 locus, the human RASGRF1-associated CpG rich regions do not exhibit differential methylation in a parent-of-origin manner.

  11. Differential DNA methylation and lymphocyte proportions in a Costa Rican high longevity region.

    PubMed

    McEwen, Lisa M; Morin, Alexander M; Edgar, Rachel D; MacIsaac, Julia L; Jones, Meaghan J; Dow, William H; Rosero-Bixby, Luis; Kobor, Michael S; Rehkopf, David H

    2017-01-01

    The Nicoya Peninsula in Costa Rica has one of the highest old-age life expectancies in the world, but the underlying biological mechanisms of this longevity are not well understood. As DNA methylation is hypothesized to be a component of biological aging, we focused on this malleable epigenetic mark to determine its association with current residence in Nicoya versus elsewhere in Costa Rica. Examining a population's unique DNA methylation pattern allows us to differentiate hallmarks of longevity from individual stochastic variation. These differences may be characteristic of a combination of social, biological, and environmental contexts. In a cross-sectional subsample of the Costa Rican Longevity and Healthy Aging Study, we compared whole blood DNA methylation profiles of residents from Nicoya (n = 48) and non-Nicoya (other Costa Rican regions, n = 47) using the Infinium HumanMethylation450 microarray. We observed a number of differences that may be markers of delayed aging, such as bioinformatically derived differential CD8+ T cell proportions. Additionally, both site- and region-specific analyses revealed DNA methylation patterns unique to Nicoyans. We also observed lower overall variability in DNA methylation in the Nicoyan population, another hallmark of younger biological age. Nicoyans represent an interesting group of individuals who may possess unique immune cell proportions as well as distinct differences in their epigenome, at the level of DNA methylation.

  12. Aberrant DNA methylation in 5' regions of DNA methyltransferase genes in aborted bovine clones.

    PubMed

    Liu, Jinghe; Liang, Xingwei; Zhu, Jiaqiao; Wei, Liang; Hou, Yi; Chen, Da-Yuan; Sun, Qing-Yuan

    2008-09-01

    High rate of abortion and developmental abnormalities is thought to be closely associated with inefficient epigenetic reprogramming of the transplanted nuclei during bovine cloning. It is known that one of the important mechanisms for epigenetic reprogramming is DNA methylation. DNA methylation is established and maintained by DNA methyltransferases (DNMTs), therefore, it is postulated that the inefficient epigenetic reprogramming of transplanted nuclei may be due to abnormal expression of DNMTs. Since DNA methylation can strongly inhibit gene expression, aberrant DNA methylation of DNMT genes may disturb gene expression. But presently, it is not clear whether the methylation abnormality of DNMT genes is related to developmental failure of somatic cell nuclear transfer embryos. In our study, we analyzed methylation patterns of the 5' regions of four DNMT genes including Dnmt3a, Dnmt3b, Dnmt1 and Dnmt2 in four aborted bovine clones. Using bisulfite sequencing method, we found that 3 out of 4 aborted bovine clones (AF1, AF2 and AF3) showed either hypermethylation or hypomethylation in the 5' regions of Dnmt3a and Dnmt3b, indicating that Dnmt3a and Dnmt3b genes are not properly reprogrammed. However, the individual AF4 exhibited similar methylation level and pattern to age-matched in vitro fertilized (IVF) fetuses. Besides, we found that the 5' regions of Dnmt1 and Dnmt2 were nearly completely unmethylated in all normal adults, IVF fetuses, sperm and aborted clones. Together, our results suggest that the aberrant methylation of Dnmt3a and Dnmt3b 5' regions is probably associated with the high abortion of bovine clones.

  13. Novel regions of acquired uniparental disomy discovered in acute myeloid leukemia.

    PubMed

    Gupta, Manu; Raghavan, Manoj; Gale, Rosemary E; Chelala, Claude; Allen, Christopher; Molloy, Gael; Chaplin, Tracy; Linch, David C; Cazier, Jean-Baptiste; Young, Bryan D

    2008-09-01

    The acquisition of uniparental disomy (aUPD) in acute myeloid leukemia (AML) results in homozygosity for known gene mutations. Uncovering novel regions of aUPD has the potential to identify previously unknown mutational targets. We therefore aimed to develop a map of the regions of aUPD in AML. Here, we have analyzed a large set of diagnostic AML samples (n = 454) from young adults (age: 15-55 years) using genotype arrays. Acquired UPD was found in 17% of the samples with a nonrandom distribution particularly affecting chromosome arms 13q, 11p, and 11q. Novel recurrent regions of aUPD were uncovered at 2p, 17p, 2q, 17q, 1p, and Xq. Overall, aUPDs were observed across all cytogenetic risk groups, although samples with aUPD13q (5.4% of samples) belonged exclusively to the intermediate-risk group as defined by cytogenetics. All cases with a high FLT3-ITD level, measured previously, had aUPD13q covering the FLT3 gene. Significantly, none of the samples with FLT3-ITD(-)/FLT3-TKD(+) mutation exhibited aUPD13q. Of the 119 aUPDs observed, the majority (87%) were due to mitotic recombination while only 13% were due to nondisjunction. This study demonstrates aUPD is a frequent and significant finding in AML and pinpoints regions that may contain novel mutational targets.

  14. The differentially methylated region of MEG8 is hypermethylated in patients with Temple syndrome.

    PubMed

    Bens, Susanne; Kolarova, Julia; Gillessen-Kaesbach, Gabriele; Buiting, Karin; Beygo, Jasmin; Caliebe, Almuth; Ammerpohl, Ole; Siebert, Reiner

    2015-10-01

    To investigate the DNA-methylation levels in the newly described MEG8 differentially methylated region (DMR) in the imprinted cluster in 14q32 in patients with Temple syndrome. We included three patients with Temple syndrome which were studied by Infinium HumanMethylation450 BeadChips, locus-specific bisulfite-pyrosequencing, methylation-specific-MLPA and microsatellite analyses. The tag-CpG of the MEG8-DMR was investigated using the Infinium HumanMethylation450 BeadChip. In all three patients, the identical pattern of DNA-hypermethylation of the MEG8-DMR was observed along with DNA-hypomethylation of the IG-DMR and MEG3-DMR. Based on the observed MEG8-DMR DNA-hypermethylation and previously published data, we conclude that DNA-methylation of the MEG3- and MEG8-DMR is functionally dependent on the DNA-methylation pattern of the IG-DMR. The observed combination of epimutations is predicted to be associated with bi-allelic MEG3 and MEG8 expression in individuals with Temple syndrome.

  15. Differentially Methylated Genomic Regions in Birth-Weight Discordant Twin Pairs.

    PubMed

    Chen, Mubo; Baumbach, Jan; Vandin, Fabio; Röttger, Richard; Barbosa, Eudes; Dong, Mingchui; Frost, Morten; Christiansen, Lene; Tan, Qihua

    2016-03-01

    Poor nutrition during critical growth phases may alter the structural and physiologic development of vital organs thus "programming" the susceptibility to adult-onset diseases and disease-related health conditions. Epigenome-wide association studies have been performed in birth-weight discordant twin pairs to find evidence for such "programming" effects, but no significant results emerged. We further investigated this issue using a new computational approach: Instead of probing single genomic sites for significant alterations in epigenetic marks, we scan for differentially methylated genomic regions. Whole genome DNA methylation levels were measured in whole blood from 150 pairs of adult identical twins discordant for birth-weight. Intrapair differential DNA methylation was associated with qualitative (large or small) and quantitative (percentage) birth-weight discordance at each genomic site using regression models adjusting for age and sex. Based on the regression results, genomic regions with consistent alteration patterns of DNA methylation were located and tested for significant robustness using computational permutation tests. This yielded an interesting genomic region on chromosome 1, which is significantly differentially methylated for quantitative birth-weight discordance. The region covers two genes (TYW3 and CRYZ) both reportedly associated with metabolism. We conclude that prenatal conditions for birth-weight discordance may result in persistent epigenetic modifications potentially affecting even adult health.

  16. DNA Methylation Analysis of HTR2A Regulatory Region in Leukocytes of Autistic Subjects.

    PubMed

    Hranilovic, Dubravka; Blazevic, Sofia; Stefulj, Jasminka; Zill, Peter

    2016-02-01

    Disturbed brain and peripheral serotonin homeostasis is often found in subjects with autism spectrum disorder (ASD). The role of the serotonin receptor 2A (HTR2A) in the regulation of central and peripheral serotonin homeostasis, as well as its altered expression in autistic subjects, have implicated the HTR2A gene as a major candidate for the serotonin disturbance seen in autism. Several studies, yielding so far inconclusive results, have attempted to associate autism with a functional SNP -1438 G/A (rs6311) in the HTR2A promoter region, while possible contribution of epigenetic mechanisms, such as DNA methylation, to HTR2A dysregulation in autism has not yet been investigated. In this study, we compared the mean DNA methylation within the regulatory region of the HTR2A gene between autistic and control subjects. DNA methylation was analysed in peripheral blood leukocytes using bisulfite conversion and sequencing of the HTR2A region containing rs6311 polymorphism. Autistic subjects of rs6311 AG genotype displayed higher mean methylation levels within the analysed region than the corresponding controls (P < 0.05), while there was no statistically significant difference for AA and GG carriers. Our study provides preliminary evidence for increased HTR2A promoter methylation in leukocytes of a portion of adult autistic subjects, indicating that epigenetic mechanisms might contribute to HTR2A dysregulation observed in individuals with ASD. © 2015 International Society for Autism Research, Wiley Periodicals, Inc.

  17. Hospital-acquired infections in Italy: a region wide prevalence study.

    PubMed

    Zotti, C M; Messori Ioli, G; Charrier, L; Arditi, G; Argentero, P A; Biglino, A; Farina, E C; Moiraghi Ruggenini, A; Reale, R; Romagnoli, S; Serra, R; Soranzo, M L; Valpreda, M; Hospital Coordinator Group

    2004-02-01

    Between October and December 2000, a region-wide prevalence study of hospital-acquired infections (HAI) was conducted in all public hospitals (59 facilities with ca. 16000 beds; 560000 admission yearly) in Piemonte Region, Italy, and in the one hospital of the neighbouring autonomous region of Valle d'Aosta. The study population comprised a total of 9467 patients hospitalized for at least 24 h. The prevalence of HAI was 7.84%, with marked differences in prevalence among the participating hospitals (range: 0-47.8%). The higher relative frequency of urinary tract infections (UTI; 52.7%) was due to the inclusion of urine cultures obtained on the day of the study from asymptomatic UTI in catheterized patients. A significant correlation was found with major risk factors related to medical procedures (urinary catheter, mechanical ventilation, surgical drainage, intravascular catheters). Patients with HAI were found to be older and to have a greater mean length of stay in hospital. Multiple logistic regression analyses showed that lack of independence, indwelling urinary catheter and mechanical ventilation were the risk factors more significantly associated with HAI. The use of antibiotics, in particular prophylactic agents used in surgery (cephalosporins, glycopeptides), provided an incentive for corrective intervention in antibiotic administration and in training of healthcare workers.

  18. Age-associated hyper-methylated regions in the human brain overlap with bivalent chromatin domains.

    PubMed

    Watson, Corey T; Disanto, Giulio; Sandve, Geir Kjetil; Breden, Felix; Giovannoni, Gavin; Ramagopalan, Sreeram V

    2012-01-01

    Recent associations between age-related differentially methylated sites and bivalently marked chromatin domains have implicated a role for these genomic regions in aging and age-related diseases. However, the overlap between such epigenetic modifications has so far only been identified with respect to age-associated hyper-methylated sites in blood. In this study, we observed that age-associated differentially methylated sites characterized in the human brain were also highly enriched in bivalent domains. Analysis of hyper- vs. hypo-methylated sites partitioned by age (fetal, child, and adult) revealed that enrichment was significant for hyper-methylated sites identified in children and adults (child, fold difference = 2.28, P = 0.0016; adult, fold difference = 4.73, P = 4.00 × 10(-5)); this trend was markedly more pronounced in adults when only the top 100 most significantly hypo- and hyper-methylated sites were considered (adult, fold difference = 10.7, P = 2.00 × 10(-5)). Interestingly, we found that bivalently marked genes overlapped by age-associated hyper-methylation in the adult brain had strong involvement in biological functions related to developmental processes, including neuronal differentiation. Our findings provide evidence that the accumulation of methylation in bivalent gene regions with age is likely to be a common process that occurs across tissue types. Furthermore, particularly with respect to the aging brain, this accumulation might be targeted to loci with important roles in cell differentiation and development, and the closing off of these developmental pathways. Further study of these genes is warranted to assess their potential impact upon the development of age-related neurological disorders.

  19. De novo identification of differentially methylated regions in the human genome.

    PubMed

    Peters, Timothy J; Buckley, Michael J; Statham, Aaron L; Pidsley, Ruth; Samaras, Katherine; V Lord, Reginald; Clark, Susan J; Molloy, Peter L

    2015-01-01

    The identification and characterisation of differentially methylated regions (DMRs) between phenotypes in the human genome is of prime interest in epigenetics. We present a novel method, DMRcate, that fits replicated methylation measurements from the Illumina HM450K BeadChip (or 450K array) spatially across the genome using a Gaussian kernel. DMRcate identifies and ranks the most differentially methylated regions across the genome based on tunable kernel smoothing of the differential methylation (DM) signal. The method is agnostic to both genomic annotation and local change in the direction of the DM signal, removes the bias incurred from irregularly spaced methylation sites, and assigns significance to each DMR called via comparison to a null model. We show that, for both simulated and real data, the predictive performance of DMRcate is superior to those of Bumphunter and Probe Lasso, and commensurate with that of comb-p. For the real data, we validate all array-derived DMRs from the candidate methods on a suite of DMRs derived from whole-genome bisulfite sequencing called from the same DNA samples, using two separate phenotype comparisons. The agglomeration of genomically localised individual methylation sites into discrete DMRs is currently best served by a combination of DM-signal smoothing and subsequent threshold specification. The findings also suggest the design of the 450K array shows preference for CpG sites that are more likely to be differentially methylated, but its overall coverage does not adequately reflect the depth and complexity of methylation signatures afforded by sequencing. For the convenience of the research community we have created a user-friendly R software package called DMRcate, downloadable from Bioconductor and compatible with existing preprocessing packages, which allows others to apply the same DMR-finding method on 450K array data.

  20. Probe Lasso: a novel method to rope in differentially methylated regions with 450K DNA methylation data.

    PubMed

    Butcher, Lee M; Beck, Stephan

    2015-01-15

    The speed and resolution at which we can scour the genome for DNA methylation changes has improved immeasurably in the last 10years and the advent of the Illumina 450K BeadChip has made epigenome-wide association studies (EWAS) a reality. The resulting datasets are conveniently formatted to allow easy alignment of significant hits to genes and genetic features, however; methods that parse significant hits into discreet differentially methylated regions (DMRs) remain a challenge to implement. In this paper we present details of a novel DMR caller, the Probe Lasso: a flexible window based approach that gathers neighbouring significant-signals to define clear DMR boundaries for subsequent in-depth analysis. The method is implemented in the R package ChAMP (Morris et al., 2014) and returns sets of DMRs according to user-tuned levels of probe filtering (e.g., inclusion of sex chromosomes, polymorphisms) and probe-lasso size distribution. Using a sub-sample of colon cancer- and healthy colon-samples from TCGA we show that Probe Lasso shifts DMR calling away from just probe-dense regions, and calls a range of DMR sizes ranging from tens-of-bases to tens-of-kilobases in scale. Moreover, using TCGA data we show that Probe Lasso leverages more information from the array and highlights a potential role of hypomethylated transcription factor binding motifs not discoverable using a basic, fixed-window approach.

  1. Probe Lasso: A novel method to rope in differentially methylated regions with 450K DNA methylation data

    PubMed Central

    Butcher, Lee M.; Beck, Stephan

    2015-01-01

    The speed and resolution at which we can scour the genome for DNA methylation changes has improved immeasurably in the last 10 years and the advent of the Illumina 450K BeadChip has made epigenome-wide association studies (EWAS) a reality. The resulting datasets are conveniently formatted to allow easy alignment of significant hits to genes and genetic features, however; methods that parse significant hits into discreet differentially methylated regions (DMRs) remain a challenge to implement. In this paper we present details of a novel DMR caller, the Probe Lasso: a flexible window based approach that gathers neighbouring significant-signals to define clear DMR boundaries for subsequent in-depth analysis. The method is implemented in the R package ChAMP (Morris et al., 2014) and returns sets of DMRs according to user-tuned levels of probe filtering (e.g., inclusion of sex chromosomes, polymorphisms) and probe-lasso size distribution. Using a sub-sample of colon cancer- and healthy colon-samples from TCGA we show that Probe Lasso shifts DMR calling away from just probe-dense regions, and calls a range of DMR sizes ranging from tens-of-bases to tens-of-kilobases in scale. Moreover, using TCGA data we show that Probe Lasso leverages more information from the array and highlights a potential role of hypomethylated transcription factor binding motifs not discoverable using a basic, fixed-window approach. PMID:25461817

  2. Restoration of CpG Methylation in The Egf Promoter Region during Rat Liver Regeneration

    PubMed Central

    Deming, Li; Ziwei, Li; Xueqiang, Guo; Cunshuan, Xu

    2015-01-01

    Epidermal growth factor (EGF) is an important factor for healing after tissue damage in diverse experimental models. It plays an important role in liver regeneration (LR). The objective of this experiment is to investigate the methylation variation of 10 CpG sites in the Egf promoter region and their relevance to Egf expression during rat liver regenera- tion. As a follow up of our previous study, rat liver tissue was collected after rat 2/3 partial hepatectomy (PH) during the re-organization phase (from days 14 to days 28). Liver DNA was extracted and modified by sodium bisulfate. The methylation status of 10 CpG sites in Egf promoter region was determined using bisulfite sequencing polymerase chain reaction (PCR), as BSP method. The results showed that 3 (sites 3, 4 and 9) out of 10 CpG sites have strikingly methylation changes during the re-organization phase compared to the regeneration phase (from 2 hours to 168 hours, P=0.002, 0.048 and 0.018, respectively). Our results showed that methylation modification of CpGs in the Egf promoter region could be restored to the status before PH operation and changes of methylation didn’t affect Egf mRNA expression during the re-organization phase. PMID:26464832

  3. DNA Methylation of Regulatory Regions of Imprinted Genes at Birth and Its Relation to Infant Temperament

    PubMed Central

    Fuemmeler, Bernard F.; Lee, Chien-Ti; Soubry, Adelheid; Iversen, Edwin S.; Huang, Zhiqing; Murtha, Amy P.; Schildkraut, Joellen M.; Jirtle, Randy L.; Murphy, Susan K.; Hoyo, Cathrine

    2016-01-01

    BACKGROUND DNA methylation of the differentially methylated regions (DMRs) of imprinted genes is relevant to neurodevelopment. METHODS DNA methylation status of the DMRs of nine imprinted genes in umbilical cord blood leukocytes was analyzed in relation to infant behaviors and temperament (n = 158). RESULTS MEG3 DMR levels were positively associated with internalizing (β = 0.15, P = 0.044) and surgency (β = 0.19, P = 0.018) behaviors, after adjusting for birth weight, gender, gestational age at birth, maternal age at delivery, race/ethnicity, education level, smoking status, parity, and a history of anxiety or depression. Higher methylation levels at the intergenic MEG3-IG methylation regions were associated with surgency (β = 0.28, P = 0.0003) and PEG3 was positively related to externalizing (β = 0.20, P = 0.01) and negative affectivity (β = 0.18, P = 0.02). CONCLUSION While the small sample size limits inference, these pilot data support gene-specific associations between epigenetic differences in regulatory regions of imprinted domains at birth and later infant temperament. PMID:27920589

  4. Mortality differences among hospitalized patients with community-acquired pneumonia in three world regions: results from the Community-Acquired Pneumonia Organization (CAPO) International Cohort Study.

    PubMed

    Arnold, Forest W; Wiemken, Timothy L; Peyrani, Paula; Ramirez, Julio A; Brock, Guy N

    2013-07-01

    Community-acquired pneumonia (CAP) causes considerable worldwide mortality, but limited data compare the mortality in different regions of the world. Our objective was to determine if there was a difference in mortality among hospitalized patients with CAP in three continental regions of the world. This was a cohort study of patients hospitalized for CAP between November 2001 and December 2011 from 70 institutions in 16 countries in US/Canada, Europe and Latin America; the Community-Acquired Pneumonia Organization (CAPO) international database. The primary outcome was mortality, and factors of interest included world region, processes of care, severity of disease, associated pathogen, specific comorbidities, and antimicrobial therapy. Multivariable logistic regression was performed to adjust for confounding effects on differences in mortality between regions. Patients were analyzed separately based on their intensive care unit admission status. A total of 6371 patients were reviewed. Latin America had the highest mortality (13.3%) followed by Europe (9.1%) and the USA/Canada (7.3%) (P < 0.001 for differences between regions). Important confounding variables included comorbidities (i.e., congestive heart failure, cerebrovascular disease), elevated blood urea nitrogen level, antimicrobial therapy (macrolide or fluoroquinolone use), and whether the patient had prior vaccinations (influenza, pneumococcal). After adjustment for confounding variables, estimated differences in mortality between the three regions were significantly reduced for both patients in the ICU and the ward. There was an observed discrepancy in CAP mortality between three world regions. Identified factors that contributed to these differences included incidence of H1N1 infection, elevated BUN, cerebrovascular disease, macrolide use, fluoroquinolone use, and vaccinations. Treatment regimen (fluoroquinolone and macrolide use) and preventive measures (vaccinations) were variables that may be modified

  5. Differential DNA Methylation Regions in Cytokine and Transcription Factor Genomic Loci Associate with Childhood Physical Aggression

    PubMed Central

    Provençal, Nadine; Suderman, Matthew J.; Caramaschi, Doretta; Wang, Dongsha; Hallett, Michael; Vitaro, Frank

    2013-01-01

    Background Animal and human studies suggest that inflammation is associated with behavioral disorders including aggression. We have recently shown that physical aggression of boys during childhood is strongly associated with reduced plasma levels of cytokines IL-1α, IL-4, IL-6, IL-8 and IL-10, later in early adulthood. This study tests the hypothesis that there is an association between differential DNA methylation regions in cytokine genes in T cells and monocytes DNA in adult subjects and a trajectory of physical aggression from childhood to adolescence. Methodology/Principal Findings We compared the methylation profiles of the entire genomic loci encompassing the IL-1α, IL-6, IL-4, IL-10 and IL-8 and three of their regulatory transcription factors (TF) NFkB1, NFAT5 and STAT6 genes in adult males on a chronic physical aggression trajectory (CPA) and males with the same background who followed a normal physical aggression trajectory (control group) from childhood to adolescence. We used the method of methylated DNA immunoprecipitation with comprehensive cytokine gene loci and TF loci microarray hybridization, statistical analysis and false discovery rate correction. We found differentially methylated regions to associate with CPA in both the cytokine loci as well as in their transcription factors loci analyzed. Some of these differentially methylated regions were located in known regulatory regions whereas others, to our knowledge, were previously unknown as regulatory areas. However, using the ENCODE database, we were able to identify key regulatory elements in many of these regions that indicate that they might be involved in the regulation of cytokine expression. Conclusions We provide here the first evidence for an association between differential DNA methylation in cytokines and their regulators in T cells and monocytes and male physical aggression. PMID:23977113

  6. Evaluation of a functional epigenetic approach to identify promoter region methylation in phaeochromocytoma and neuroblastoma.

    PubMed

    Margetts, Caroline D E; Morris, Mark; Astuti, Dewi; Gentle, Dean C; Cascon, Alberto; McRonald, Fiona E; Catchpoole, Daniel; Robledo, Mercedes; Neumann, Hartmut P H; Latif, Farida; Maher, Eamonn R

    2008-09-01

    The molecular genetics of inherited phaeochromocytoma have received considerable attention, but the somatic genetic and epigenetic events that characterise tumourigenesis in sporadic phaeochromocytomas are less well defined. Previously, we found considerable overlap between patterns of promoter region tumour suppressor gene (TSG) hypermethylation in two neural crest tumours, neuroblastoma and phaeochromocytoma. In order to identify candidate biomarkers and epigenetically inactivated TSGs in phaeochromocytoma and neuroblastoma, we characterised changes in gene expression in three neuroblastoma cell lines after treatment with the demethylating agent 5-azacytidine. Promoter region methylation status was then determined for 28 genes that demonstrated increased expression after demethylation. Three genes HSP47, homeobox A9 (HOXA9) and opioid binding protein (OPCML) were methylated in >10% of phaeochromocytomas (52, 17 and 12% respectively). Two of the genes, epithelial membrane protein 3 (EMP3) and HSP47, demonstrated significantly more frequent methylation in neuroblastoma than phaeochromocytoma. These findings extend epigenotype of phaeochromocytoma and identify candidate genes implicated in sporadic phaeochromocytoma tumourigenesis.

  7. Evaluation of a functional epigenetic approach to identify promoter region methylation in phaeochromocytoma and neuroblastoma

    PubMed Central

    Margetts, Caroline D E; Morris, Mark; Astuti, Dewi; Gentle, Dean C; Cascon, Alberto; McRonald, Fiona E; Catchpoole, Daniel; Robledo, Mercedes; Neumann, Hartmut P H; Latif, Farida; Maher, Eamonn R

    2008-01-01

    The molecular genetics of inherited phaeochromocytoma have received considerable attention, but the somatic genetic and epigenetic events that characterise tumourigenesis in sporadic phaeochromocytomas are less well defined. Previously, we found considerable overlap between patterns of promoter region tumour suppressor gene (TSG) hypermethylation in two neural crest tumours, neuroblastoma and phaeochromocytoma. In order to identify candidate biomarkers and epigenetically inactivated TSGs in phaeochromocytoma and neuroblastoma, we characterised changes in gene expression in three neuroblastoma cell lines after treatment with the demethylating agent 5-azacytidine. Promoter region methylation status was then determined for 28 genes that demonstrated increased expression after demethylation. Three genes HSP47, homeobox A9 (HOXA9) and opioid binding protein (OPCML) were methylated in >10% of phaeochromocytomas (52, 17 and 12% respectively). Two of the genes, epithelial membrane protein 3 (EMP3) and HSP47, demonstrated significantly more frequent methylation in neuroblastoma than phaeochromocytoma. These findings extend epigenotype of phaeochromocytoma and identify candidate genes implicated in sporadic phaeochromocytoma tumourigenesis. PMID:18499731

  8. Aberrant methylation of the major breakpoint cluster region in chronic myeloid leukemia.

    PubMed

    Litz, C E; Vos, J A; Copenhaver, C M

    1996-09-15

    Isolated hypomethylated sites exist in the major breakpoint cluster region (M-bcr) where most Philadelphia chromosome (Ph) breakpoints are located. Twenty of 50 (40%) chronic myeloid leukemia (CML) patients were found to have aberrant hypermethylation of these sites on the rearranged M-bcr when compared with control marrows. The aberrancy correlated strongly with M-bcr breakpoint location; 19 of 20 cases had breakpoints located 5' of the M-bcr Sca I site, and 28 of 30 cases with normal M-bcr methylation had breakpoints located 3' of the M-bcr Sca I site. Sequence analysis of the Ph M-bcr breakpoints failed to find an M-bcr nucleotide position that delineated the transition between abnormally and normally methylated cases, indicating that the translocation of a critical M-bcr sequence was not responsible for the methylation abnormality. In 3 of 8 CML patients, cells without the t(9;22) were found to have abnormally methylated, unrearranged M-bcrs. The data indicate that abnormally methylated rearranged M-bcrs are present in CML cases with Ph breakpoints 5' of the M-bcr Sca I site and that the M-bcr in Ph- cells of patients with CML may also be abnormally methylated.

  9. Injury Region and Risk of Hospital-Acquired Pneumonia Among Pediatric Trauma Patients.

    PubMed

    Cutler, Gretchen J; Kharbanda, Anupam B; Nowak, Jeffrey; Ortega, Henry W

    2017-03-01

    To describe the relationship between injury region and risk of hospital-acquired pneumonia (HAP) in pediatric trauma patients. Analyses included patients <19 years of age from the National Trauma Data Bank, during 2009-2011. Multivariable logistic regression was used to examine the association between injury region and odds of developing HAP stratified by age group. A total of 71 377 patients were eligible for analysis, and 1818 patients developed pneumonia. In adjusted regression models both younger (11-15 years) and older (16-18 years) adolescents with multisite injuries including the head and neck had higher odds of developing HAP compared with adolescents with isolated head and neck injuries (odds ratio [OR] = 2.04, 95% confidence interval [CI] 1.34-3.10; OR = 1.47, 95% CI 1.14-1.89, respectively), and younger adolescents with multisite injuries not involving the head and neck also had higher odds of developing HAP (OR = 1.97, 95% CI 1.08-3.60). We found no significant association between injury region and risk of HAP in children <11 years of age. Younger and older adolescents with firearm (OR = 1.85, 95% CI 1.00-3.42; OR = 1.39, 95% CI 1.02-1.88, respectively) or pulmonary (OR = 3.78, 95% CI 1.26-11.3; OR = 2.56, 95% CI 1.01-6.51, respectively) injuries had higher odds of developing HAP compared with those with motor vehicle collision injuries. Adolescent trauma patients with multisite injuries including the head and neck have a higher risk of developing HAP compared with those with isolated head and neck injuries. We identified several risk factors that can be used to inform future research focused on identifying subgroups at high risk for the development of HAP. Copyright © 2017 by the American Academy of Pediatrics.

  10. Identification of imprinting regulators at the Meg3 differentially methylated region.

    PubMed

    McMurray, Erin N; Schmidt, Jennifer V

    2012-09-01

    Genomic imprinting at the Delta-like 1 (Dlk1)-Maternally expressed gene 3 (Meg3) locus is regulated by the Meg3 differentially methylated region (DMR), but the mechanism by which this DMR acts is unknown. The goal of this study was to analyze the Meg3 DMR during imprinting establishment and maintenance for the presence of histone modifications and trans-acting DNA binding proteins using chromatin immunoprecipitation. In embryonic stem (ES) cells, where Meg3 is biallelically expressed, the DMR showed variable DNA methylation, with biallelic methylation at one region but paternal allele-specific methylation at another. All histone modifications detected at the Meg3 DMR of ES cells were biallelic. In embryonic day 12.5 (e12.5) embryos, where Meg3 is maternally expressed, the paternal Meg3 DMR was methylated, and activating histone modifications were specific to the maternal DMR. DNA-binding proteins that represent potential regulatory factors were identified in both ES cells and embryos.

  11. Region-specific DNA methylation in the preimplantation embryo as a target for genomic plasticity.

    PubMed

    Thurston, A; Lucas, E S; Allegrucci, C; Steele, W; Young, L E

    2007-09-01

    It has been long known that the unique genetic sequence each embryo inherits is not the sole determinant of phenotype. However, only recently have epigenetic modifications to DNA been implicated in providing potential developmental plasticity to the embryonic and fetal genome, with environmental influences directly altering the epigenetic modifications that contribute to tissue-specific gene regulation. Most is known about the potential environmental regulation of DNA methylation, epigenetic addition of methyl groups to cytosine residues in DNA that acts in the long-term silencing of affected sequences. While most attention has been paid to the methylation of imprinted gene sequences, in terms of developmental plasticity there are many more parts of the genome that are methylated and that could be affected. This review explores the distribution of cytosine methylation in the genome and discusses the potential effects of regional plasticity on subsequent development. Widening our consideration of potentially plastic regions is likely to greatly enhance our understanding of how individuals are shaped not only by DNA sequence, but by the environment in which pluripotent embryonic cells are transformed into the many cell types of the body.

  12. DNA Methylation Analysis of BRD1 Promoter Regions and the Schizophrenia rs138880 Risk Allele

    PubMed Central

    Dyrvig, Mads; Qvist, Per; Lichota, Jacek; Larsen, Knud; Nyegaard, Mette; Børglum, Anders D.

    2017-01-01

    The bromodomain containing 1 gene, BRD1 is essential for embryogenesis and CNS development. It encodes a protein that participates in histone modifying complexes and thereby regulates the expression of a large number of genes. Genetic variants in the BRD1 locus show association with schizophrenia and bipolar disorder and risk alleles in the promoter region correlate with reduced BRD1 expression. Insights into the transcriptional regulation of BRD1 and the pathogenic mechanisms associated with BRD1 risk variants, however, remain sparse. By studying transcripts in human HeLa and SH-SY5Y cells we provide evidence for differences in relative expression of BRD1 transcripts with three alternative 5’ UTRs (exon 1C, 1B, and 1A). We further show that expression of these transcript variants covaries negatively with DNA methylation proportions in their upstream promoter regions suggesting that promoter usage might be regulated by DNA methylation. In line with findings that the risk allele of the rs138880 SNP in the BRD1 promoter region correlates with reduced BRD1 expression, we find that it is also associated with moderate regional BRD1 promoter hypermethylation in both adipose tissue and blood. Importantly, we demonstrate by inspecting available DNA methylation and expression data that these regions undergo changes in methylation during fetal brain development and that differences in their methylation proportions in fetal compared to postnatal frontal cortex correlate significantly with BRD1 expression. These findings suggest that BRD1 may be dysregulated in both the developing and mature brain of risk allele carriers. Finally, we demonstrate that commonly used mood stabilizers Lithium, Valproate, and Carbamazepine affect the expression of BRD1 in SH-SY5Y cells. Altogether this study indicates a link between genetic risk and epigenetic dysregulation of BRD1 which raises interesting perspectives for targeting the mechanisms pharmacologically. PMID:28095495

  13. Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells

    PubMed Central

    Devailly, Guillaume; Grandin, Mélodie; Perriaud, Laury; Mathot, Pauline; Delcros, Jean-Guy; Bidet, Yannick; Morel, Anne-Pierre; Bignon, Jean-Yves; Puisieux, Alain; Mehlen, Patrick; Dante, Robert

    2015-01-01

    DNA methylation is thought to induce transcriptional silencing through the combination of two mechanisms: the repulsion of transcriptional activators unable to bind their target sites when methylated, and the recruitment of transcriptional repressors with specific affinity for methylated DNA. The Methyl CpG Binding Domain proteins MeCP2, MBD1 and MBD2 belong to the latter category. Here, we present MBD2 ChIPseq data obtained from the endogenous MBD2 in an isogenic cellular model of oncogenic transformation of human mammary cells. In immortalized (HMEC-hTERT) or transformed (HMLER) cells, MBD2 was found in a large proportion of methylated regions and associated with transcriptional silencing. A redistribution of MBD2 on methylated DNA occurred during oncogenic transformation, frequently independently of local DNA methylation changes. Genes downregulated during HMEC-hTERT transformation preferentially gained MBD2 on their promoter. Furthermore, depletion of MBD2 induced an upregulation of MBD2-bound genes methylated at their promoter regions, in HMLER cells. Among the 3,160 genes downregulated in transformed cells, 380 genes were methylated at their promoter regions in both cell lines, specifically associated by MBD2 in HMLER cells, and upregulated upon MBD2 depletion in HMLER. The transcriptional MBD2-dependent downregulation occurring during oncogenic transformation was also observed in two additional models of mammary cell transformation. Thus, the dynamics of MBD2 deposition across methylated DNA regions was associated with the oncogenic transformation of human mammary cells. PMID:26007656

  14. Identification of a DNA methylation-independent imprinting control region at the Arabidopsis MEDEA locus.

    PubMed

    Wöhrmann, Heike J P; Gagliardini, Valeria; Raissig, Michael T; Wehrle, Wendelin; Arand, Julia; Schmidt, Anja; Tierling, Sascha; Page, Damian R; Schöb, Hanspeter; Walter, Jörn; Grossniklaus, Ueli

    2012-08-15

    Genomic imprinting is exclusive to mammals and seed plants and refers to parent-of-origin-dependent, differential transcription. As previously shown in mammals, studies in Arabidopsis have implicated DNA methylation as an important hallmark of imprinting. The current model suggests that maternally expressed imprinted genes, such as MEDEA (MEA), are activated by the DNA glycosylase DEMETER (DME), which removes DNA methylation established by the DNA methyltransferase MET1. We report the systematic functional dissection of the MEA cis-regulatory region, resulting in the identification of a 200-bp fragment that is necessary and sufficient to mediate MEA activation and imprinted expression, thus containing the imprinting control region (ICR). Notably, imprinted MEA expression mediated by this ICR is independent of DME and MET1, consistent with the lack of any significant DNA methylation in this region. This is the first example of an ICR without differential DNA methylation, suggesting that factors other than DME and MET1 are required for imprinting at the MEA locus.

  15. Identification of a DNA methylation-independent imprinting control region at the Arabidopsis MEDEA locus

    PubMed Central

    Wöhrmann, Heike J.P.; Gagliardini, Valeria; Raissig, Michael T.; Wehrle, Wendelin; Arand, Julia; Schmidt, Anja; Tierling, Sascha; Page, Damian R.; Schöb, Hanspeter; Walter, Jörn; Grossniklaus, Ueli

    2012-01-01

    Genomic imprinting is exclusive to mammals and seed plants and refers to parent-of-origin-dependent, differential transcription. As previously shown in mammals, studies in Arabidopsis have implicated DNA methylation as an important hallmark of imprinting. The current model suggests that maternally expressed imprinted genes, such as MEDEA (MEA), are activated by the DNA glycosylase DEMETER (DME), which removes DNA methylation established by the DNA methyltransferase MET1. We report the systematic functional dissection of the MEA cis-regulatory region, resulting in the identification of a 200-bp fragment that is necessary and sufficient to mediate MEA activation and imprinted expression, thus containing the imprinting control region (ICR). Notably, imprinted MEA expression mediated by this ICR is independent of DME and MET1, consistent with the lack of any significant DNA methylation in this region. This is the first example of an ICR without differential DNA methylation, suggesting that factors other than DME and MET1 are required for imprinting at the MEA locus. PMID:22855791

  16. Indices of methylation in sperm DNA from fertile men differ between distinct geographical regions.

    PubMed

    Consales, C; Leter, G; Bonde, J P E; Toft, G; Eleuteri, P; Moccia, T; Budillon, A; Jönsson, B A G; Giwercman, A; Pedersen, H S; Ludwicki, J K; Zviezdai, V; Heederik, D; Spanò, M

    2014-09-01

    Which are the main determinants, if any, of sperm DNA methylation levels? Geographical region resulted associated with the sperm methylation status assessed on genome-wide repetitive sequences. DNA methylation level, assessed on repetitive sequences from peripheral blood lymphocyte, can vary with age, gender, alcohol consumption and white blood cell counts. A cross-sectional study. Individual data were collected from 269 young healthy men of proven fertility living in three geographical regions: Inuits from Greenland, Caucasians from Warsaw (Poland) and Kharkiv (Ukraine). Semen samples were collected between May 2002 and February 2004 and aliquots were immediately frozen. We estimated sperm DNA global methylation level (DGML) in two ways. First DNA methylation in repetitive DNA sequences (LINE-1, Satα and Alu) was quantified by PCR pyrosequencing after bisulfite conversion and second by flow cytometry (FCM) using fluorescently labeled monoclonal antibodies anti-5-methylcytosine. We analyzed whether personal characteristics and habits, body mass index, semen quality parameters, sperm chromatin integrity, biomarkers of accessory gland function and the plasma concentration of reproductive hormones were associated with sperm DNA methylation levels in men. Associations were evaluated by analysis of variance and linear regression analyses. The geographical location emerged as the main determinant when using the methylation level in repetitive sequences. FCM DGML results were not associated with those from repetitive sequence analysis. No other consistent associations between methylation markers and the assessed variables were identified across countries. The methods used are only surrogates of the actual sperm methylome and the methylation levels at individual specific loci were not explored. Sperm DGML is relatively independent from semen quality parameters and is a new candidate biomarker for epidemiological studies of the impact of environmental contaminants on male

  17. Methylation status of the major breakpoint cluster region in Philadelphia chromosome negative leukemias.

    PubMed

    Litz, C E; McClure, J S; Coad, J E; Goldfarb, A N; Brunning, R D

    1992-01-01

    It has been shown that a 600 bp long cluster of cell lineage specific hypomethylated sites in the major breakpoint cluster region (M-bcr) on chromosome 22 exists in hematopoietic cells. To determine possible relationships between methylation patterns within the M-bcr and the stage of hematopoietic cell development, the M-bcr methylation status of 39 patients with leukemia and lymphoma and two patients with myelodysplastic syndrome with non-rearranged M-bcrs was examined by BgIII-HpaII digestion. In the myeloid malignancies, the presence of a hypermethylated 4.8 kb BgIII-BgIII M-bcr allele was directly proportional to the combined myeloblast and promyelocyte percentage of the specimen, whereas the presence of a 2.5 kb BgIII-HpaII allele was directly proportional to the combined percentage of monocytic cells and neutrophils. All five acute monoblastic leukemias showed a methylation pattern that closely resembled neutrophils. All of thirteen surface immunoglobulin positive B-cell malignancies showed a distinct methylation pattern consisting of three or more BgIII-HpaII restriction fragments of 2.5 kb or less in length. The B-cell precursor leukemias showed heterogeneous M-bcr methylation patterns, with four of seven showing a B-cell pattern and three showing a hypermethylated pattern with 4.8, 3.1/3.0 and/or 2.5 kb BgIII-HpaII M-bcr alleles. It is concluded that the M-bcr methylation status is related to the maturation of the neutrophil series; the surface immunoglobulin positive B-cell malignancies are characterized by a distinct, extreme hypomethylation pattern of the M-bcr; and the B-cell precursor malignancies appear to have a heterogeneous M-bcr methylation pattern.

  18. Impact on prognosis of the regional distribution of MGMT methylation with respect to the CpG island methylator phenotype and age in glioma patients.

    PubMed

    Mur, Pilar; Rodríguez de Lope, Ángel; Díaz-Crespo, Francisco Javier; Hernández-Iglesias, Teresa; Ribalta, Teresa; Fiaño, Concepción; García, Juan Fernando; Rey, Juan Antonio; Mollejo, Manuela; Meléndez, Bárbara

    2015-05-01

    Clinical and molecular prognostic factors in gliomas include age, IDH mutation, the glioma CpG island methylator phenotype (G-CIMP+) and promoter methylation of the O(6)-methylguanine DNA-methyltransferase (MGMT) gene. Among these markers, a predictive value was reported in glioblastomas (GBM) for MGMT promoter methylation, in particular in elderly GBM patients. In this study, methylation data from 46 glioma samples with the Illumina 450K platform were obtained and extended using external data to include a total of 247 glioma samples. Methylation analysis of the whole MGMT gene with this platform revealed two strongly survival-associated CpG regions within the promoter and the gene body, which were confirmed in a reported dataset of high grade-gliomas. Methylation at the promoter (CpG 25, cg12981137 and the prognostic model MGMT-STP27) and at the gene body CpG 165 (cg07933035), were significantly associated with better overall survival, and strongly correlated with G-CIMP+ status. In this series, the prognostic value of MGMT methylation at the promoter was not observed in G-CIMP- cases, although around 50 % of them were MGMT-methylated. These results were also obtained in an homogeneously-treated series of chemoradiated G-CIMP- GBMs analyzed by MSP and qMSP, and confirmed in a reported pyrosequencing-analyzed series of gliomas. Interestingly, in contrast to the MGMT promoter, gene body methylation was of prognostic value in G-CIMP-patients older than 65 years. Our study highlights the relevance of the prognostic value of the different regions of methylation throughout the MGMT gene that could be affected by specific G-CIMP profiles and age groups.

  19. Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA

    PubMed Central

    Blackledge, Neil P.; Long, Hannah K.; Zhou, Jin C.; Kriaucionis, Skirmantas; Patient, Roger; Klose, Robert J.

    2012-01-01

    Across vertebrate genomes methylation of cytosine residues within the context of CpG dinucleotides is a pervasive epigenetic mark that can impact gene expression and has been implicated in various developmental and disease-associated processes. Several biochemical approaches exist to profile DNA methylation, but recently an alternative approach based on profiling non-methylated CpGs was developed. This technique, called CxxC affinity purification (CAP), uses a ZF-CxxC (CxxC) domain to specifically capture DNA containing clusters of non-methylated CpGs. Here we describe a new CAP approach, called biotinylated CAP (Bio-CAP), which eliminates the requirement for specialized equipment while dramatically improving and simplifying the CxxC-based DNA affinity purification. Importantly, this approach isolates non-methylated DNA in a manner that is directly proportional to the density of non-methylated CpGs, and discriminates non-methylated CpGs from both methylated and hydroxymethylated CpGs. Unlike conventional CAP, Bio-CAP can be applied to nanogram quantities of genomic DNA and in a magnetic format is amenable to efficient parallel processing of samples. Furthermore, Bio-CAP can be applied to genome-wide profiling of non-methylated DNA with relatively small amounts of input material. Therefore, Bio-CAP is a simple and streamlined approach for characterizing regions of the non-methylated DNA, whether at specific target regions or genome wide. PMID:22156374

  20. H19 Imprinting Control Region Methylation Requires an Imprinted Environment Only in the Male Germ Line ▿

    PubMed Central

    Gebert, Claudia; Kunkel, David; Grinberg, Alexander; Pfeifer, Karl

    2010-01-01

    The 2.4-kb H19 imprinting control region (H19ICR) is required to establish parent-of-origin-specific epigenetic marks and expression patterns at the Igf2/H19 locus. H19ICR activity is regulated by DNA methylation. The ICR is methylated in sperm but not in oocytes, and this paternal chromosome-specific methylation is maintained throughout development. We recently showed that the H19ICR can work as an ICR even when inserted into the normally nonimprinted alpha fetoprotein locus. Paternal but not maternal copies of the ICR become methylated in somatic tissue. However, the ectopic ICR remains unmethylated in sperm. To extend these findings and investigate the mechanisms that lead to methylation of the H19ICR in the male germ line, we characterized novel mouse knock-in lines. Our data confirm that the 2.4-kb element is an autonomously acting ICR whose function is not dependent on germ line methylation. Ectopic ICRs become methylated in the male germ line, but the timing of methylation is influenced by the insertion site and by additional genetic information. Our results support the idea that DNA methylation is not the primary genomic imprint and that the H19ICR insertion is sufficient to transmit parent-of-origin-dependent DNA methylation patterns independent of its methylation status in sperm. PMID:20038532

  1. Differential Methylation of the HPV 16 Upstream Regulatory Region during Epithelial Differentiation and Neoplastic Transformation

    PubMed Central

    Vinokurova, Svetlana; von Knebel Doeberitz, Magnus

    2011-01-01

    High risk human papillomaviruses are squamous epitheliotropic viruses that may cause cervical and other cancers. HPV replication depends on squamous epithelial differentiation. Transformation of HPV-infected cells goes along with substantial alteration of the viral gene expression profile and preferentially occurs at transformation zones usually at the uterine cervix. Methylation of the viral genome may affect regulatory features that control transcription and replication of the viral genome. Therefore, we analyzed the methylation pattern of the HPV16 upstream regulatory region (URR) during squamous epithelial differentiation and neoplastic transformation and analyzed how shifts in the HPV URR methylome may affect viral gene expression and replication. HPV 16 positive biopsy sections encompassing all stages of an HPV infection (latent, permissive and transforming) were micro-dissected and DNA was isolated from cell fractions representing the basal, intermediate, and superficial cell layers, each, as well as from transformed p16INK4a-positive cells. We observed fundamental changes in the methylation profile of transcription factor binding sites in the HPV16 upstream regulatory region linked to the squamous epithelial differentiation stage. Squamous epithelial transformation indicated by p16INK4a overexpression was associated with methylation of the distal E2 binding site 1 leading to hyper-activation of the HPV 16 URR. Adjacent normal but HPV 16-infected epithelial areas retained hyper-methylated HPV DNA suggesting that these viral genomes were inactivated. These data suggest that distinct shifts of the HPV 16 methylome are linked to differentiation dependent transcription and replication control and may trigger neoplastic transformation. PMID:21915330

  2. Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions.

    PubMed

    Tang, Man-Hung; Varadan, Vinay; Kamalakaran, Sitharthan; Zhang, Michael Q; Dimitrova, Nevenka; Hicks, James

    2012-01-01

    Solid tumors exhibit chromosomal rearrangements resulting in gain or loss of multiple chromosomal loci (copy number variation, or CNV), and translocations that occasionally result in the creation of novel chimeric genes. In the case of breast cancer, although most individual tumors each have unique CNV landscape, the breakpoints, as measured over large datasets, appear to be non-randomly distributed in the genome. Breakpoints show a significant regional concentration at genomic loci spanning perhaps several megabases. The proximal cause of these breakpoint concentrations is a subject of speculation, but is, as yet, largely unknown. To shed light on this issue, we have performed a bio-statistical analysis on our previously published data for a set of 119 breast tumors and normal controls (Wiedswang et al., 2003), where each sample has both high-resolution CNV and methylation data. The method examined the distribution of closeness of breakpoint regions with differentially methylated regions (DMR), coupled with additional genomic parameters, such as repeat elements and designated "fragile sites" in the reference genome. Through this analysis, we have identified a set of 93 regional loci called breakpoint enriched DMR (BEDMRs) characterized by altered DNA methylation in cancer compared to normal cells that are associated with frequent breakpoint concentrations within a distance of 1 Mb. BEDMR loci are further associated with local hypomethylation (66%), concentrations of the Alu SINE repeats within 3 Mb (35% of the cases), and tend to occur near a number of cancer related genes such as the protocadherins, AKT1, DUB3, GAB2. Furthermore, BEDMRs seem to deregulate members of the histone gene family and chromatin remodeling factors, e.g., JMJD1B, which might affect the chromatin structure and disrupt coordinate signaling and repair. From this analysis we propose that preference for chromosomal breakpoints is related to genome structure coupled with alterations in DNA

  3. Major Chromosomal Breakpoint Intervals in Breast Cancer Co-Localize with Differentially Methylated Regions

    PubMed Central

    Eric Tang, Man-Hung; Varadan, Vinay; Kamalakaran, Sitharthan; Zhang, Michael Q.; Dimitrova, Nevenka; Hicks, James

    2012-01-01

    Solid tumors exhibit chromosomal rearrangements resulting in gain or loss of multiple chromosomal loci (copy number variation, or CNV), and translocations that occasionally result in the creation of novel chimeric genes. In the case of breast cancer, although most individual tumors each have unique CNV landscape, the breakpoints, as measured over large datasets, appear to be non-randomly distributed in the genome. Breakpoints show a significant regional concentration at genomic loci spanning perhaps several megabases. The proximal cause of these breakpoint concentrations is a subject of speculation, but is, as yet, largely unknown. To shed light on this issue, we have performed a bio-statistical analysis on our previously published data for a set of 119 breast tumors and normal controls (Wiedswang et al., 2003), where each sample has both high-resolution CNV and methylation data. The method examined the distribution of closeness of breakpoint regions with differentially methylated regions (DMR), coupled with additional genomic parameters, such as repeat elements and designated “fragile sites” in the reference genome. Through this analysis, we have identified a set of 93 regional loci called breakpoint enriched DMR (BEDMRs) characterized by altered DNA methylation in cancer compared to normal cells that are associated with frequent breakpoint concentrations within a distance of 1 Mb. BEDMR loci are further associated with local hypomethylation (66%), concentrations of the Alu SINE repeats within 3 Mb (35% of the cases), and tend to occur near a number of cancer related genes such as the protocadherins, AKT1, DUB3, GAB2. Furthermore, BEDMRs seem to deregulate members of the histone gene family and chromatin remodeling factors, e.g., JMJD1B, which might affect the chromatin structure and disrupt coordinate signaling and repair. From this analysis we propose that preference for chromosomal breakpoints is related to genome structure coupled with alterations in

  4. Genome-wide DNA methylation profiling identifies a folate-sensitive region of differential methylation upstream of ZFP57-imprinting regulator in humans.

    PubMed

    Amarasekera, Manori; Martino, David; Ashley, Sarah; Harb, Hani; Kesper, Dörthe; Strickland, Deborah; Saffery, Richard; Prescott, Susan L

    2014-09-01

    Folate intake during pregnancy may affect the regulation of DNA methylation during fetal development. The genomic regions in the offspring that may be sensitive to folate exposure during in utero development have not been characterized. Using genome-scale profiling, we investigated DNA methylation in 2 immune cell types (CD4(+) and antigen-presenting cells) isolated from neonatal cord blood, selected on the basis of in utero folate exposure. High-folate (HF; n=11) and low-folate (LF; n=12) groups were selected from opposite extremes of maternal serum folate levels measured in the last trimester of pregnancy. A comparison of these groups revealed differential methylation at 7 regions across the genome. By far, the biggest effect observed was hypomethylation of a 923 bp region 3 kb upstream of the ZFP57 transcript, a regulator of DNA methylation during development, observed in both cell types. Levels of H3/H4 acetylation at ZFP57 promoter and ZFP57 mRNA expression were higher in CD4(+) cells in the HF group relative to the LF group. Hypomethylation at this region was replicated in an independent sample set. These data suggest that exposure to folate has effects on the regulation of DNA methylation during fetal development, and this may be important for health and disease.

  5. DNA methylation of the LIN28 pseudogene family.

    PubMed

    Davis, Aaron P; Benninghoff, Abby D; Thomas, Aaron J; Sessions, Benjamin R; White, Kenneth L

    2015-04-11

    DNA methylation directs the epigenetic silencing of selected regions of DNA, including the regulation of pseudogenes, and is widespread throughout the genome. Pseudogenes are decayed copies of duplicated genes that have spread throughout the genome by transposition. Pseudogenes are transcriptionally silenced by DNA methylation, but little is known about how pseudogenes are targeted for methylation or how methylation levels are maintained in different tissues. We employed bisulfite next generation sequencing to examine the methylation status of the LIN28 gene and four processed pseudogenes derived from LIN28. The objective was to determine whether LIN28 pseudogenes maintain the same pattern of methylation as the parental gene or acquire a methylation pattern independent of the gene of origin. In this study, we determined that the methylation status of LIN28 pseudogenes does not resemble the pattern evident for the LIN28 gene, but rather these pseudogenes appear to acquire methylation patterns independent of the parental gene. Furthermore, we observed that methylation levels of the examined pseudogenes correlate to the location of insertion within the genome. LIN28 pseudogenes inserted into gene bodies were highly methylated in all tissues examined. In contrast, pseudogenes inserted into genomic regions that are not proximal to genes were differentially methylated in various tissue types. Our analysis suggests that Lin28 pseudogenes do not acquire patterns of tissue-specific methylation as for the parental gene, but rather are methylated in patterns specific to the local genomic environment into which they were inserted.

  6. Healthcare-acquired infections in rehabilitation units of the Lombardy Region, Italy.

    PubMed

    Tinelli, M; Mannino, S; Lucchi, S; Piatti, A; Pagani, L; D'Angelo, R; Villa, M; Trezzi, L; Di Stefano, M G; Pavan, A; Macchi, L

    2011-08-01

    Little data are available on the frequency and risk factors for infection in patients in rehabilitation units. This was a 2-year retrospective cohort study conducted in 131 rehabilitation units (RUs) of the Lombardy Region, including those for patients requiring musculoskeletal, cardiac, respiratory, neurological and general geriatric rehabilitation. RUs were stratified into three groups by infection rate calculated from administrative data, and a random sample of RUs in each group was selected for analysis. Discharges from these RUs were randomly selected for chart review, and healthcare-acquired infection was confirmed using CDC/NHSN definitions. A logistic regression analysis explored the association among demographic variables of age, sex, type of rehabilitation unit, Charlson comorbidity score, and location prior to RU admission for selected infections. For the 3,028 discharges from 28 RUs, hospital administrative data had a sensitivity of 0.45 and a positive predictive value of 0.89 to identify infections in the chart review. At least one infection occurred in 14.9% of patient discharges, with 71% of infections being urinary, 8.0% respiratory, and 5% skin and soft tissue. Urinary infection was associated with female sex [odds ratio (OR) 1.48, 95% confidence interval (CI) 1.13-1.93], age 75-85 years (OR 2.21, 95% CI 1.12-4.34), Charlson comorbidity score of ≥3 (OR 1.54, 95% CI 1.10-2.17), and the transfer from acute care (OR 1.45, 95% CI 1.04-2.02). For respiratory infection, male sex (OR 3.06, 95% CI 1.51-6.18), comorbidity score of 1 or 2 (OR 2.16, 95% CI 1.08-4.36), and transfer from a healthcare setting other than an acute care hospital were independent risks (OR 3.14, 95% CI 1.15-8.53). Infections are common in residents of these rehabilitation units, and risk factors may differ with type of infection. The proportion of infections which may be prevented and effective prevention strategies need to be determined.

  7. Redundant mechanisms to form silent chromatin at pericentromeric regions rely on BEND3 and DNA methylation.

    PubMed

    Saksouk, Nehmé; Barth, Teresa K; Ziegler-Birling, Celine; Olova, Nelly; Nowak, Agnieszka; Rey, Elodie; Mateos-Langerak, Julio; Urbach, Serge; Reik, Wolf; Torres-Padilla, Maria-Elena; Imhof, Axel; Déjardin, Jérome; Simboeck, Elisabeth

    2014-11-20

    Constitutive heterochromatin is typically defined by high levels of DNA methylation and H3 lysine 9 trimethylation (H3K9Me3), whereas facultative heterochromatin displays DNA hypomethylation and high H3 lysine 27 trimethylation (H3K27Me3). The two chromatin types generally do not coexist at the same loci, suggesting mutual exclusivity. During development or in cancer, pericentromeric regions can adopt either epigenetic state, but the switching mechanism is unknown. We used a quantitative locus purification method to characterize changes in pericentromeric chromatin-associated proteins in mouse embryonic stem cells deficient for either the methyltransferases required for DNA methylation or H3K9Me3. DNA methylation controls heterochromatin architecture and inhibits Polycomb recruitment. BEND3, a protein enriched on pericentromeric chromatin in the absence of DNA methylation or H3K9Me3, allows Polycomb recruitment and H3K27Me3, resulting in a redundant pathway to generate repressive chromatin. This suggests that BEND3 is a key factor in mediating a switch from constitutive to facultative heterochromatin.

  8. Increased Frequency of CpG Island Methylator Phenotype and CDH1 Methylation in a Gastric Cancer High-Risk Region of China1

    PubMed Central

    Zhang, Kai-Li; Sun, Yuan; Li, Yan; Liu, Ming; Qu, Bo; Cui, Shu-Hong; Kong, Qing-You; Chen, Xiao-Yan; Li, Hong; Liu, Jia

    2008-01-01

    This study aimed to profile the methylation statuses of CDH1/E-cadherin and five CpG island methylator phenotype (CIMP)-associated genes (p16, hMLH1, MINT1, MINT2, and MINT31) in gastric specimens of 47 Dalian long-term residents with and 31 without gastric cancers (GCs). CIMP patterns were classified as CIMP-H with over three methylated genes, CIMP-L with one to two methylated genes, and CIMP-N without methylation. Of 47 GC cases, 24 (51.1%) were CIMP-H, 18 (38.3%) were CIMP-L, and 5 (10.6%) were CIMP-N, whereas 5 of 21 (23.8%) premalignant lesions were CIMP-H and 15 (71.4%) were CIMP-L. CIMP-L was found in 75% (12/16) of GC-adjacent mucosa and in 38.7% (12/31) of mucosa from GC-free patients. CDH1 methylation occurred in 48.9% (23/47) of cancer, in 23.8% (5/21) of premalignant, and in 25% (4/16) of noncancerous tissues and was correlated with patients' age (P = .01), lymph node metastasis, and CIMP severity (P = .000–.028). Our results demonstrated that the frequencies of CIMP-H in Dalian GCs, CIMP-L, and p16 methylation in GC-adjacent tissues and in GC-free mucosa were much higher than those reported previously, indicating the elevated methylation pressure in this GC high-risk region. The close correlation between CDH1 methylation and CIMP severity suggests the necessity of their combination in GC prevention and earlier diagnosis. PMID:18607505

  9. IRF7 gene expression profile and methylation of its promoter region in patients with systemic sclerosis.

    PubMed

    Rezaei, Ramazan; Mahmoudi, Mahdi; Gharibdoost, Farhad; Kavosi, Hoda; Dashti, Navid; Imeni, Vahideh; Jamshidi, Ahmadreza; Aslani, Saeed; Mostafaei, Shayan; Vodjgani, Mohammad

    2017-09-26

    The aim of the current study was to evaluate if methylation status of CpG sites of interferon regulatory factor 7 (IRF7) promoter in peripheral blood mononuclear cells (PBMCs) of systemic sclerosis (SSc) patients is involved in pathogenesis of the disease. PBMCs were isolated from whole blood of 50 SSc patients and 30 controls. After the extraction of total RNA and DNA contents from PBMCs, complementary DNA (cDNA) was synthesized. Afterwards, quantitative analysis of IRF7 messenger RNA (mRNA) was conducted by real-time polymerase chain reaction (PCR). To evaluate the methylation status of the promoter region of IRF7 gene, PCR products of bisulfite-treated DNA from SSc patients and controls were sequenced. The mRNA expression of IRF7 in PBMCs from patients compared with controls was significantly upregulated. While limited cutaneous SSc patients expressed the mRNA of IRF7 higher than controls, the diffuse cutaneous SSc group did not demonstrate significantly increased expression in comparison to controls. Insignificant promoter hypomethylation of IRF7 was observed in SSc patients compared with the control group. However, CpG2 hypomethylation was significantly associated with increased SSc risk. Furthermore, overall promoter methylation and mRNA level of IRF7 were significantly correlated with each other. Nonetheless, none of them correlated with Rodnan score of SSc patients. There was significant difference in IRF7 mRNA expression between CpG8 methylated and unmethylated SSc patients. Moreover, the difference of methylation and expression was not significant between anti-nuclear antibody (ANA)-positive and ANA-negative SSc patients. It is suggested that hypomethylation of the IRF7 promoter might play a role in SSc pathogenesis, probably through promoting the IRF7 expression in PBMCs of patients with SSc. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

  10. Patterns of methylation heritability in a genome-wide analysis of four brain regions

    PubMed Central

    Quon, Gerald; Lippert, Christoph; Heckerman, David; Listgarten, Jennifer

    2013-01-01

    DNA methylation has been implicated in a number of diseases and other phenotypes. It is, therefore, of interest to identify and understand the genetic determinants of methylation and epigenomic variation. We investigated the extent to which genetic variation in cis-DNA sequence explains variation in CpG dinucleotide methylation in publicly available data for four brain regions from unrelated individuals, finding that 3–4% of CpG loci assayed were heritable, with a mean estimated narrow-sense heritability of 30% over the heritable loci. Over all loci, the mean estimated heritability was 3%, as compared with a recent twin-based study reporting 18%. Heritable loci were enriched for open chromatin regions and binding sites of CTCF, an influential regulator of transcription and chromatin architecture. Additionally, heritable loci were proximal to genes enriched in several known pathways, suggesting a possible functional role for these loci. Our estimates of heritability are conservative, and we suspect that the number of identified heritable loci will increase as the methylome is assayed across a broader range of cell types and the density of the tested loci is increased. Finally, we show that the number of heritable loci depends on the window size parameter commonly used to identify candidate cis-acting single-nucleotide polymorphism variants. PMID:23303775

  11. metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data

    PubMed Central

    Jühling, Frank; Kretzmer, Helene; Bernhart, Stephan H.; Otto, Christian; Stadler, Peter F.; Hoffmann, Steve

    2016-01-01

    The detection of differentially methylated regions (DMRs) is a necessary prerequisite for characterizing different epigenetic states. We present a novel program, metilene, to identify DMRs within whole-genome and targeted data with unrivaled specificity and sensitivity. A binary segmentation algorithm combined with a two-dimensional statistical test allows the detection of DMRs in large methylation experiments with multiple groups of samples in minutes rather than days using off-the-shelf hardware. metilene outperforms other state-of-the-art tools for low coverage data and can estimate missing data. Hence, metilene is a versatile tool to study the effect of epigenetic modifications in differentiation/development, tumorigenesis, and systems biology on a global, genome-wide level. Whether in the framework of international consortia with dozens of samples per group, or even without biological replicates, it produces highly significant and reliable results. PMID:26631489

  12. Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells.

    PubMed

    Devailly, Guillaume; Grandin, Mélodie; Perriaud, Laury; Mathot, Pauline; Delcros, Jean-Guy; Bidet, Yannick; Morel, Anne-Pierre; Bignon, Jean-Yves; Puisieux, Alain; Mehlen, Patrick; Dante, Robert

    2015-07-13

    DNA methylation is thought to induce transcriptional silencing through the combination of two mechanisms: the repulsion of transcriptional activators unable to bind their target sites when methylated, and the recruitment of transcriptional repressors with specific affinity for methylated DNA. The Methyl CpG Binding Domain proteins MeCP2, MBD1 and MBD2 belong to the latter category. Here, we present MBD2 ChIPseq data obtained from the endogenous MBD2 in an isogenic cellular model of oncogenic transformation of human mammary cells. In immortalized (HMEC-hTERT) or transformed (HMLER) cells, MBD2 was found in a large proportion of methylated regions and associated with transcriptional silencing. A redistribution of MBD2 on methylated DNA occurred during oncogenic transformation, frequently independently of local DNA methylation changes. Genes downregulated during HMEC-hTERT transformation preferentially gained MBD2 on their promoter. Furthermore, depletion of MBD2 induced an upregulation of MBD2-bound genes methylated at their promoter regions, in HMLER cells. Among the 3,160 genes downregulated in transformed cells, 380 genes were methylated at their promoter regions in both cell lines, specifically associated by MBD2 in HMLER cells, and upregulated upon MBD2 depletion in HMLER. The transcriptional MBD2-dependent downregulation occurring during oncogenic transformation was also observed in two additional models of mammary cell transformation. Thus, the dynamics of MBD2 deposition across methylated DNA regions was associated with the oncogenic transformation of human mammary cells. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function.

    PubMed

    Schröder, Christopher; Leitão, Elsa; Wallner, Stefan; Schmitz, Gerd; Klein-Hitpass, Ludger; Sinha, Anupam; Jöckel, Karl-Heinz; Heilmann-Heimbach, Stefanie; Hoffmann, Per; Nöthen, Markus M; Steffens, Michael; Ebert, Peter; Rahmann, Sven; Horsthemke, Bernhard

    2017-07-26

    There is increasing evidence for inter-individual methylation differences at CpG dinucleotides in the human genome, but the regional extent and function of these differences have not yet been studied in detail. For identifying regions of common methylation differences, we used whole genome bisulfite sequencing data of monocytes from five donors and a novel bioinformatic strategy. We identified 157 differentially methylated regions (DMRs) with four or more CpGs, almost none of which has been described before. The DMRs fall into different chromatin states, where methylation is inversely correlated with active, but not repressive histone marks. However, methylation is not correlated with the expression of associated genes. High-resolution single nucleotide polymorphism (SNP) genotyping of the five donors revealed evidence for a role of cis-acting genetic variation in establishing methylation patterns. To validate this finding in a larger cohort, we performed genome-wide association studies (GWAS) using SNP genotypes and 450k array methylation data from blood samples of 1128 individuals. Only 30/157 (19%) DMRs include at least one 450k CpG, which shows that these arrays miss a large proportion of DNA methylation variation. In most cases, the GWAS peak overlapped the CpG position, and these regions are enriched for CREB group, NF-1, Sp100 and CTCF binding motifs. In two cases, there was tentative evidence for a trans-effect by KRAB zinc finger proteins. Allele-specific DNA methylation occurs in discrete chromosomal regions and is driven by genetic variation in cis and trans, but in general has little effect on gene expression.

  14. DNA methylation analysis on satellite I region in blastocysts obtained from somatic cell cloned cattle.

    PubMed

    Yamanaka, Ken-Ichi; Kaneda, Masahiro; Inaba, Yasushi; Saito, Koji; Kubota, Kaiyu; Sakatani, Miki; Sugimura, Satoshi; Imai, Kei; Watanabe, Shinya; Takahashi, Masashi

    2011-08-01

    Many observations have been made on cloned embryos and on adult clones by somatic cell nuclear transfer (SCNT), but it is still unclear whether the progeny of cloned animals is presenting normal epigenetic status. Here, in order to accumulate the information for evaluating the normality of cloned cattle, we analyzed the DNA methylation status on satellite I region in blastocysts obtained from cloned cattle. Embryos were produced by artificial insemination (AI) to non-cloned or cloned dams using semen from non-cloned or cloned sires. After 7 days of AI, embryos at blastocyst stage were collected by uterine flushing. The DNA methylation levels in embryos obtained by using semen and/or oocytes from cloned cattle were similar to those in in vivo embryos from non-cloned cattle. In contrast, the DNA methylation levels in SCNT embryos were significantly higher (P < 0.01) than those in in vivo embryos from non-cloned and cloned cattle, approximately similar to those in somatic cells used as donor cells. Thus, this study provides useful information that epigenetic status may be normal in the progeny of cloned cattle, suggesting the normality of germline cells in cloned cattle. 2011 The Authors. Animal Science Journal © 2011 Japanese Society of Animal Science.

  15. Region-specific RNA m(6)A methylation represents a new layer of control in the gene regulatory network in the mouse brain.

    PubMed

    Chang, Mengqi; Lv, Hongyi; Zhang, Weilong; Ma, Chunhui; He, Xue; Zhao, Shunli; Zhang, Zhi-Wei; Zeng, Yi-Xin; Song, Shuhui; Niu, Yamei; Tong, Wei-Min

    2017-09-01

    N(6)-methyladenosine (m(6)A) is the most abundant epitranscriptomic mark found on mRNA and has important roles in various physiological processes. Despite the relatively high m(6)A levels in the brain, its potential functions in the brain remain largely unexplored. We performed a transcriptome-wide methylation analysis using the mouse brain to depict its region-specific methylation profile. RNA methylation levels in mouse cerebellum are generally higher than those in the cerebral cortex. Heterogeneity of RNA methylation exists across different brain regions and different types of neural cells including the mRNAs to be methylated, their methylation levels and methylation site selection. Common and region-specific methylation have different preferences for methylation site selection and thereby different impacts on their biological functions. In addition, high methylation levels of fragile X mental retardation protein (FMRP) target mRNAs suggest that m(6)A methylation is likely to be used for selective recognition of target mRNAs by FMRP in the synapse. Overall, we provide a region-specific map of RNA m(6)A methylation and characterize the distinct features of specific and common methylation in mouse cerebellum and cerebral cortex. Our results imply that RNA m(6)A methylation is a newly identified element in the region-specific gene regulatory network in the mouse brain. © 2017 The Authors.

  16. Differentially methylated regions in maternal and paternal uniparental disomy for chromosome 7

    PubMed Central

    Hannula-Jouppi, Katariina; Muurinen, Mari; Lipsanen-Nyman, Marita; Reinius, Lovisa E; Ezer, Sini; Greco, Dario; Kere, Juha

    2014-01-01

    DNA methylation is a hallmark of genomic imprinting and differentially methylated regions (DMRs) are found near and in imprinted genes. Imprinted genes are expressed only from the maternal or paternal allele and their normal balance can be disrupted by uniparental disomy (UPD), the inheritance of both chromosomes of a chromosome pair exclusively from only either the mother or the father. Maternal UPD for chromosome 7 (matUPD7) results in Silver-Russell syndrome (SRS) with typical features and growth retardation, but no gene has been conclusively implicated in SRS. In order to identify novel DMRs and putative imprinted genes on chromosome 7, we analyzed eight matUPD7 patients, a segmental matUPD7q31-qter, a rare patUPD7 case and ten controls on the Infinium HumanMethylation450K BeadChip with 30 017 CpG methylation probes for chromosome 7. Genome-scale analysis showed highly significant clustering of DMRs only on chromosome 7, including the known imprinted loci GRB10, SGCE/PEG10, and PEG/MEST. We found ten novel DMRs on chromosome 7, two DMRs for the predicted imprinted genes HOXA4 and GLI3 and one for the disputed imprinted gene PON1. Quantitative RT-PCR on blood RNA samples comparing matUPD7, patUPD7, and controls showed differential expression for three genes with novel DMRs, HOXA4, GLI3, and SVOPL. Allele specific expression analysis confirmed maternal only expression of SVOPL and imprinting of HOXA4 was supported by monoallelic expression. These results present the first comprehensive map of parent-of-origin specific DMRs on human chromosome 7, suggesting many new imprinted sites. PMID:24247273

  17. Normal mode analyses of methyl palmitate all-trans and disordered forms in wagging progressive region.

    PubMed

    Ishioka, Tsutomu; Yan, Wenhong; Strauss, Herbert L; Snyder, Robert G

    2003-03-01

    Normal mode analyses are made for methyl palmitate molecule having all-trans or conformational disorders around the ester head group, in order to explain characteristic observed frequency shifts in the wagging progressive region between all-trans and disorder chains in triglyceride molecules. It was found that one gauche conformation at C(alpha)-C(beta) position and 90 degrees rotation of the ester head group in an alkyl chain produce frequency shifts for twisting mode as observed. For wagging modes, contamination of the disorders around the head group makes assignments change and apparent frequency shifts occur.

  18. Methylome analysis reveals alterations in DNA methylation in the regulatory regions of left ventricle development genes in human dilated cardiomyopathy.

    PubMed

    Jo, Bong-Seok; Koh, In-Uk; Bae, Jae-Bum; Yu, Ho-Yeong; Jeon, Eun-Seok; Lee, Hae-Young; Kim, Jae-Joong; Choi, Murim; Choi, Sun Shim

    2016-08-01

    Dilated cardiomyopathy (DCM) is one of the main causes of heart failure (called cardiomyopathies) in adults. Alterations in epigenetic regulation (i.e., DNA methylation) have been implicated in the development of DCM. Here, we identified a total of 1828 differentially methylated probes (DMPs) using the Infinium 450K HumanMethylation Bead chip by comparing the methylomes between 18 left ventricles and 9 right ventricles. Alterations in DNA methylation levels were observed mainly in lowly methylated regions corresponding to promoter-proximal regions, which become hypermethylated in severely affected left ventricles. Subsequent mRNA microarray analysis showed that the effect of DNA methylation on gene expression regulation is not unidirectional but is controlled by the functional sub-network context. DMPs were significantly enriched in the transcription factor binding sites (TFBSs) we tested. Alterations in DNA methylation were specifically enriched in the cis-regulatory regions of cardiac development genes, the majority of which are involved in ventricular development (e.g., TBX5 and HAND1). Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  19. CTCFL/BORIS Is a Methylation-Independent DNA-Binding Protein That Preferentially Binds to the Paternal H19 Differentially Methylated Region

    PubMed Central

    Nguyen, Phuongmai; Cui, Hengmi; Bisht, Kheem S.; Sun, Lunching; Patel, Krish; Lee, Richard S.; Kugoh, Hiroyuki; Oshimura, Mitsuo; Feinberg, Andrew P.; Gius, David

    2009-01-01

    The CTCF paralog BORIS (brother of the regulator of imprinted sites) is an insulator DNA-binding protein thought to play a role in chromatin organization and gene expression. Under normal physiologic conditions, BORIS is predominantly expressed during embryonic male germ cell development; however, it is also expressed in tumors and tumor cell lines and, as such, has been classified as a cancer-germline or cancer-testis gene. It has been suggested that BORIS may be a pro-proliferative factor, whereas CTCF favors antiproliferation. BORIS and CTCF share similar zinc finger DNA-binding domains and seem to bind to identical target sequences. Thus, one critical question is the mechanism governing the DNA-binding specificity of these two proteins when both are present in tumor cells. Chromatin immunoprecipitation (ChIP) in HCT116 cells and their hypermethylated variant showed that BORIS binds to methylated DNA sequences, whereas CTCF binds to unmethylated DNA. Electromobility shift assays, using both whole-cell extracts and in vitro translated CTCF and BORIS protein, and methylation-specific ChIP PCR showed that BORIS is a methylation-independent DNA-binding protein. Finally, experiments in murine hybrid cells containing either the maternal or paternal human chromosome 11 showed that BORIS preferentially binds to the methylated paternal H19 differentially methylated region, suggesting a mechanism in which the affinity of CTCF for the unmethylated maternal allele directs the DNA binding of BORIS toward the paternal allele. PMID:18632606

  20. Epididymal Region-Specific miRNA Expression and DNA Methylation and Their Roles in Controlling Gene Expression in Rats

    PubMed Central

    Hu, Shuanggang; Zhang, Jinsong; Xie, Shengsong; Ma, Wubin; Ni, Minjie; Tang, Chunhua; Zhou, Lu; Zhou, Yuchuan; Liu, Mofang; Li, Yixue; Zhang, Yonglian

    2015-01-01

    Region-specific gene expression is an intriguing feature of the mammalian epididymis. This unique property is essential for sperm maturation and storage, and it also implicates stringent and multi-level regulations of gene expression. Over the past decade, the androgen-driven activation of epididymal gene transcription has been extensively studied. However, it still remains largely unexplored whether and how other regulatory mechanisms, such as miRNAs and DNA methylation, are involved in controlling regional gene expression in the epididymis. Using microarray-based approaches, we studied the regional miRNA expression and DNA methylation profiles in 4 distinct epididymal regions (initial segment, caput, corpus and cauda) of rats. We found that the miR-200 family members were more expressed in caput, compared with cauda. By GSEA analysis, the differential expression of miR-200 family between caput and cauda was shown to be negatively correlated with their predicted target genes, among which 4 bona fide targets were verified by luciferase reporter assay. Predicted target genes of miR-200 family have enriched functions in anti-apoptosis, cell transportation and development, implying the regional diversity in epididymal functions. On the other hand, we revealed epididymal DNA methylation of 2002 CpG islands and 2771 gene promoters (-3.88-0.97kb), among which 1350 (67.43%) CpG islands and 2095 (75.60%) promoters contained region-specific DNA methylation. We observed significant and distinct functional enrichment in genes with specifically methylated promoters in each epididymal regions, but these DNA methylations did not show significant correlation with repressed gene transcription in the mature epididymis. Conclusively, we investigated the regional miRNA expression and DNA methylation in the rat epididymis and revealed a potential role of miR-200 family in gene expression regulation between caput and cauda. This may contribute to the distinct physiological function in

  1. Human bocavirus infection diagnosed serologically among children admitted to hospital with community-acquired pneumonia in a tropical region.

    PubMed

    Nascimento-Carvalho, Cristiana M; Cardoso, Maria-Regina A; Meriluoto, Mira; Kemppainen, Kaisa; Kantola, Kalle; Ruuskanen, Olli; Hedman, Klaus; Söderlund-Venermo, Maria

    2012-02-01

    Human bocavirus (HBoV) is a human virus associated with respiratory disease in children. Limited information is available on acute infection with HBoV among children admitted to hospital with community-acquired pneumonia in tropical regions and the current diagnosis is inadequate. The aims were to diagnose and describe acute HBoV infections among children hospitalized for community-acquired pneumonia. In Salvador, Brazil, 277 children with community-acquired pneumonia were prospectively enrolled. Paired serum samples were tested by IgG, IgM, and IgG-avidity enzyme immunoassays (EIAs) using recombinant HBoV VP2. HBoV DNA was detected in nasopharyngeal aspirates and serum by a quantitative polymerase-chain reaction (PCR). HBoV DNA was detected in nasopharyngeal aspirates of 62/268 (23%) children and 156/273 (57%) were seropositive. Acute primary HBoV infection was reliably diagnosed (bearing at least two acute markers: Positive IgM, a fourfold increase/conversion of IgG, low IgG avidity or viremia) in 21 (8%) of 273 patients, 90% of 20 had HBoV DNA in nasopharyngeal aspirates, 83% with a high DNA load. The median age of infection with HBoV was 16 months, range 5-36. Community-acquired pneumonia was confirmed radiographically in 85% of 20 patients with acute HBoV infection diagnosed serologically. HBoV DNA was found in nasopharyngeal aspirates of 42/246(17%) children without an acute primary HBoV infection and available nasopharyngeal aspirate. Four children with HBoV secondary immune responses were detected, lacking both IgM and viremia. HBoV infection was diagnosed accurately in children aged 5-36 months with community-acquired pneumonia confirmed radiographically. PCR of nasopharyngeal aspirates is not a reliable marker of acute HBoV infection.

  2. Alcohol, one-carbon nutrient intake, and risk of colorectal cancer according to tumor methylation level of IGF2 differentially methylated region.

    PubMed

    Nishihara, Reiko; Wang, Molin; Qian, Zhi Rong; Baba, Yoshifumi; Yamauchi, Mai; Mima, Kosuke; Sukawa, Yasutaka; Kim, Sun A; Inamura, Kentaro; Zhang, Xuehong; Wu, Kana; Giovannucci, Edward L; Chan, Andrew T; Fuchs, Charles S; Ogino, Shuji; Schernhammer, Eva S

    2014-12-01

    Although a higher consumption of alcohol, which is a methyl-group antagonist, was previously associated with colorectal cancer risk, mechanisms remain poorly understood. We hypothesized that excess alcohol consumption might increase risk of colorectal carcinoma with hypomethylation of insulin-like growth factor 2 (IGF2) differentially methylated region-0 (DMR0), which was previously associated with a worse prognosis. With the use of a molecular pathologic epidemiology database in 2 prospective cohort studies, the Nurses' Health Study and Health Professionals Follow-up Study, we examined the association between alcohol intake and incident colorectal cancer according to the tumor methylation level of IGF2 DMR0. Duplication-method Cox proportional cause-specific hazards regression for competing risk data were used to compute HRs and 95% CIs. In addition, we investigated intakes of vitamin B-6, vitamin B-12, methionine, and folate as exposures. During 3,206,985 person-years of follow-up, we identified 993 rectal and colon cancer cases with an available tumor DNA methylation status. Compared with no alcohol consumption, the consumption of ≥15 g alcohol/d was associated with elevated risk of colorectal cancer with lower levels of IGF2 DMR0 methylation [within the first and second quartiles: HRs of 1.55 (95% CI: 1.08, 2.24) and 2.11 (95% CI: 1.44, 3.07), respectively]. By contrast, alcohol consumption was not associated with cancer with higher levels of IGF2 DMR0 methylation. The association between alcohol and cancer risk differed significantly by IGF2 DMR0 methylation level (P-heterogeneity = 0.006). The association of vitamin B-6, vitamin B-12, and folate intakes with cancer risk did not significantly differ according to IGF2 DMR0 methylation level (P-heterogeneity > 0.2). Higher alcohol consumption was associated with risk of colorectal cancer with IGF2 DMR0 hypomethylation but not risk of cancer with high-level IGF2 DMR0 methylation. The association between alcohol

  3. Alcohol, one-carbon nutrient intake, and risk of colorectal cancer according to tumor methylation level of IGF2 differentially methylated region123456

    PubMed Central

    Nishihara, Reiko; Wang, Molin; Qian, Zhi Rong; Baba, Yoshifumi; Yamauchi, Mai; Mima, Kosuke; Sukawa, Yasutaka; Kim, Sun A; Inamura, Kentaro; Zhang, Xuehong; Wu, Kana; Giovannucci, Edward L; Chan, Andrew T; Fuchs, Charles S; Ogino, Shuji; Schernhammer, Eva S

    2014-01-01

    Background: Although a higher consumption of alcohol, which is a methyl-group antagonist, was previously associated with colorectal cancer risk, mechanisms remain poorly understood. Objective: We hypothesized that excess alcohol consumption might increase risk of colorectal carcinoma with hypomethylation of insulin-like growth factor 2 (IGF2) differentially methylated region-0 (DMR0), which was previously associated with a worse prognosis. Design: With the use of a molecular pathologic epidemiology database in 2 prospective cohort studies, the Nurses’ Health Study and Health Professionals Follow-up Study, we examined the association between alcohol intake and incident colorectal cancer according to the tumor methylation level of IGF2 DMR0. Duplication-method Cox proportional cause-specific hazards regression for competing risk data were used to compute HRs and 95% CIs. In addition, we investigated intakes of vitamin B-6, vitamin B-12, methionine, and folate as exposures. Results: During 3,206,985 person-years of follow-up, we identified 993 rectal and colon cancer cases with an available tumor DNA methylation status. Compared with no alcohol consumption, the consumption of ≥15 g alcohol/d was associated with elevated risk of colorectal cancer with lower levels of IGF2 DMR0 methylation [within the first and second quartiles: HRs of 1.55 (95% CI: 1.08, 2.24) and 2.11 (95% CI: 1.44, 3.07), respectively]. By contrast, alcohol consumption was not associated with cancer with higher levels of IGF2 DMR0 methylation. The association between alcohol and cancer risk differed significantly by IGF2 DMR0 methylation level (P-heterogeneity = 0.006). The association of vitamin B-6, vitamin B-12, and folate intakes with cancer risk did not significantly differ according to IGF2 DMR0 methylation level (P-heterogeneity > 0.2). Conclusions: Higher alcohol consumption was associated with risk of colorectal cancer with IGF2 DMR0 hypomethylation but not risk of cancer with high

  4. Sexual epigenetics: gender-specific methylation of a gene in the sex determining region of Populus balsamifera

    PubMed Central

    Bräutigam, Katharina; Soolanayakanahally, Raju; Champigny, Marc; Mansfield, Shawn; Douglas, Carl; Campbell, Malcolm M.; Cronk, Quentin

    2017-01-01

    Methylation has frequently been implicated in gender determination in plants. The recent discovery of the sex determining region (SDR) of balsam poplar, Populus balsamifera, pinpointed 13 genes with differentiated X and Y copies. We tested these genes for differential methylation using whole methylome sequencing of xylem tissue of multiple individuals grown under field conditions in two common gardens. The only SDR gene to show a marked pattern of gender-specific methylation is PbRR9, a member of the two component response regulator (type-A) gene family, involved in cytokinin signalling. It is an ortholog of Arabidopsis genes ARR16 and ARR17. The strongest patterns of differential methylation (mostly male-biased) are found in the putative promoter and the first intron. The 4th intron is strongly methylated in both sexes and the 5th intron is unmethylated in both sexes. Using a statistical learning algorithm we find that it is possible accurately to assign trees to gender using genome-wide methylation patterns alone. The strongest predictor is the region coincident with PbRR9, showing that this gene stands out against all genes in the genome in having the strongest sex-specific methylation pattern. We propose the hypothesis that PbRR9 has a direct, epigenetically mediated, role in poplar sex determination. PMID:28345647

  5. The Extent to Which Methyl Salicylate Is Required for Signaling Systemic Acquired Resistance Is Dependent on Exposure to Light after Infection1[OA

    PubMed Central

    Liu, Po-Pu; von Dahl, Caroline C.; Klessig, Daniel F.

    2011-01-01

    Systemic acquired resistance (SAR) is a state of heightened defense to a broad spectrum of pathogens that is activated throughout a plant following local infection. Development of SAR requires the translocation of one or more mobile signals from the site of infection through the vascular system to distal (systemic) tissues. The first such signal identified was methyl salicylate (MeSA) in tobacco (Nicotiana tabacum). Subsequent studies demonstrated that MeSA also serves as a SAR signal in Arabidopsis (Arabidopsis thaliana) and potato (Solanum tuberosum). By contrast, another study suggested that MeSA is not required for SAR in Arabidopsis and raised questions regarding its signaling role in tobacco. Differences in experimental design, including the developmental age of the plants, the light intensity, and/or the strain of bacterial pathogen, were proposed to explain these conflicting results. Here, we demonstrate that the length of light exposure that plants receive after the primary infection determines the extent to which MeSA is required for SAR signaling. When the primary infection occurred late in the day and as a result infected plants received very little light exposure before entering the night/dark period, MeSA and its metabolizing enzymes were essential for SAR development. In contrast, when infection was done in the morning followed by 3.5 h or more of exposure to light, SAR developed in the absence of MeSA. However, MeSA was generally required for optimal SAR development. In addition to resolving the conflicting results concerning MeSA and SAR, this study underscores the importance of environmental factors on the plant’s response to infection. PMID:22021417

  6. DNA methylation patterns of behavior-related gene promoter regions dissect the gray wolf from domestic dog breeds.

    PubMed

    Banlaki, Zsofia; Cimarelli, Giulia; Viranyi, Zsofia; Kubinyi, Eniko; Sasvari-Szekely, Maria; Ronai, Zsolt

    2017-06-01

    A growing body of evidence highlights the relationship between epigenetics, especially DNA methylation, and population divergence as well as speciation. However, little is known about how general the phenomenon of epigenetics-wise separation of different populations is, or whether population assignment is, possible based on solely epigenetic marks. In the present study, we compared DNA methylation profiles between four different canine populations: three domestic dog breeds and their ancestor the gray wolf. Altogether, 79 CpG sites constituting the 65 so-called CpG units located in the promoter regions of genes affecting behavioral and temperamental traits (COMT, HTR1A, MAOA, OXTR, SLC6A4, TPH1, WFS1)-regions putatively targeted during domestication and breed selection. Methylation status of buccal cells was assessed using EpiTYPER technology. Significant inter-population methylation differences were found in 52.3% of all CpG units investigated. DNA methylation profile-based hierarchical cluster analysis indicated an unambiguous segregation of wolf from domestic dog. In addition, one of the three dog breeds (Golden Retriever) investigated also formed a separate, autonomous group. The findings support that population segregation is interrelated with shifts in DNA methylation patterns, at least in putative selection target regions, and also imply that epigenetic profiles could provide a sufficient basis for population assignment of individuals.

  7. Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array

    PubMed Central

    2013-01-01

    Background DNA methylation has been recognized as a key mechanism in cell differentiation. Various studies have compared tissues to characterize epigenetically regulated genomic regions, but due to differences in study design and focus there still is no consensus as to the annotation of genomic regions predominantly involved in tissue-specific methylation. We used a new algorithm to identify and annotate tissue-specific differentially methylated regions (tDMRs) from Illumina 450k chip data for four peripheral tissues (blood, saliva, buccal swabs and hair follicles) and six internal tissues (liver, muscle, pancreas, subcutaneous fat, omentum and spleen with matched blood samples). Results The majority of tDMRs, in both relative and absolute terms, occurred in CpG-poor regions. Further analysis revealed that these regions were associated with alternative transcription events (alternative first exons, mutually exclusive exons and cassette exons). Only a minority of tDMRs mapped to gene-body CpG islands (13%) or CpG islands shores (25%) suggesting a less prominent role for these regions than indicated previously. Implementation of ENCODE annotations showed enrichment of tDMRs in DNase hypersensitive sites and transcription factor binding sites. Despite the predominance of tissue differences, inter-individual differences in DNA methylation in internal tissues were correlated with those for blood for a subset of CpG sites in a locus- and tissue-specific manner. Conclusions We conclude that tDMRs preferentially occur in CpG-poor regions and are associated with alternative transcription. Furthermore, our data suggest the utility of creating an atlas cataloguing variably methylated regions in internal tissues that correlate to DNA methylation measured in easy accessible peripheral tissues. PMID:23919675

  8. Septin 9 promoter region methylation in free circulating DNA-potential role in noninvasive diagnosis of lung cancer: preliminary report.

    PubMed

    Powrózek, Tomasz; Krawczyk, Paweł; Kucharczyk, Tomasz; Milanowski, Janusz

    2014-04-01

    Currently, there are no sensitive diagnostic tests that could allow early detection of lung cancer. Among some cancer patients, epigenetic changes in the nature of methylation of different gene promoter regions are observed, which affect expression of suppressor genes such as septin 9 (SEPT9). Due to the ability of detecting these changes in free circulating DNA in peripheral blood, such genes may become ideal markers in early and noninvasive diagnostics of cancer. Methylation of SEPT9 promoter region in plasma DNA is observed frequently in colorectal cancer patients. The aim of the study was to define the frequency of SEPT9 promoter methylation in lung cancer patients and evaluation of usefulness of this marker in early diagnostic of lung cancer. Plasma samples were obtained from 70 untreated patients with different lung cancer pathological diagnosis and disease stage and from 100 healthy individuals. DNA was isolated from peripheral blood plasma and was then subjected to bisulfitation, purification and elution using Abbott mSEPT9 Detection Kit. Methylation level was assessed by real-time PCR with the use of specific SEPT9 promoter methylation probe. Each sample was assayed in the presence of positive and negative control. SEPT9 promoter methylation was detected in 31 (44.3% of the whole studied group) of lung cancer patients finding the result positive when methylation was detected in 1 out of 3 repetitions of each test sample determinations. The marker was present in patients with different pathological diagnosis and disease stage. Analysis of SEPT9 promoter region methylation may be useful in early diagnosis of lung cancer.

  9. Role of DNA methylation in expression control of the IKZF3-GSDMA region in human epithelial cells.

    PubMed

    Moussette, Sanny; Al Tuwaijri, Abeer; Kohan-Ghadr, Hamid-Reza; Elzein, Samar; Farias, Raquel; Bérubé, Julie; Ho, Bianca; Laprise, Catherine; Goodyer, Cynthia G; Rousseau, Simon; Naumova, Anna K

    2017-01-01

    Chromosomal region 17q12-q21 is associated with asthma and harbors regulatory polymorphisms that influence expression levels of all five protein-coding genes in the region: IKAROS family zinc finger 3 (Aiolos) (IKZF3), zona pellucida binding protein 2 (ZPBP2), ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3), and gasdermins A and B (GSDMA, GSDMB). Furthermore, DNA methylation in this region has been implicated as a potential modifier of the genetic risk of asthma development. To further characterize the effect of DNA methylation, we examined the impact of treatment with DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-dC) that causes DNA demethylation, on expression and promoter methylation of the five 17q12-q21 genes in the human airway epithelium cell line NuLi-1, embryonic kidney epithelium cell line 293T and human adenocarcinoma cell line MCF-7. 5-aza-dC treatment led to upregulation of expression of GSDMA in all three cell lines. ZPBP2 was upregulated in NuLi-1, but remained repressed in 293T and MCF-7 cells, whereas ORMDL3 was upregulated in 293T and MCF-7 cells, but not NuLi-1. Upregulation of ZPBP2 and GSDMA was accompanied by a decrease in promoter methylation. Moreover, 5-aza-dC treatment modified allelic expression of ZPBP2 and ORMDL3 suggesting that different alleles may respond differently to treatment. We also identified a polymorphic CTCF-binding site in intron 1 of ORMDL3 carrying a CG SNP rs4065275 and determined its methylation level. The site's methylation was unaffected by 5-aza-dC treatment in NuLi-1 cells. We conclude that modest changes (8-13%) in promoter methylation levels of ZPBP2 and GSDMA may cause substantial changes in RNA levels and that allelic expression of ZPBP2 and ORMDL3 is mediated by DNA methylation.

  10. Role of DNA methylation in expression control of the IKZF3-GSDMA region in human epithelial cells

    PubMed Central

    Kohan-Ghadr, Hamid-Reza; Elzein, Samar; Farias, Raquel; Bérubé, Julie; Ho, Bianca; Laprise, Catherine; Goodyer, Cynthia G.; Rousseau, Simon

    2017-01-01

    Chromosomal region 17q12-q21 is associated with asthma and harbors regulatory polymorphisms that influence expression levels of all five protein-coding genes in the region: IKAROS family zinc finger 3 (Aiolos) (IKZF3), zona pellucida binding protein 2 (ZPBP2), ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3), and gasdermins A and B (GSDMA, GSDMB). Furthermore, DNA methylation in this region has been implicated as a potential modifier of the genetic risk of asthma development. To further characterize the effect of DNA methylation, we examined the impact of treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5-aza-dC) that causes DNA demethylation, on expression and promoter methylation of the five 17q12-q21 genes in the human airway epithelium cell line NuLi-1, embryonic kidney epithelium cell line 293T and human adenocarcinoma cell line MCF-7. 5-aza-dC treatment led to upregulation of expression of GSDMA in all three cell lines. ZPBP2 was upregulated in NuLi-1, but remained repressed in 293T and MCF-7 cells, whereas ORMDL3 was upregulated in 293T and MCF-7 cells, but not NuLi-1. Upregulation of ZPBP2 and GSDMA was accompanied by a decrease in promoter methylation. Moreover, 5-aza-dC treatment modified allelic expression of ZPBP2 and ORMDL3 suggesting that different alleles may respond differently to treatment. We also identified a polymorphic CTCF-binding site in intron 1 of ORMDL3 carrying a CG SNP rs4065275 and determined its methylation level. The site’s methylation was unaffected by 5-aza-dC treatment in NuLi-1 cells. We conclude that modest changes (8–13%) in promoter methylation levels of ZPBP2 and GSDMA may cause substantial changes in RNA levels and that allelic expression of ZPBP2 and ORMDL3 is mediated by DNA methylation. PMID:28241063

  11. Nuclear matrix attachment regions antagonize methylation-dependent repression of long-range enhancer–promoter interactions

    PubMed Central

    Forrester, William C.; Fernández, Luis A.; Grosschedl, Rudolf

    1999-01-01

    The immunoglobulin intragenic μ enhancer region acts as a locus control region that mediates transcriptional activation over large distances in germ line transformation assays. In transgenic mice, but not in transfected tissue culture cells, the activation of a variable region (VH) promoter by the μ enhancer is dependent on flanking nuclear matrix attachment regions (MARs). Here, we examine the effects of DNA methylation, which occurs in early mouse development, on the function of the μ enhancer and the MARs. We find that methylation of rearranged μ genes in vitro, before transfection, represses the ability of the μ enhancer to activate the VH promoter over the distance of 1.2 kb. However, methylation does not affect enhancer-mediated promoter activation over a distance of 150 bp. In methylated DNA templates, the μ enhancer alone induces only local chromatin remodeling, whereas in combination with MARs, the μ enhancer generates an extended domain of histone acetylation. These observations provide evidence that DNA methylation impairs the distance independence of enhancer function and thereby imposes a requirement for additional regulatory elements, such as MARs, which facilitate long-range chromatin remodeling. PMID:10580007

  12. Epigenetic approach to early-onset Parkinson's disease: low methylation status of SNCA and PARK2 promoter regions.

    PubMed

    Eryilmaz, Isil Ezgi; Cecener, Gulsah; Erer, Sevda; Egeli, Unal; Tunca, Berrin; Zarifoglu, Mehmet; Elibol, Bulent; Bora Tokcaer, Ayse; Saka, Esen; Demirkiran, Meltem; Akbostanci, Cenk; Dogu, Okan; Colakoglu, Beril; Kenangil, Gulay; Kaleagasi, Hakan

    2017-08-22

    Background and aim The effect of epigenetic modifications in the genes related to Parkinson's disease (PD) is still unclear. In the present study, we investigated methylation status of SNCA and PARK2 genes in patients with early-onset Parkinson's disease (EOPD). Materials and methods The promoter region methylation status of SNCA and PARK2 genes was evaluated by methylation specific-PCR (MSP) in 91 patients with EOPD and 52 healthy individuals. Results The methylation of SNCA and PARK2 promoter regions were significantly lower in EOPD patients compared to the control group (P = 0.013 and P = 0.03, respectively). We also found that the methylation status of the SNCA might be associated with positive family history of PD (P = 0.042). Conclusion Although it should be supported by further analysis, based on the results of the present study, the methylation status of SNCA and PARK2 genes might contribute to EOPD pathogenesis.

  13. High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions.

    PubMed

    Krebs, Arnaud R; Dessus-Babus, Sophie; Burger, Lukas; Schübeler, Dirk

    2014-09-26

    The majority of mammalian promoters are CpG islands; regions of high CG density that require protection from DNA methylation to be functional. Importantly, how sequence architecture mediates this unmethylated state remains unclear. To address this question in a comprehensive manner, we developed a method to interrogate methylation states of hundreds of sequence variants inserted at the same genomic site in mouse embryonic stem cells. Using this assay, we were able to quantify the contribution of various sequence motifs towards the resulting DNA methylation state. Modeling of this comprehensive dataset revealed that CG density alone is a minor determinant of their unmethylated state. Instead, these data argue for a principal role for transcription factor binding sites, a prediction confirmed by testing synthetic mutant libraries. Taken together, these findings establish the hierarchy between the two cis-encoded mechanisms that define the DNA methylation state and thus the transcriptional competence of CpG islands.

  14. Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities

    PubMed Central

    de Ridder, Jeroen; Meysman, Pieter; Oluwagbemi, Olugbenga; Abeel, Thomas

    2014-01-01

    Contributing to a student organization, such as the International Society for Computational Biology Student Council (ISCB-SC) and its Regional Student Group (RSG) program, takes time and energy. Both are scarce commodities, especially when you are trying to find your place in the world of computational biology as a graduate student. It comes as no surprise that organizing ISCB-SC-related activities sometimes interferes with day-to-day research and shakes up your priority list. However, we unanimously agree that the rewards, both in the short as well as the long term, make the time spent on these extracurricular activities more than worth it. In this article, we will explain what makes this so worthwhile: soft skills. PMID:24992198

  15. Soft skills: an important asset acquired from organizing regional student group activities.

    PubMed

    de Ridder, Jeroen; Meysman, Pieter; Oluwagbemi, Olugbenga; Abeel, Thomas

    2014-07-01

    Contributing to a student organization, such as the International Society for Computational Biology Student Council (ISCB-SC) and its Regional Student Group (RSG) program, takes time and energy. Both are scarce commodities, especially when you are trying to find your place in the world of computational biology as a graduate student. It comes as no surprise that organizing ISCB-SC-related activities sometimes interferes with day-to-day research and shakes up your priority list. However, we unanimously agree that the rewards, both in the short as well as the long term, make the time spent on these extracurricular activities more than worth it. In this article, we will explain what makes this so worthwhile: soft skills.

  16. Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions.

    PubMed

    Keravnou, Anna; Ioannides, Marios; Tsangaras, Kyriakos; Loizides, Charalambos; Hadjidaniel, Michael D; Papageorgiou, Elisavet A; Kyriakou, Skevi; Antoniou, Pavlos; Mina, Petros; Achilleos, Achilleas; Neofytou, Maria; Kypri, Elena; Sismani, Carolina; Koumbaris, George; Patsalis, Philippos C

    2016-11-11

    DNA methylation is an epigenetic marker that has been shown to vary significantly across different tissues. Taking advantage of the methylation differences between placenta-derived cell-free DNA and maternal blood, several groups employed different approaches for the discovery of fetal-specific biomarkers. The aim of this study was to analyse whole-genome fetal and maternal methylomes in order to identify and confirm the presence of differentially methylated regions (DMRs). We have initially utilized methylated DNA immunoprecipitation (MeDIP) and next-generation sequencing (NGS) to identify genome-wide DMRs between chorionic villus sampling (CVS) and female non-pregnant plasma (PL) and peripheral blood (WBF) samples. Next, using specific criteria, 331 fetal-specific DMRs were selected and confirmed in eight CVS, eight WBF and eight PL samples by combining MeDIP and in-solution targeted enrichment followed by NGS. Results showed higher enrichment in CVS samples as compared to both WBF and PL samples, confirming the distinct methylation levels between fetal and maternal DNA for the selected DMRs. We have successfully implemented a novel approach for the discovery and confirmation of a significant number of fetal-specific DMRs by combining for the first time MeDIP and in-solution targeted enrichment followed by NGS. The implementation of this double-enrichment approach is highly efficient and enables the detailed analysis of multiple DMRs by targeted NGS. Also, this is, to our knowledge, the first reported application of MeDIP on plasma samples, which leverages the implementation of our enrichment methodology in the detection of fetal abnormalities in maternal plasma.

  17. Methylation and expression analyses of Pallister-Killian syndrome reveal partial dosage compensation of tetrasomy 12p and hypomethylation of gene-poor regions on 12p

    PubMed Central

    Davidsson, Josef; Johansson, Bertil

    2016-01-01

    ABSTRACT To ascertain the epigenomic features, i.e., the methylation, non-coding RNA, and gene expression patterns, associated with gain of i(12p) in Pallister-Killian syndrome (PKS), we investigated single cell clones, harboring either disomy 12 or tetrasomy 12p, from a patient with PKS. The i(12p)-positive cells displayed a characteristic expression and methylation signature. Of all the genes on 12p, 13% were overexpressed, including the ATN1, COPS7A, and NECAP1 genes in 12p13.31, a region previously implicated in PKS. However, the median expression fold change (1.3) on 12p was lower than expected by tetrasomy 12p. Thus, partial dosage compensation occurs in cells with i(12p). The majority (89%) of the significantly deregulated genes were not situated on 12p, indicating that global perturbation of gene expression is a key pathogenetic event in PKS. Three genes—ATP6V1G1 in 9q32, GMPS in 3q25.31, and TBX5 in 12q24.21—exhibited concomitant hypermethylation and decreased expression. The i(12p)-positive cells displayed global hypomethylation of gene-poor regions on 12p, a footprint previously associated with constitutional and acquired gains of whole chromosomes as well as with X-chromosome inactivation in females. We hypothesize that this non-genic hypomethylation is associated with chromatin processing that facilitates cellular adaptation to excess genetic material. PMID:26890086

  18. Methylation and expression analyses of Pallister-Killian syndrome reveal partial dosage compensation of tetrasomy 12p and hypomethylation of gene-poor regions on 12p.

    PubMed

    Davidsson, Josef; Johansson, Bertil

    2016-03-03

    To ascertain the epigenomic features, i.e., the methylation, non-coding RNA, and gene expression patterns, associated with gain of i(12p) in Pallister-Killian syndrome (PKS), we investigated single cell clones, harboring either disomy 12 or tetrasomy 12p, from a patient with PKS. The i(12p)-positive cells displayed a characteristic expression and methylation signature. Of all the genes on 12p, 13% were overexpressed, including the ATN1, COPS7A, and NECAP1 genes in 12p13.31, a region previously implicated in PKS. However, the median expression fold change (1.3) on 12p was lower than expected by tetrasomy 12p. Thus, partial dosage compensation occurs in cells with i(12p). The majority (89%) of the significantly deregulated genes were not situated on 12p, indicating that global perturbation of gene expression is a key pathogenetic event in PKS. Three genes-ATP6V1G1 in 9q32, GMPS in 3q25.31, and TBX5 in 12q24.21-exhibited concomitant hypermethylation and decreased expression. The i(12p)-positive cells displayed global hypomethylation of gene-poor regions on 12p, a footprint previously associated with constitutional and acquired gains of whole chromosomes as well as with X-chromosome inactivation in females. We hypothesize that this non-genic hypomethylation is associated with chromatin processing that facilitates cellular adaptation to excess genetic material.

  19. swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing

    PubMed Central

    Shao, Qianzhi; Liu, Qi; Chen, BingYu; Huang, Dongsheng

    2015-01-01

    DNA methylation is a widespread epigenetic modification that plays an essential role in gene expression through transcriptional regulation and chromatin remodeling. The emergence of whole genome bisulfite sequencing (WGBS) represents an important milestone in the detection of DNA methylation. Characterization of differential methylated regions (DMRs) is fundamental as well for further functional analysis. In this study, we present swDMR (http://sourceforge.net/projects/swdmr/) for the comprehensive analysis of DMRs from whole genome methylation profiles by a sliding window approach. It is an integrated tool designed for WGBS data, which not only implements accessible statistical methods to perform hypothesis test adapted to two or more samples without replicates, but false discovery rate was also controlled by multiple test correction. Downstream analysis tools were also provided, including cluster, annotation and visualization modules. In summary, based on WGBS data, swDMR can produce abundant information of differential methylated regions. As a convenient and flexible tool, we believe swDMR will bring us closer to unveil the potential functional regions involved in epigenetic regulation. PMID:26176536

  20. Placental hydroxymethylation vs methylation at the imprinting control region 2 on chromosome 11p15.5.

    PubMed

    Magalhães, H R; Leite, S B P; Paz, C C P de; Duarte, G; Ramos, E S

    2013-10-22

    In addition to methylated cytosines (5-mCs), hydroxymethylcytosines (5-hmCs) are present in CpG dinucleotide-enriched regions and some transcription regulator binding sites. Unlike methylation, hydroxymethylation does not result in silencing of gene expression, and the most commonly used methods to study methylation, such as techniques based on restriction enzymatic digestion and/or bisulfite modification, are unable to distinguish between them. Genomic imprinting is a process of gene regulation where only one member of an allelic pair is expressed depending on the parental origin. Chromosome 11p15.5 has an imprinting control region (ICR2) that includes a differentially methylated region (KvDMR1) that guarantees parent-specific gene expression. The objective of the present study was to determine the presence of 5-hmC at the KvDMR1 in human placentas. We analyzed 16 third-trimester normal human placentas (chorionic villi). We compared two different methods based on real-time PCR after enzymatic digestion. The first method distinguished methylation from hydroxymethylation, while the other method did not. Unlike other methylation studies, subtle variations of methylation in ICRs could represent a drastic deregulation of the expression of imprinted genes, leading to important phenotypic consequences, and the presence of hydroxymethylation could interfere with the results of many studies. We observed agreement between the results of both methods, indicating the absence of hydroxymethylation at the KvDMR1 in third-trimester placentas. To the best of our knowledge, this is the first study describing the investigation of hydroxymethylation in human placenta using a genomic imprinting model.

  1. Placental hydroxymethylation vs methylation at the imprinting control region 2 on chromosome 11p15.5

    PubMed Central

    Magalhães, H.R.; Leite, S.B.P.; de Paz, C.C.P.; Duarte, G.; Ramos, E.S.

    2013-01-01

    In addition to methylated cytosines (5-mCs), hydroxymethylcytosines (5-hmCs) are present in CpG dinucleotide-enriched regions and some transcription regulator binding sites. Unlike methylation, hydroxymethylation does not result in silencing of gene expression, and the most commonly used methods to study methylation, such as techniques based on restriction enzymatic digestion and/or bisulfite modification, are unable to distinguish between them. Genomic imprinting is a process of gene regulation where only one member of an allelic pair is expressed depending on the parental origin. Chromosome 11p15.5 has an imprinting control region (ICR2) that includes a differentially methylated region (KvDMR1) that guarantees parent-specific gene expression. The objective of the present study was to determine the presence of 5-hmC at the KvDMR1 in human placentas. We analyzed 16 third-trimester normal human placentas (chorionic villi). We compared two different methods based on real-time PCR after enzymatic digestion. The first method distinguished methylation from hydroxymethylation, while the other method did not. Unlike other methylation studies, subtle variations of methylation in ICRs could represent a drastic deregulation of the expression of imprinted genes, leading to important phenotypic consequences, and the presence of hydroxymethylation could interfere with the results of many studies. We observed agreement between the results of both methods, indicating the absence of hydroxymethylation at the KvDMR1 in third-trimester placentas. To the best of our knowledge, this is the first study describing the investigation of hydroxymethylation in human placenta using a genomic imprinting model. PMID:24270911

  2. Identification of the methylation preference region in heterogeneous nuclear ribonucleoprotein K by protein arginine methyltransferase 1 and its implication in regulating nuclear/cytoplasmic distribution

    SciTech Connect

    Chang, Yuan-I; Hsu, Sheng-Chieh; Chau, Gar-Yang; Huang, Chi-Ying F.; Sung, Jung-Sung; Hua, Wei-Kai; Lin, Wey-Jinq

    2011-01-21

    Research highlights: {yields} Verifying by direct methylation assay the substrate sites of PRMT1 in the hnRNP K protein. {yields} Identifying the preferred PMRT1 methylation regions in hnRNP K by kinetic analysis. {yields} Linking methylation in regulating nuclear localization of hnRNP K. -- Abstract: Protein arginine methylation plays crucial roles in numerous cellular processes. Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a multi-functional protein participating in a variety of cellular functions including transcription and RNA processing. HnRNP K is methylated at multiple sites in the glycine- and arginine-rich (RGG) motif. Using various RGG domain deletion mutants of hnRNP K as substrates, here we show by direct methylation assay that protein arginine methyltransferase 1 (PRMT1) methylated preferentially in a.a. 280-307 of the RGG motif. Kinetic analysis revealed that deletion of a.a. 280-307, but not a.a. 308-327, significantly inhibited rate of methylation. Importantly, nuclear localization of hnRNP K was significantly impaired in mutant hnRNP K lacking the PRMT1 methylation region or upon pharmacological inhibition of methylation. Together our results identify preferred PRMT1 methylation sequences of hnRNP K by direct methylation assay and implicate a role of arginine methylation in regulating intracellular distribution of hnRNP K.

  3. Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies

    PubMed Central

    Prischi, Filippo

    2017-01-01

    Abstract Methylation of cytosine is an epigenetic mark involved in the regulation of transcription, usually associated with transcriptional repression. In mammals, methylated cytosines are found predominantly in CpGs but in plants non-CpG methylation (in the CpHpG or CpHpH contexts, where H is A, C or T) is also present and is associated with the transcriptional silencing of transposable elements. In addition, CpG methylation is found in coding regions of active genes. In the absence of the demethylase of lysine 9 of histone 3 (IBM1), a subset of body-methylated genes acquires non-CpG methylation. This was shown to alter their expression and affect plant development. It is not clear why only certain body-methylated genes gain non-CpG methylation in the absence of IBM1 and others do not. Here we describe a link between CpG methylation and the establishment of methylation in the CpHpG context that explains the two classes of body-methylated genes. We provide evidence that external cytosines of CpCpG sites can only be methylated when internal cytosines are methylated. CpCpG sites methylated in both cytosines promote spreading of methylation in the CpHpG context in genes protected by IBM1. In contrast, CpCpG sites remain unmethylated in IBM1-independent genes and do not promote spread of CpHpG methylation. PMID:28053115

  4. Alteration of methylation status in the ATXN3 gene promoter region is linked to the SCA3/MJD.

    PubMed

    Wang, Chunrong; Peng, Huirong; Li, Jiada; Ding, Dongxue; Chen, Zhao; Long, Zhe; Peng, Yun; Zhou, Xin; Ye, Wei; Li, Kai; Xu, Qian; Ai, Sanxi; Song, Chengyuan; Weng, Ling; Qiu, Rong; Xia, Kun; Tang, Beisha; Jiang, Hong

    2017-05-01

    DNA methylation has been acknowledged as one of the key epigenetic mechanisms involved in the regulation of gene expression and genomic functions. Alteration of the DNA methylation level has been linked to modification of the disease progression and instability regulation of certain disease-causing repeats in neurodegenerative diseases. In this study, blood samples collected from spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD) patients versus control were used to explore the potential link of DNA methylation levels at ATXN3 gene promoter to the pathogenesis of SCA3/MJD. We found that the methylation levels in the ATXN3 promoter were significantly higher in SCA3/MJD patients relative to the controls. Furthermore, higher methylation levels were detected in the SCA3/MJD patients with earlier age at onset and the families with an intergenerational CAG repeats instability. In addition, the first CpG island of the ATXN3 promoter served as the main regulation region of DNA methylation. These findings suggested that an epigenetic change may contribute to the pathogenesis of the SCA3/MJD and provide potential therapeutic targets for CAG repeats-based diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Methylation of BRCA1 promoter region is associated with unfavorable prognosis in women with early-stage breast cancer.

    PubMed

    Hsu, Nicholas C; Huang, Ya-Fang; Yokoyama, Kazunari K; Chu, Pei-Yi; Chen, Fang-Ming; Hou, Ming-Feng

    2013-01-01

    BRCA1-associated breast cancers are associated with particular features such as early onset, poor histological differentiation, and hormone receptor negativity. Previous studies conducted in Taiwanese population showed that the mutation of BRCA1 gene does not play a significant role in the occurrence of breast cancer. The present study explored methylation of BRCA1 promoter and its relationship to clinical features and outcome in Taiwanese breast cancer patients. Tumor specimens from a cohort of 139 early-stage breast cancer patients were obtained during surgery before adjuvant treatment for DNA extraction. Methylation of BRCA1 promoter region was determined by methylation-specific PCR and the results were related to clinical features and outcome of patients using statistical analysis. Methylation of the BRCA1 promoter was detected in 78 (56%) of the 139 tumors. Chi-square analysis indicated that BRCA1 promoter methylation correlated significantly with triple-negative (ER-/PR-/HER2-) status of breast cancer patients (p = 0.041). The Kaplan-Meier method showed that BRCA1 promoter methylation was significantly associated with poor overall survival (p = 0.026) and disease-free survival (p = 0.001). Multivariate analysis which incorporated variables of patients' age, tumor size, grade, and lymph node metastasis revealed that BRCA1 promoter methylation was associated with overall survival (p = 0.027; hazard ratio, 16.38) and disease-free survival (p = 0.003; hazard ratio, 12.19) [corrected].Our findings underscore the clinical relevance of the methylation of BRCA1 promoter in Taiwanese patients with early-stage breast cancer.

  6. Differential DNA Methylation Regions in Adult Human Sperm following Adolescent Chemotherapy: Potential for Epigenetic Inheritance

    PubMed Central

    Shnorhavorian, Margarett; Schwartz, Stephen M.; Stansfeld, Barbara; Sadler-Riggleman, Ingrid; Beck, Daniel

    2017-01-01

    Background The potential that adolescent chemotherapy can impact the epigenetic programming of the germ line to influence later life adult fertility and promote epigenetic inheritance was investigated. Previous studies have demonstrated a number of environmental exposures such as abnormal nutrition and toxicants can promote sperm epigenetic changes that impact offspring. Methods Adult males approximately ten years after pubertal exposure to chemotherapy were compared to adult males with no previous exposure. Sperm were collected to examine differential DNA methylation regions (DMRs) between the exposed and control populations. Gene associations and correlations to genetic mutations (copy number variation) were also investigated. Methods and Findings A signature of statistically significant DMRs was identified in the chemotherapy exposed male sperm. The DMRs, termed epimutations, were found in CpG desert regions of primarily 1 kilobase size. Observations indicate adolescent chemotherapy exposure can promote epigenetic alterations that persist in later life. Conclusions This is the first observation in humans that an early life chemical exposure can permanently reprogram the spermatogenic stem cell epigenome. The germline (i.e., sperm) epimutations identified suggest chemotherapy has the potential to promote epigenetic inheritance to the next generation. PMID:28146567

  7. CpG methylation at GATA elements in the regulatory region of CCR3 positively correlates with CCR3 transcription.

    PubMed

    Uhm, Tae Gi; Lee, Seol Kyung; Kim, Byung Soo; Kang, Jin Hyun; Park, Choon Sik; Rhim, Tai Youn; Chang, Hun Soo; Kim, Do Jin; Chung, Il Yup

    2012-04-30

    DNA methylation may regulate gene expression by restricting the access of transcription factors. We have previously demonstrated that GATA-1 regulates the transcription of the CCR3 gene by dynamically interacting with both positively and negatively acting GATA elements of high affinity binding in the proximal promoter region including exon 1. Exon 1 has three CpG sites, two of which are positioned at the negatively acting GATA elements. We hypothesized that the methylation of these two CpGs sites might preclude GATA-1 binding to the negatively acting GATA elements and, as a result, increase the availability of GATA-1 to the positively acting GATA element, thereby contributing to an increase in GATA-1-mediated transcription of the gene. To this end, we determined the methylation of the three CpG sites by bisulfate pyrosequencing in peripheral blood eosinophils, cord blood (CB)-derived eosinophils, PBMCs, and cell lines that vary in CCR3 mRNA expression. Our results demonstrated that methylation of CpG sites at the negatively acting GATA elements severely reduced GATA-1 binding and augmented transcription activity in vitro. In agreement, methylation of these CpG sites positively correlated with CCR3 mRNA expression in the primary cells and cell lines examined. Interestingly, methylation patterns of these three CpG sites in CB-derived eosinophils mostly resembled those in peripheral blood eosinophils. These results suggest that methylation of CpG sites at the GATA elements in the regulatory regions fine-tunes CCR3 transcription.

  8. Methylation of Promoter Regions of Genes of the Human Intrauterine Renin Angiotensin System and Their Expression

    PubMed Central

    Sykes, Shane D.; Mitchell, Carolyn; Pringle, Kirsty G.; Wang, Yu; Zakar, Tamas; Lumbers, Eugenie R.

    2015-01-01

    The intrauterine renin angiotensin system (RAS) is implicated in placentation and labour onset. Here we investigate whether promoter methylation of RAS genes changes with gestation or labour and if it affects gene expression. Early gestation amnion and placenta were studied, as were term amnion, decidua, and placenta collected before labour (at elective caesarean section) or after spontaneous labour and delivery. The expression and degree of methylation of the prorenin receptor (ATP6AP2), angiotensin converting enzyme (ACE), angiotensin II type 1 receptor (AGTR1), and two proteases that can activate prorenin (kallikrein, KLK1, and cathepsin D, CTSD) were measured by qPCR and a DNA methylation array. There was no effect of gestation or labour on the methylation of RAS genes and CTSD. Amnion and decidua displayed strong correlations between the percent hypermethylation of RAS genes and CTSD, suggestive of global methylation. There were no correlations between the degree of methylation and mRNA abundance of any genes studied. KLK1 was the most methylated gene and the proportion of hypermethylated KLK1 alleles was lower in placenta than decidua. The presence of intermediate methylated alleles of KLK1 in early gestation placenta and in amnion after labour suggests that KLK1 methylation is uniquely dynamic in these tissues. PMID:25918528

  9. Brain region-specific methylation in the promoter of the murine oxytocin receptor gene is involved in its expression regulation.

    PubMed

    Harony-Nicolas, Hala; Mamrut, Shimrat; Brodsky, Leonid; Shahar-Gold, Hadar; Barki-Harrington, Liza; Wagner, Shlomo

    2014-01-01

    Oxytocin is a nine amino acid neuropeptide that is known to play a critical role in fetal expulsion and breast-feeding, and has been recently implicated in mammalian social behavior. The actions of both central and peripheral oxytocin are mediated through the oxytocin receptor (Oxtr), which is encoded by a single gene. In contrast to the highly conserved expression of oxytocin in specific hypothalamic nuclei, the expression of its receptor in the brain is highly diverse among different mammalian species or even within individuals of the same species. The diversity in the pattern of brain Oxtr expression among mammals is thought to contribute to the broad range of social systems and organizations. Yet, the mechanisms underlying this diversity are poorly understood. DNA methylation is a major epigenetic mechanism that regulates gene transcription, and has been linked to reduced expression levels of the Oxtr in individuals with autism. Here we hypothesize that DNA methylation is involved in the expression regulation of Oxtr in the mouse brain. By combining bisulfite DNA conversion and Next-Generation Sequencing we found that specific CpG sites are differentially methylated between distinct brain regions expressing different levels of Oxtr mRNA. Some of these CpG sites are located within putative binding sites of transcription factors known to regulate Oxtr expression, including estrogen receptor α (ERα) and SP1. Specifically, methylation of the SP1 site was found to positively correlate with Oxtr expression. Furthermore, we revealed that the methylation levels of these sites in the various brain regions predict the relationship between ERα and Oxtr mRNA levels. Collectively, our results suggest that brain region-specific expression of the mouse Oxtr gene is epigenetically regulated by DNA methylation of its promoter. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Clinicopathologic Risk Factor Distributions for MLH1 Promoter Region Methylation in CIMP-Positive Tumors.

    PubMed

    Levine, A Joan; Phipps, Amanda I; Baron, John A; Buchanan, Daniel D; Ahnen, Dennis J; Cohen, Stacey A; Lindor, Noralane M; Newcomb, Polly A; Rosty, Christophe; Haile, Robert W; Laird, Peter W; Weisenberger, Daniel J

    2016-01-01

    The CpG island methylator phenotype (CIMP) is a major molecular pathway in colorectal cancer. Approximately 25% to 60% of CIMP tumors are microsatellite unstable (MSI-H) due to DNA hypermethylation of the MLH1 gene promoter. Our aim was to determine if the distributions of clinicopathologic factors in CIMP-positive tumors with MLH1 DNA methylation differed from those in CIMP-positive tumors without DNA methylation of MLH1. We assessed the associations between age, sex, tumor-site, MSI status BRAF and KRAS mutations, and family colorectal cancer history with MLH1 methylation status in a large population-based sample of CIMP-positive colorectal cancers defined by a 5-marker panel using unconditional logistic regression to assess the odds of MLH1 methylation by study variables. Subjects with CIMP-positive tumors without MLH1 methylation were significantly younger, more likely to be male, and more likely to have distal colon or rectal primaries and the MSI-L phenotype. CIMP-positive MLH1-unmethylated tumors were significantly less likely than CIMP-positive MLH1-methylated tumors to harbor a BRAF V600E mutation and significantly more likely to harbor a KRAS mutation. MLH1 methylation was associated with significantly better overall survival (HR, 0.50; 95% confidence interval, 0.31-0.82). These data suggest that MLH1 methylation in CIMP-positive tumors is not a completely random event and implies that there are environmental or genetic determinants that modify the probability that MLH1 will become methylated during CIMP pathogenesis. MLH1 DNA methylation status should be taken into account in etiologic studies. ©2015 American Association for Cancer Research.

  11. Clinicopathological risk factor distributions for MLH1 promoter region methylation in CIMP positive tumors

    PubMed Central

    Levine, A. Joan; Phipps, Amanda I.; Baron, John A.; Buchanan, Daniel D.; Ahnen, Dennis J.; Cohen, Stacey A.; Lindor, Noralane M.; Newcomb, Polly A.; Rosty, Christophe; Haile, Robert W.; Laird, Peter W.; Weisenberger, Daniel J.

    2015-01-01

    Background The CpG Island Methylator Phenotype (CIMP) is a major molecular pathway in colorectal cancer (CRC). Approximately 25% to 60% of CIMP tumors are microsatellite unstable (MSI-H) due to DNA hypermethylation of the MLH1 gene promoter. Our aim was to determine if the distributions of clinicopathologic factors in CIMP-positive tumors with MLH1 DNA methylation differed from those in CIMP-positive tumors without DNA methylation of MLH1. Methods We assessed the associations between age, sex, tumor-site, MSI status BRAF and KRAS mutations and family CRC history with MLH1 methylation status in a large population-based sample of CIMP-positive CRCs defined by a 5-marker panel using unconditional logistic regression to assess the odds of MLH1 methylation by study variables. Results Subjects with CIMP-positive tumors without MLH1 methylation were significantly younger, more likely to be male, more likely to have distal colon or rectal primaries and the MSI-L phenotype. CIMP-positive MLH1-unmethylated tumors were significantly less likely than CIMP-positive MLH1-methylated tumors to harbor a BRAF V600E mutation and significantly more likely to harbor a KRAS mutation. MLH1 methylation was associated with significantly better overall survival (HR=0.50; 95% Confidence Interval (0.31, 0.82)). Conclusions These data suggest that MLH1 methylation in CIMP-positive tumors is not a completely random event and implies that there are environmental or genetic determinants that modify the probability that MLH1 will become methylated during CIMP pathogenesis. Impact MLH1 DNA methylation status should be taken into account in etiologic studies. PMID:26512054

  12. Case Report: Molecular Confirmation of Lobomycosis in an Italian Traveler Acquired in the Amazon Region of Venezuela.

    PubMed

    Beltrame, Anna; Danesi, Patrizia; Farina, Claudio; Orza, Pierantonio; Perandin, Francesca; Zanardello, Claudia; Rodari, Paola; Staffolani, Silvia; Bisoffi, Zeno

    2017-09-25

    Lobomycosis is a chronic skin mycosis endemic in Amazon regions characterized by chronic nodular or keloidal lesions caused by Lacazia loboi, an uncultivable fungus. Imported cases in nonendemic countries are rare and diagnosed after years. We describe a case of lobomycosis in a healthy 55-year-old Italian traveler who had acquired the infection during 5-day-honeymoon in the Amazon region of Venezuela in 1999. Several weeks after return, he recalled pruritus and papular skin lesions on the left lower limb, subsequently evolving to a plaque-like lesion. Blastomycosis and cryptococcosis were hypothesized based on microscopic morphology of yeast-like bodies found in three consecutive biopsies, although fungal cultures were always negative. In 2016, exfoliative cytology and a biopsy specimen examination showed round yeast-like organisms (6-12 μm), isolated or in a chain, connected by short tubular projections fulfilling the morphologic diagnostic criteria of Lacazia spp. The microscopic diagnosis was confirmed by molecular identification.

  13. Epigenetics in Schizophrenia: A Pilot Study of Global DNA Methylation in Different Brain Regions Associated with Higher Cognitive Functions

    PubMed Central

    Alelú-Paz, Raúl; Carmona, Francisco J.; Sanchez-Mut, José V.; Cariaga-Martínez, Ariel; González-Corpas, Ana; Ashour, Nadia; Orea, Maria J.; Escanilla, Ana; Monje, Alfonso; Guerrero Márquez, Carmen; Saiz-Ruiz, Jerónimo; Esteller, Manel; Ropero, Santiago

    2016-01-01

    Attempts to discover genes that are involved in the pathogenesis of major psychiatric disorders have been frustrating and often fruitless. Concern is building about the need to understand the complex ways in which nature and nurture interact to produce mental illness. We analyze the epigenome in several brain regions from schizophrenic patients with severe cognitive impairment using high-resolution (450K) DNA methylation array. We identified 139 differentially methylated CpG sites included in known and novel candidate genes sequences as well as in and intergenic sequences which functions remain unknown. We found that altered DNA methylation is not restricted to a particular region, but includes others such as CpG shelves and gene bodies, indicating the presence of different DNA methylation signatures depending on the brain area analyzed. Our findings suggest that epimutations are not relatables between different tissues or even between tissues' regions, highlighting the need to adequately study brain samples to obtain reliable data concerning the epigenetics of schizophrenia. PMID:27746755

  14. Epigenetics in Schizophrenia: A Pilot Study of Global DNA Methylation in Different Brain Regions Associated with Higher Cognitive Functions.

    PubMed

    Alelú-Paz, Raúl; Carmona, Francisco J; Sanchez-Mut, José V; Cariaga-Martínez, Ariel; González-Corpas, Ana; Ashour, Nadia; Orea, Maria J; Escanilla, Ana; Monje, Alfonso; Guerrero Márquez, Carmen; Saiz-Ruiz, Jerónimo; Esteller, Manel; Ropero, Santiago

    2016-01-01

    Attempts to discover genes that are involved in the pathogenesis of major psychiatric disorders have been frustrating and often fruitless. Concern is building about the need to understand the complex ways in which nature and nurture interact to produce mental illness. We analyze the epigenome in several brain regions from schizophrenic patients with severe cognitive impairment using high-resolution (450K) DNA methylation array. We identified 139 differentially methylated CpG sites included in known and novel candidate genes sequences as well as in and intergenic sequences which functions remain unknown. We found that altered DNA methylation is not restricted to a particular region, but includes others such as CpG shelves and gene bodies, indicating the presence of different DNA methylation signatures depending on the brain area analyzed. Our findings suggest that epimutations are not relatables between different tissues or even between tissues' regions, highlighting the need to adequately study brain samples to obtain reliable data concerning the epigenetics of schizophrenia.

  15. Association between DNA Methylation of the BDNF Promoter Region and Clinical Presentation in Alzheimer's Disease

    PubMed Central

    Nagata, Tomoyuki; Kobayashi, Nobuyuki; Ishii, Jumpei; Shinagawa, Shunichiro; Nakayama, Ritsuko; Shibata, Nobuto; Kuerban, Bolati; Ohnuma, Tohru; Kondo, Kazuhiro; Arai, Heii; Yamada, Hisashi; Nakayama, Kazuhiko

    2015-01-01

    Background/Aims In the present study, we examined whether DNA methylation of the brain-derived neurotrophic factor (BDNF) promoter is associated with the manifestation and clinical presentation of Alzheimer's disease (AD). Methods Of 20 patients with AD and 20 age-matched normal controls (NCs), the DNA methylation of the BDNF promoter (measured using peripheral blood samples) was completely analyzed in 12 patients with AD and 6 NCs. The resulting methylation levels were compared statistically. Next, we investigated the correlation between the DNA methylation levels and the clinical presentation of AD. Results The total methylation ratio (in %) of the 20 CpG sites was significantly higher in the AD patients (5.08 ± 5.52%) than in the NCs (2.09 ± 0.81%; p < 0.05). Of the 20 CpG sites, the methylation level at the CpG4 site was significantly higher in the AD subjects than in the NCs (p < 0.05). Moreover, the methylation level was significantly and negatively correlated with some neuropsychological test subscores (registration, recall, and prehension behavior scores; p < 0.05). Conclusion These results suggest that the DNA methylation of the BDNF promoter may significantly influence the manifestation of AD and might be associated with its neurocognitive presentation. PMID:25873928

  16. CALCULATED MOLECULAR STRUCTURES AND POTENTIAL ENERGY FUNCTIONS OF PAHS WITH METHYL CROWDING IN THE BAY REGION AND THEIR METABOLITES: COMPARISON TO EXPERIMENTAL STRUCTURES

    EPA Science Inventory

    Calculated molecular structures and potential energy functions ofP AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures

    PAHs with methyl group substitution near a bay region represent a class of chemicals associated with ...

  17. CALCULATED MOLECULAR STRUCTURES AND POTENTIAL ENERGY FUNCTIONS OF PAHS WITH METHYL CROWDING IN THE BAY REGION AND THEIR METABOLITES: COMPARISON TO EXPERIMENTAL STRUCTURES

    EPA Science Inventory

    Abstract Title: Calculated molecular structures and potential energy functions of P AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures.

    Abstract:
    PAHs with methyl group substitution near a bay region represent a cl...

  18. CALCULATED MOLECULAR STRUCTURES AND POTENTIAL ENERGY FUNCTIONS OF PAHS WITH METHYL CROWDING IN THE BAY REGION AND THEIR METABOLITES: COMPARISON TO EXPERIMENTAL STRUCTURES

    EPA Science Inventory

    Calculated molecular structures and potential energy functions ofP AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures

    PAHs with methyl group substitution near a bay region represent a class of chemicals associated with ...

  19. Differentially Methylated Region-Representational Difference Analysis (DMR-RDA): A Powerful Method to Identify DMRs in Uncharacterized Genomes.

    PubMed

    Sasheva, Pavlina; Grossniklaus, Ueli

    2017-01-01

    Over the last years, it has become increasingly clear that environmental influences can affect the epigenomic landscape and that some epigenetic variants can have heritable, phenotypic effects. While there are a variety of methods to perform genome-wide analyses of DNA methylation in model organisms, this is still a challenging task for non-model organisms without a reference genome. Differentially methylated region-representational difference analysis (DMR-RDA) is a sensitive and powerful PCR-based technique that isolates DNA fragments that are differentially methylated between two otherwise identical genomes. The technique does not require special equipment and is independent of prior knowledge about the genome. It is even applicable to genomes that have high complexity and a large size, being the method of choice for the analysis of plant non-model systems.

  20. Regional development of glutamate-N-methyl-D-aspartate receptor sites in asphyxiated newborn infants.

    PubMed

    Andersen, D L; Tannenberg, A E; Burke, C J; Dodd, P R

    1998-04-01

    The N-methyl-D-aspartate (NMDA) subclass of glutamate receptors was examined in newborn infants dying between 25 weeks' gestation and term, either from acute cerebral hypoxia, or from other noncerebral conditions incompatible with life. Frontal, occipital, temporal, and motor cortex tissue samples were obtained at autopsy (post mortem delay: median, 45.9 hr; range, 24-96 hr) and frozen for subsequent [3H]MK801 homogenate binding assays. Whereas no significant variation was observed in ligand affinity (KD), in all cases receptor density (BMAX) increased with gestational age, in occipital cortex (27 weeks, BMAX = 222 +/- 44 fmol x mg protein(-1); 39 weeks, 439 +/- 42 fmol x mg protein[-1]), but not in motor or temporal cortex. The gestational-age increase also occurred in control frontal cortex (27 weeks, 284 +/- 80; 39 weeks, 567 +/- 40 fmol x mg protein[-1]), but was significantly less marked in frontal cortex in hypoxia cases (27 weeks, 226 +/- 90; 39 weeks, 326 +/- 47 fmol x mg protein[-1]). In all cortical areas except temporal, the maximal response to glutamate did not vary across case groups. Hypoxia cases showed an increased response to glutamate enhancement selectively in temporal cortex. Binding site density did not correlate with degree of hypoxia as assessed pathologically, suggesting that receptor differences preceded the hypoxic episode. Regional differences in glutamate-NMDA receptor sites may underlie increased vulnerability to hypoxia at birth.

  1. Exposure of mouse embryos to ethanol during preimplantation development: effect on DNA methylation in the h19 imprinting control region.

    PubMed

    Haycock, Philip C; Ramsay, Michéle

    2009-10-01

    In the present study, it was hypothesized that disruption of imprinting control in the H19/Igf2 domain may be a mechanism of ethanol-induced growth retardation-a key clinical feature of the fetal alcohol spectrum disorders (FASD). To test this prediction, genomic bisulphite sequencing was carried out on 473 bp of the H19 imprinting control region in DNA obtained from midgestation F(1) hybrid mouse embryos (C57BL/6 x Mus musculus castaneus) exposed to ethanol during preimplantation development. Although ethanol-exposed placentae and embryos were severely growth retarded in comparison with saline-treated controls, DNA methylation at paternal and maternal alleles was unaffected in embryos. However, paternal alleles were significantly less methylated in ethanol-treated placentae in comparison with saline-treated controls. Partial correlations suggested that the relationship between ethanol and placental weight partly depended on DNA methylation at a CCCTC-binding factor site on the paternal allele in placentae, suggesting a novel mechanism of ethanol-induced growth retardation. In contrast, partial correlations suggested that embryo growth retardation was independent of placental growth retardation. Relaxation of allele-specific DNA methylation in control placentae in comparison with control embryos was also observed, consistent with a model of imprinting in which 1) regulation of allele-specific DNA methylation in the placenta depends on a stochastic interplay between silencer and enhancer chromatin assembly factors and 2) imprinting control mechanisms in the embryo are more robust to environmental perturbations.

  2. High fructose consumption induces DNA methylation at PPARα and CPT1A promoter regions in the rat liver

    SciTech Connect

    Ohashi, Koji; Munetsuna, Eiji; Yamada, Hiroya; Ando, Yoshitaka; Yamazaki, Mirai; Taromaru, Nao; Nagura, Ayuri; Ishikawa, Hiroaki; Suzuki, Koji; Teradaira, Ryoji; Hashimoto, Shuji

    2015-12-04

    DNA methylation status is affected by environmental factors, including nutrition. Fructose consumption is considered a risk factor for the conditions that make up metabolic syndrome such as dyslipidemia. However, the pathogenetic mechanism by which fructose consumption leads to metabolic syndrome is unclear. Based on observations that epigenetic modifications are closely related to induction of metabolic syndrome, we hypothesized that fructose-induced metabolic syndrome is caused by epigenetic alterations. Male SD rats were designated to receive water or 20% fructose solution for 14 weeks. mRNA levels for peroxisome proliferator-activated receptor alpha (PPARα) and carnitine palmitoyltransferase 1A (CPT1A) was analyzed using Real-time PCR. Restriction digestion and real-time PCR (qAMP) was used for the analysis of DNA methylation status. Hepatic lipid accumulation was also observed by fructose intake. Fructose feeding also significantly decreased mRNA levels for PPARα and CPT1A. qAMP analysis demonstrated the hypermethylation of promoter regions of PPARα and CTP1A genes. Fructose-mediated attenuated gene expression may be mediated by alterations of DNA methylation status, and pathogenesis of metabolic syndrome induced by fructose relates to DNA methylation status. - Highlights: • No general consensus has been reached regarding the molecular mechanisms of the pathogenesis of fructose-induced diseases. • Significant increase in hepatic total methylation level was observed after fructose-supplemented feeding. • Fructose feeding significantly decreased mRNA levels for PPARα and CPT1A. • qAMP analysis demonstrated the hypermethylation of promoter regions of PPARα and CTP1A genes. • Fructose-mediated attenuated gene expression may be mediated by alterations of DNA methylation status in rat liver.

  3. Optimal vaccination and bednet maintenance for the control of malaria in a region with naturally acquired immunity.

    PubMed

    Prosper, Olivia; Ruktanonchai, Nick; Martcheva, Maia

    2014-07-21

    Following over two decades of research, the malaria vaccine candidate RTS,S has reached the final stages of vaccine trials, demonstrating an efficacy of roughly 50% in young children. Regions with high malaria prevalence tend to have high levels of naturally acquired immunity (NAI) to severe malaria; NAI is caused by repeated exposure to infectious bites and results in large asymptomatic populations. To address concerns about how these vaccines will perform in regions with existing NAI, we developed a simple malaria model incorporating vaccination and NAI. Typically, if the basic reproduction number (R0) for malaria is greater than unity, the disease will persist; otherwise, the disease will become extinct. However, analysis of this model revealed that NAI, compounded by a subpopulation with only partial protection to malaria, may render vaccination efforts ineffective and potentially detrimental to malaria control, by increasing R0 and increasing the likelihood of malaria persistence even when R0<1. The likelihood of this scenario increases when non-immune infected individuals are treated disproportionately compared with partially immune individuals - a plausible scenario since partially immune individuals are more likely to be asymptomatically infected. Consequently, we argue that active case-detection of asymptomatic infections is a critical component of an effective malaria control program. We then investigated optimal vaccination and bednet control programs under two endemic settings with varying levels of naturally acquired immunity: a typical setting under which prevalence decays when R0<1, and a setting in which subthreshold endemic equilibria exist. A qualitative comparison of the optimal control results under the first setting revealed that the optimal policy differs depending on whether the goal is to reduce total morbidity, or to reduce clinical infections. Furthermore, this comparison dictates that control programs should place less effort in

  4. DNA-methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control

    PubMed Central

    Betts, Matthew J.; Carrillo-de-Santa-Pau, Enrique; Doose, Gero; Gutwein, Jana; Richter, Julia; Hovestadt, Volker; Huang, Bingding; Rico, Daniel; Jühling, Frank; Kolarova, Julia; Lu, Qianhao; Otto, Christian; Wagener, Rabea; Arnolds, Judith; Burkhardt, Birgit; Claviez, Alexander; Drexler, Hans G.; Eberth, Sonja; Eils, Roland; Flicek, Paul; Haas, Siegfried; Humme, Michael; Karsch, Dennis; Kerstens, Hinrik H.D.; Klapper, Wolfram; Kreuz, Markus; Lawerenz, Chris; Lenzek, Dido; Loeffler, Markus; López, Cristina; MacLeod, Roderick A.F.; Martens, Joost H.A.; Kulis, Marta; Martín-Subero, José Ignacio; Möller, Peter; Nage, Inga; Picelli, Simone; Vater, Inga; Rohde, Marius; Rosenstiel, Philip; Rosolowski, Maciej; Russell, Robert B.; Schilhabel, Markus; Schlesner, Matthias; Stadler, Peter F.; Szczepanowski, Monika; Trümper, Lorenz; Stunnenberg, Hendrik G.; Küppers, Ralf; Ammerpohl, Ole; Lichter, Peter; Siebert, Reiner; Hoffmann, Steve; Radlwimmer, Bernhard

    2017-01-01

    In spite of both having features of germinal center B-cells, Burkitt lymphomas and follicular lymphomas are biologically and clinically quite diverse. We here performed whole genome bisulfite, genome and transcriptome sequencing from 13 IG-MYC-translocation positive Burkitt lymphoma, 9 BCL2-translocation positive follicular lymphoma and four normal germinal center B-cell samples. Comparison of Burkitt and follicular lymphoma samples revealed differential methylation of intragenic regions that strongly correlated with expression of associated genes, e.g. genes active in germinal center dark zone and light zone B-cells. Integrative pathway analyses of regions differentially methylated between Burkitt and follicular lymphoma implicated DNA methylation to cooperate with somatic mutation of sphingosine-phosphate signaling, as well as the TCF3/ID3 and SWI/SNF complexes in a large fraction of Burkitt lymphomas. Taken together, our results demonstrate a tight connection between somatic mutation, DNA methylation and transcriptional control in key B-cell pathways deregulated differentially between Burkitt and other germinal center B-cell lymphomas. PMID:26437030

  5. A methylation status analysis of the apomixis-specific region in Paspalum spp. suggests an epigenetic control of parthenogenesis.

    PubMed

    Podio, Maricel; Cáceres, Maria E; Samoluk, Sergio S; Seijo, José G; Pessino, Silvina C; Ortiz, Juan Pablo A; Pupilli, Fulvio

    2014-12-01

    Apomixis, a clonal plant reproduction by seeds, is controlled in Paspalum spp. by a single locus which is blocked in terms of recombination. Partial sequence analysis of the apomixis locus revealed structural features of heterochromatin, namely the presence of repetitive elements, gene degeneration, and de-regulation. To test the epigenetic control of apomixis, a study on the distribution of cytosine methylation at the apomixis locus and the effect of artificial DNA demethylation on the mode of reproduction was undertaken in two apomictic Paspalum species. The 5-methylcytosine distribution in the apomixis-controlling genomic region was studied in P. simplex by methylation-sensitive restriction fragment length polymorphism (RFLP) analysis and in P. notatum by fluorescene in situ hybridization (FISH). The effect of DNA demethylation was studied on the mode of reproduction of P. simplex by progeny test analysis of apomictic plants treated with the demethylating agent 5'-azacytidine. A high level of cytosine methylation was detected at the apomixis-controlling genomic region in both species. By analysing a total of 374 open pollination progeny, it was found that artificial demethylation had little or no effect on apospory, whereas it induced a significant depression of parthenogenesis. The results suggested that factors controlling repression of parthenogenesis might be inactivated in apomictic Paspalum by DNA methylation.

  6. LMethyR-SVM: Predict Human Enhancers Using Low Methylated Regions based on Weighted Support Vector Machines

    PubMed Central

    Xu, Jingting; Hu, Hong; Dai, Yang

    2016-01-01

    Background The identification of enhancers is a challenging task. Various types of epigenetic information including histone modification have been utilized in the construction of enhancer prediction models based on a diverse panel of machine learning schemes. However, DNA methylation profiles generated from the whole genome bisulfite sequencing (WGBS) have not been fully explored for their potential in enhancer prediction despite the fact that low methylated regions (LMRs) have been implied to be distal active regulatory regions. Method In this work, we propose a prediction framework, LMethyR-SVM, using LMRs identified from cell-type-specific WGBS DNA methylation profiles and a weighted support vector machine learning framework. In LMethyR-SVM, the set of cell-type-specific LMRs is further divided into three sets: reliable positive, like positive and likely negative, according to their resemblance to a small set of experimentally validated enhancers in the VISTA database based on an estimated non-parametric density distribution. Then, the prediction model is obtained by solving a weighted support vector machine. Results We demonstrate the performance of LMethyR-SVM by using the WGBS DNA methylation profiles derived from the human embryonic stem cell type (H1) and the fetal lung fibroblast cell type (IMR90). The predicted enhancers are highly conserved with a reasonable validation rate based on a set of commonly used positive markers including transcription factors, p300 binding and DNase-I hypersensitive sites. In addition, we show evidence that the large fraction of the LMethyR-SVM predicted enhancers are not predicted by ChromHMM in H1 cell type and they are more enriched for the FANTOM5 enhancers. Conclusion Our work suggests that low methylated regions detected from the WGBS data are useful as complementary resources to histone modification marks in developing models for the prediction of cell-type-specific enhancers. PMID:27662487

  7. Functional DNA methylation in a transcript specific 3′UTR region of TrkB associates with suicide

    PubMed Central

    Maussion, Gilles; Yang, Jennie; Suderman, Matthew; Diallo, Alpha; Nagy, Corina; Arnovitz, Mitchell; Mechawar, Naguib; Turecki, Gustavo

    2014-01-01

    Previous studies indicate that a subgroup of suicide completers has low cortical brain expression levels of TrkB-T1, a TrkB gene transcript that is highly expressed in astrocytes. Epigenetic modifications, including methylation changes in the TrkB promoter, partially explain TrkB-T1 low expression levels in brain tissue from suicide completers. The aim of this study was to investigate whether methylation changes in other regions of the TrkB gene could also contribute to the significant downregulation of the TrkB-T1 transcript observed in the brain of suicide completers. Methylation levels were assessed on BA8/9 from suicide completers expressing low TrkB-T1 transcript levels and controls, using custom-made Agilent arrays tiling the whole TrkB gene. After statistical correction for multiple testing, five probes located in the TrkB-T1 3′UTR region were found hypermethylated in the frontal cortex of suicide completers. These results were validated for four CpGs spanning a 150 bp sequence by cloning and Sanger sequencing bisulfite treated DNA. We found a significant correlation between the methylation level at these four CpGs and TrkB-T1 expression in BA8/9. Site-specific hypermethylation on this 3′UTR sequence induced decreased luciferase activity in reporter gene cell assays. Site-specific differential methylation in the TrkB-T1 3′UTR region associates with functional changes in TrkB-T1 expression and may play a significant role in the important decrease of cortical TrkB-T1 expression observed among suicide completers. PMID:24802768

  8. Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population

    PubMed Central

    Yang, Tsun-Po; Pidsley, Ruth; Nisbet, James; Glass, Daniel; Mangino, Massimo; Zhai, Guangju; Zhang, Feng; Valdes, Ana; Shin, So-Youn; Dempster, Emma L.; Murray, Robin M.; Grundberg, Elin; Hedman, Asa K.; Nica, Alexandra; Small, Kerrin S.; Dermitzakis, Emmanouil T.; McCarthy, Mark I.; Mill, Jonathan; Spector, Tim D.; Deloukas, Panos

    2012-01-01

    Age-related changes in DNA methylation have been implicated in cellular senescence and longevity, yet the causes and functional consequences of these variants remain unclear. To elucidate the role of age-related epigenetic changes in healthy ageing and potential longevity, we tested for association between whole-blood DNA methylation patterns in 172 female twins aged 32 to 80 with age and age-related phenotypes. Twin-based DNA methylation levels at 26,690 CpG-sites showed evidence for mean genome-wide heritability of 18%, which was supported by the identification of 1,537 CpG-sites with methylation QTLs in cis at FDR 5%. We performed genome-wide analyses to discover differentially methylated regions (DMRs) for sixteen age-related phenotypes (ap-DMRs) and chronological age (a-DMRs). Epigenome-wide association scans (EWAS) identified age-related phenotype DMRs (ap-DMRs) associated with LDL (STAT5A), lung function (WT1), and maternal longevity (ARL4A, TBX20). In contrast, EWAS for chronological age identified hundreds of predominantly hyper-methylated age DMRs (490 a-DMRs at FDR 5%), of which only one (TBX20) was also associated with an age-related phenotype. Therefore, the majority of age-related changes in DNA methylation are not associated with phenotypic measures of healthy ageing in later life. We replicated a large proportion of a-DMRs in a sample of 44 younger adult MZ twins aged 20 to 61, suggesting that a-DMRs may initiate at an earlier age. We next explored potential genetic and environmental mechanisms underlying a-DMRs and ap-DMRs. Genome-wide overlap across cis-meQTLs, genotype-phenotype associations, and EWAS ap-DMRs identified CpG-sites that had cis-meQTLs with evidence for genotype–phenotype association, where the CpG-site was also an ap-DMR for the same phenotype. Monozygotic twin methylation difference analyses identified one potential environmentally-mediated ap-DMR associated with total cholesterol and LDL (CSMD1). Our results suggest that in a

  9. Regional brain structural dysmorphology in human immunodeficiency virus infection: effects of acquired immune deficiency syndrome, alcoholism, and age.

    PubMed

    Pfefferbaum, Adolf; Rosenbloom, Margaret J; Sassoon, Stephanie A; Kemper, Carol A; Deresinski, Stanley; Rohlfing, Torsten; Sullivan, Edith V

    2012-09-01

    Human immunodeficiency virus (HIV) infection and alcoholism each carries liability for disruption of brain structure and function integrity. Despite considerable prevalence of HIV-alcoholism comorbidity, few studies examined the potentially heightened burden of disease comorbidity. Participants were 342 men and women: 110 alcoholics, 59 with HIV infection, 65 with HIV infection and alcoholism, and 108 healthy control subjects. This design enabled examination of independent and combined effects of HIV infection and alcoholism along with other factors (acquired immune deficiency syndrome [AIDS]-defining events, hepatitis C infection, age) on regional brain volumes derived from T1-weighted magnetic resonance images. Brain volumes, expressed as Z scores corrected for intracranial volume and age, were measured in 20 tissue and 5 ventricular and sulcal regions. The most profound and consistent volume deficits occurred with alcohol use disorders, notable in the cortical mantle, insular and anterior cingulate cortices, thalamus, corpus callosum, and frontal sulci. The HIV-only group had smaller thalamic and larger frontal sulcal volumes than control subjects. HIV disease-related factors associated with greater volume abnormalities included CD4 cell count nadir, clinical staging, history of AIDS-defining events, infection age, and current age. Longer sobriety and less lifetime alcohol consumption were predictive of attenuated brain volume abnormalities in both alcohol groups. Having HIV infection with alcoholism and AIDS had an especially poor outcome on brain structures. That longer periods of sobriety and less lifetime alcohol consumption were predictive of attenuated brain volume abnormalities encourages the inclusion of alcohol recovery efforts in HIV/AIDS therapeutic settings. Copyright © 2012 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  10. Whole-Genome Bisulfite Sequencing of Human Pancreatic Islets Reveals Novel Differentially Methylated Regions in Type 2 Diabetes Pathogenesis.

    PubMed

    Volkov, Petr; Bacos, Karl; Ofori, Jones K; Esguerra, Jonathan Lou S; Eliasson, Lena; Rönn, Tina; Ling, Charlotte

    2017-04-01

    Current knowledge about the role of epigenetics in type 2 diabetes (T2D) remains limited. Only a few studies have investigated DNA methylation of selected candidate genes or a very small fraction of genomic CpG sites in human pancreatic islets, the tissue of primary pathogenic importance for diabetes. Our aim was to characterize the whole-genome DNA methylation landscape in human pancreatic islets, to identify differentially methylated regions (DMRs) in diabetic islets, and to investigate the function of DMRs in islet biology. Here, we performed whole-genome bisulfite sequencing, which is a comprehensive and unbiased method to study DNA methylation throughout the genome at a single nucleotide resolution, in pancreatic islets from donors with T2D and control subjects without diabetes. We identified 25,820 DMRs in islets from individuals with T2D. These DMRs cover loci with known islet function, e.g., PDX1, TCF7L2, and ADCY5 Importantly, binding sites previously identified by ChIP-seq for islet-specific transcription factors, enhancer regions, and different histone marks were enriched in the T2D-associated DMRs. We also identified 457 genes, including NR4A3, PARK2, PID1, SLC2A2, and SOCS2, that had both DMRs and significant expression changes in T2D islets. To mimic the situation in T2D islets, candidate genes were overexpressed or silenced in cultured β-cells. This resulted in impaired insulin secretion, thereby connecting differential methylation to islet dysfunction. We further explored the islet methylome and found a strong link between methylation levels and histone marks. Additionally, DNA methylation in different genomic regions and of different transcript types (i.e., protein coding, noncoding, and pseudogenes) was associated with islet expression levels. Our study provides a comprehensive picture of the islet DNA methylome in individuals with and without diabetes and highlights the importance of epigenetic dysregulation in pancreatic islets and T2D

  11. Disrupted imprinting status at the H19 differentially methylated region is associated with the resorbed embryo phenotype in rats.

    PubMed

    Pathak, Shilpa; Saxena, Madhurima; D'Souza, Ryan; Balasinor, N H

    2010-01-01

    Igf2, an imprinted gene that is paternally expressed in embryos, encodes an embryonic growth factor. An important regulator of Igf2 expression is methylation of the H19 differentially methylated region (DMR). A significant association has been observed between sperm methylation status at the H19 DMR and post-implantation loss. In addition, tamoxifen treatment has been shown to increase post-implantation loss and reduce DNA methylation at the H19 DMR in rat spermatozoa. Because this DMR is a primary DMR transmitting epigenetic imprint information from the gametes to the embryo, the aim of the present study was to determine the imprinting status of H19 DMR in post-implantation normal and resorbed embryos (F(1)) and to compare it with the H19 DMR in the spermatozoa of the respective sires. Analysis of the H19 DMR revealed methylation errors in resorbed embryo that were also observed in their sires' spermatozoa in the control and tamoxifen-treated groups. Expression analysis of the reciprocally imprinted genes Igf2 and H19 showed significant downregulation of Igf2 protein without any effect on H19 transcript levels in the resorbed embryos. The results indicate an association between disrupted imprinting status at the H19 DMR in resorbed embryos and the spermatozoa from their respective sires regardless of treatment, implying a common mechanism of resorption. The results demonstrate transmission of methylation errors at the Igf2-H19 locus through the paternal germline to the subsequent generation, emphasising the role of paternal factors during embryogenesis.

  12. Alcohol and nicotine codependence-associated DNA methylation changes in promoter regions of addiction-related genes

    PubMed Central

    Xu, Hongqin; Wang, Fan; Kranzler, Henry R.; Gelernter, Joel; Zhang, Huiping

    2017-01-01

    Altered DNA methylation in addiction-related genes may modify the susceptibility to alcohol or drug dependence (AD or ND). We profiled peripheral blood DNA methylation levels of 384 CpGs in promoter regions of 82 addiction-related genes in 256 African Americans (AAs) (117 cases with AD-ND codependence and 139 controls) and 196 European Americans (103 cases with AD-ND codependence and 93 controls) using Illumina’s GoldenGate DNA methylation array assays. AD-ND codependence-associated DNA methylation changes were analyzed using linear mixed-effects models with consideration of batch effects and covariates age, sex, and ancestry proportions. Seventy CpGs (in 41 genes) showed nominally significant associations (P < 0.05) with AD-ND codependence in both AAs and EAs. One CpG (HTR2B cg27531267) was hypomethylated in AA cases (P = 7.2 × 10−5), while 17 CpGs in 16 genes (including HTR2B cg27531267) were hypermethylated in EA cases (5.6 × 10−9 ≤ P ≤ 9.5 × 10−5). Nevertheless, 13 single nucleotide polymorphisms (SNPs) nearby HTR2B cg27531267 and the interaction of these SNPs and cg27531267 did not show significant effects on AD-ND codependence in either AAs or EAs. Our study demonstrated that DNA methylation changes in addiction-related genes could be potential biomarkers for AD-ND co-dependence. Future studies need to explore whether DNA methylation alterations influence the risk of AD-ND codependence or the other way around. PMID:28165486

  13. Usefulness of DNA Methylation Levels in COASY and SPINT1 Gene Promoter Regions as Biomarkers in Diagnosis of Alzheimer’s Disease and Amnestic Mild Cognitive Impairment

    PubMed Central

    Shinagawa, Shunichiro; Nagata, Tomoyuki; Shimada, Kazuya; Shibata, Nobuto; Ohnuma, Tohru; Kasanuki, Koji; Arai, Heii; Yamada, Hisashi; Nakayama, Kazuhiko; Kondo, Kazuhiro

    2016-01-01

    In order to conduct early therapeutic interventions for Alzheimer’s disease (AD), convenient, early diagnosis markers are required. We previously reported that changes in DNA methylation levels were associated with amnestic mild cognitive impairment (aMCI) and AD. As the results suggested changes in DNA methylation levels in the COASY and SPINT1 gene promoter regions, in the present study we examined DNA methylation in these regions in normal controls (NCs, n = 30), aMCI subjects (n = 28) and AD subjects (n = 30) using methylation-sensitive high resolution melting (MS-HRM) analysis. The results indicated that DNA methylation in the two regions was significantly increased in AD and aMCI as compared to NCs (P < 0.0001, P < 0.0001, ANOVA). Further analysis suggested that DNA methylation in the COASY gene promoter region in particular could be a high sensitivity, high specificity diagnosis biomarker (COASY: sensitivity 96.6%, specificity 96.7%; SPINT1: sensitivity 63.8%, specificity 83.3%). DNA methylation in the COASY promoter region was associated with CDR Scale Sum of Boxes (CDR-SB), an indicator of dementia severity. In the SPINT1 promoter region, DNA methylation was negatively associated with age in NCs and elevated in aMCI and AD subjects positive for antibodies to Herpes simplex virus type 1 (HSV-1). These findings suggested that changes in DNA methylation in the COASY and SPINT1 promoter regions are influenced by various factors. In conclusion, DNA methylation levels in the COASY and SPINT1 promoter regions were considered to potentially be a convenient and useful biomarker for diagnosis of AD and aMCI. PMID:27992572

  14. Local genotype influences DNA methylation at two asthma-associated regions, 5q31 and 17q21, in a founder effect population.

    PubMed

    Al Tuwaijri, Abeer; Gagné-Ouellet, Valérie; Madore, Anne-Marie; Laprise, Catherine; Naumova, Anna K

    2016-04-01

    Two asthma-associated regions 17q12-q21 and 5q31.1 harbour genes that show strong effect of genotype on expression levels. DNA methylation has an important role in gene regulation; therefore, we examined DNA methylation at promoters of 12 genes from 5q31 and 17q12-q21 regions. Our goal was to determine whether DNA methylation was associated with predisposition to asthma and whether such a relationship was independent from genetic association. Using sodium bisulfite sequencing and pyrosequencing methylation assays, we examined the effect of genotype on DNA methylation in peripheral blood cells from individuals from the Saguenay-Lac-Saint-Jean asthma familial collection and lymphoblastoid cell lines. The local genotype influenced methylation levels of solute carrier family 22 (organic 3 cation/carnitine transporter) member 5 (SLC22A5), zona pellucida binding protein 2 (ZPBP2) and gasdermin A (GSDMA) promoter regions. The genotype had a dominant effect on ZPBP2 and GSDMA methylation with lower methylation levels in individuals that carry the asthma-predisposing alleles. Males also had lower methylation at the ZPBP2 promoter than females. We did not observe an effect of asthma status that would be independent of the genotype and the sex effects in the GSDMA, ZPBP2 and SLC22A5 regions; however, GSDMA and ZPBP2 data were suggestive of interaction between asthma and methylation levels in females and SLC22A5 in males. The local genotype influences methylation levels at SLC22A5 and ZPBP2 promoters independently of the asthma status. Further studies are necessary to confirm the relationship between GSDMA-ZPBP2 and SLC22A5 methylation and asthma in females and males separately. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  15. Tissue-specific methylation of individual CpG dinucleotides in the 5{prime} upstream region of the mouse catalase gene (Cas-1)

    SciTech Connect

    Pillay, I.L.; Singh, S.M.

    1994-09-01

    The intracellular antioxidant enzyme, catalase, is encoded by a gene whose level of expression in different organisms, including humans, varies with tissue-type. The {open_quotes}TATA-less{close_quotes} 5{prime} upstream region of the catalase gene, in mice and humans, contains a CpG island. Such CG-rich regions are target sites for cytosine methylation and have been implicated in tissue-specific gene expression. However, the methylation status of individual CpG dinucleotides and their significance in gene expression has not been established. A 275 bp fragment within the 5{prime} region of Cas-1 was evaluated for CpG methylation. HpaII digestion of genomic DNA, followed by polymerase chain reaction amplification (HpaII-PCR), suggests that at least one of three CCGG is not methylated in nine different somatic tissues that express this enzyme at various levels. In contrast, all three CCGG sites are methylated in DNA from sperm and spleen. Further examination of the methylation specificity of individual CCGG sites was conducted using sodium bisulfite modification of genomic DNA followed by HPaII-PCR. Sodium bisulfite modifies non-methylated cytosines to uracils, changing a CG to a TG dinucleotide. This nucleotide substitution eliminates HpaII sites and allows the methylation status of each of the CCGG sites to be assessed. The ability to discern the number and combination of methylated sites within the 5{prime} region of a gene permits the determination of a possible correlation between differential methylation patterns and temporal/spatial gene regulation. Analysis of differential methylation, using the mouse catalase gene as a model, provides further insight into CpG methylation as one mechanism of mammalian gene regulation.

  16. Detection of differentially methylated regions in whole genome bisulfite sequencing data using local Getis-Ord statistics.

    PubMed

    Wen, Yalu; Chen, Fushun; Zhang, Qingzheng; Zhuang, Yan; Li, Zhiguang

    2016-11-15

    DNA methylation is an important epigenetic modification that has essential role in gene regulation, cell differentiation and cancer development. Bisulfite sequencing is a widely used technique to obtain genome-wide DNA methylation profiles, and one of the key tasks of analyzing bisulfite sequencing data is to detect differentially methylated regions (DMRs) among samples under different treatment conditions. Although numerous tools have been proposed to detect differentially methylated single CpG site (DMC) between samples, methods for direct DMR detection, especially for complex study designs, are largely limited. We present a new software, GetisDMR, for direct DMR detection. We use beta-binomial regression to model the whole-genome bisulfite sequencing data, where variations in methylation levels and confounding effects have been accounted for. We employ a region-wise test statistic, which is derived from local Getis-Ord statistics and considers the spatial correlation between nearby CpG sites, to detect DMRs. Unlike existing methods, that attempt to infer DMRs from DMCs based on empirical criteria, we provide statistical inference for direct DMR detection. Through extensive simulations and an application to two mouse datasets, we demonstrate that GetisDMR achieves better sensitivities, positive predictive values, more exact locations and better agreement of DMRs with current biological knowledge. It is available at https://github.com/DMU-lilab/GetisDMR CONTACTS: y.wen@auckland.ac.nz or zhiguangli@dlmedu.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. Abnormal Methylation Status of the GNAS Exon 1A Region in Pseudohypohyperparathyroidism Combined With Turner Syndrome.

    PubMed

    Zhu, Jie; Wang, Dong; Ren, An; Xing, Yan; Zhang, Dongliang; Wei, Jun; Yu, Ning; Xing, Xuenong; Ye, Shandong

    2015-12-01

    Pseudohypohyperparathyroidism (PHHP) is a rare type of pseudohypoparathyroidism (PHP), which seems to have a normal skeletal response to parathyroid hormone but shows renal resistance. Almost all patients with PHHP have PHP Ib, a subtype of PHP that is usually caused by GNAS methylation defects, often in exon 1A. Some features of Albright hereditary osteodystrophy can occasionally be found in patients with PHHP, but these features are also common in Turner syndrome. The authors report on an extremely rare case of a patient with PHHP and Turner syndrome, a 47-year-old woman who sought medical attention for hypocalcemia and elevated parathyroid hormone. She had no family history of hypocalcemia and no STX16 gene deletions. She had a mosaic karyotype of 46, X, del(X)(p11.4)/45, XO. Pyrosequencing was performed to determine the GNAS exon 1A methylation. The degree of methylation found in exon 1A of the patient was lower than her unaffected relatives.

  18. Epigenetic deregulation across chromosome 2q14.2 differentiates normal from prostate cancer and provides a regional panel of novel DNA methylation cancer biomarkers.

    PubMed

    Devaney, James; Stirzaker, Clare; Qu, Wenjia; Song, Jenny Z; Statham, Aaron L; Patterson, Kate I; Horvath, Lisa G; Tabor, Bruce; Coolen, Marcel W; Hulf, Toby; Kench, James G; Henshall, Susan M; Pe Benito, Ruth; Haynes, Anne-Maree; Mayor, Regina; Peinado, Miguel A; Sutherland, Robert L; Clark, Susan J

    2011-01-01

    Previously, we showed that gene suppression commonly occurs across chromosome 2q14.2 in colorectal cancer, through a process of long-range epigenetic silencing (LRES), involving a combination of DNA methylation and repressive histone modifications. We now investigate whether LRES also occurs in prostate cancer across this 4-Mb region and whether differential DNA methylation of 2q14.2 genes could provide a regional panel of prostate cancer biomarkers. We used highly sensitive DNA methylation headloop PCR assays that can detect 10 to 25 pg of methylated DNA with a specificity of at least 1:1,000, and chromatin immunoprecipitation assays to investigate regional epigenetic remodeling across 2q14.2 in prostate cancer, in a cohort of 195 primary prostate tumors and 90 matched normal controls. Prostate cancer cells exhibit concordant deacetylation and methylation of histone H3 Lysine 9 (H3K9Ac and H3K9me2, respectively), and localized DNA hypermethylation of EN1, SCTR, and INHBB and corresponding loss of H3K27me3. EN1 and SCTR were frequently methylated (65% and 53%, respectively), whereas INHBB was less frequently methylated. Consistent with LRES in colorectal cancer, we found regional epigenetic remodeling across 2q14.2 in prostate cancer. Concordant methylation of EN1 and SCTR was able to differentiate cancer from normal (P < 0.0001) and improved the diagnostic specificity of GSTP1 methylation for prostate cancer detection by 26%. For the first time we show that DNA methylation of EN1 and SCTR promoters provide potential novel biomarkers for prostate cancer detection and in combination with GSTP1 methylation can add increased specificity and sensitivity to improve diagnostic potential. ©2011 AACR.

  19. Deletions of a differentially methylated CpG island at SNRPN define a putative imprinting control region

    SciTech Connect

    Sutcliffe, J.S.,; Nakao, M.; Beaudet, A.L.

    1994-09-01

    Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are associated with paternal and maternal deficiencies, respectively, of gene expression within human chromosome 15q11-q13, and are caused by deletion, uniparental disomy, or other mutations. Four transcripts designated PAR-5, PAR-7, PAR-1 and PAR-4 were isolated and localized to a region within 300 kb telomeric to the gene encoding small nuclear ribonucleoprotein-associated polypeptide N (SNRPN). Analysis of the transcripts in cultured fibroblasts and lymphoblasts from deletion patients demonstrated that SNRPN, PAR-5 and PAR-1 are expressed exclusively from the paternal chromosome, defining an imprinted domain that spans at least 200 kb. All three imprinted transcripts were absent in cells from three PWS patients (one pair of sibs and one sporadic case) with small deletions that involve a differentially methylated CpG island containing a previously undescribed 5{prime} untranslated exon ({alpha}) of SNRPN. Methylation of the CpG island is specific for the maternal chromosome consistent with paternal expression of the imprinted domain. One deletion, which is benign when maternally transmitted, extends upstream <30 kb from the CpG island, and is associated with altered methylation centromeric to SNRPN, and loss of transcription telomeric to SNRPN, implying the presence of an imprinting control region around the CpG island containing exon {alpha}.

  20. CG methylation.

    PubMed

    Vinson, Charles; Chatterjee, Raghunath

    2012-12-01

    A striking feature of mammalian genomes is the paucity of the CG dinucleotide. There are approximately 20,000 regions termed CpG islands where CGs cluster. This represents 5% of all CGs and 1% of the genome. CpG islands are typically unmethylated and are often promoters for housekeeping genes. The remaining 95% of CG dinucleotides are disposed throughout 99% of the genome and are typically methylated and found in half of all promoters. CG methylation facilitates binding of the C/EBP family of transcription factors, proteins critical for differentiation of many tissues. This allows these proteins to localize in the methylated CG poor regions of the genome where they may produce advantageous changes in gene expression at nearby or more distant regions of the genome. In this review, our growing understanding of the consequences of CG methylation will be surveyed.

  1. DNA methylation in the NCAPH2/LMF2 promoter region is associated with hippocampal atrophy in Alzheimer's disease and amnesic mild cognitive impairment patients.

    PubMed

    Shinagawa, Shunichiro; Kobayashi, Nobuyuki; Nagata, Tomoyuki; Kusaka, Akira; Yamada, Hisashi; Kondo, Kazuhiro; Nakayama, Kazuhiko

    2016-08-26

    Several studies have noted an effect of DNA methylation on the pathogenesis of Alzheimer's disease (AD). We have already reported that DNA methylation levels in the NCAPH2/LMF2 promoter region can be a useful biomarker for the diagnosis of AD and amnesic mild cognitive impairment (aMCI). However, there is still uncertainty about the mechanism by which NCAPH2/LMF2 methylation affects the pathogenesis of AD and aMCI. In this study, we investigated relationships between NCAPH2/LMF2 methylation and other factors. AD (n=30) and aMCI (n=28) subjects were included in this study. NCAPH2/LMF2 methylation levels were measured by pyrosequencing. Correlations between methylation levels and other factors including age at onset, sex, duration of disease, education, mini-mental state examination (MMSE) and frontal assessment battery (FAB) scores, APOE genotype, degree of hippocampal atrophy, and total brain atrophy were measured. Degrees of hippocampal atrophy and total brain atrophy were measured by VSRAD (Voxel-Based Specific Regional Analysis System for Alzheimer's Disease). Regression analysis revealed that only hippocampal atrophy according to VSRAD is a significant dependent variable correlated with NCAPH2/LMF2 methylation levels. Our results suggest that DNA methylation in the NCAPH2/LMF2 promoter region is associated with hippocampal atrophy through apoptosis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  2. PCR amplification of GC-rich DNA regions using the nucleotide analog N4-methyl-2'-deoxycytidine 5'-triphosphate.

    PubMed

    Flores-Juárez, Cyntia R; González-Jasso, Eva; Antaramian, Anaid; Pless, Reynaldo C

    2016-10-01

    GC-rich DNA regions were PCR-amplified with Taq DNA polymerase using either the canonical set of deoxynucleoside triphosphates or mixtures in which the dCTP had been partially or completely replaced by its N4-methylated analog, N4-methyl-2'-deoxycytidine 5'-triphosphate (N4me-dCTP). In the case of a particularly GC-rich region (78.9% GC), the PCR mixtures containing N4me-dCTP produced the expected amplicon in high yield, while mixtures containing the canonical set of nucleotides produced numerous alternative amplicons. For another GC-rich DNA region (80.6% GC), the target amplicon was only generated by re-amplifying a gel-purified sample of the original amplicon with N4me-dCTP-containing PCR mixtures. In a direct PCR comparison on a highly GC-rich template, mixtures containing N4me-dCTP clearly performed better than did solutions containing the canonical set of nucleotides mixed with various organic additives (DMSO, betaine, or ethylene glycol) that have been reported to resolve or alleviate problems caused by secondary structures in the DNA. This nucleotide analog was also tested in PCR amplification of DNA regions with intermediate GC content, producing the expected amplicon in each case with a melting temperature (Tm) clearly below the Tm of the same amplicon synthesized exclusively with the canonical bases.

  3. Feasibility of a bilateral regional sternocleidomastoid muscular flap in the closure of a persistent acquired tracheopharyngeal fistula.

    PubMed

    Goh, Liang Chye; Santhi, Kalimuthu; Arvin, Balachandran; Mohd Razif, Mohamad Yunus

    2016-08-26

    An acquired persistent tracheopharyngeal fistula secondary to an infected tracheopharyngeal voice prosthesis is a common cause of recurrent aspiration pneumonia in a postlaryngectomy patient. We report a case of a successfully treated tracheopharyngeal fistula whereby both the sternocleidomastoid muscles were used as muscular flaps to close the defect and its outcome.

  4. Risk factors for hospital-acquired infections in teaching hospitals of Amhara regional state, Ethiopia: A matched-case control study.

    PubMed

    Yallew, Walelegn Worku; Kumie, Abera; Yehuala, Feleke Moges

    2017-01-01

    Hospital-acquired infection affects hundreds of millions of people worldwide. It is a major global issue for patient safety. Understanding the potential risk factors is important to appreciate the local context. A matched case control study design, which is the first of its kind in the study region, was undertaken to identify risk factors in teaching hospitals of Amhara regional state, Ethiopia. A matched case control study design matched with age and hospital type was used. The study was conducted in University of Gondar and Felege-Hiwot medical teaching hospital. Cases were patients who fulfilled the criteria based on CDC definition of hospital-acquired infection and controls were patients admitted to the hospital that stayed for more than 48 hours in the ward in the study period, but who did not develop infection. For one case, four controls were selected. Of 545 patients, 109 were cases and 436 were controls. Conditional logistic regression using STATA 13 was used for data analysis. The median length of stay for cases and controls was 7 and 8 days, respectively. Patients admitted in wards with the presence of medical waste container in the room had 82% less chance of developing hospital-acquired infection (AOR 0.18; 95% CI, 0.03-0.98). The odds of developing hospital-acquired infection among immune deficient patients were 2.34 times higher than their counterparts (95% CI; 1.17-4.69). Patients received antimicrobials, central vascular catheter and surgery since admission had 8.63, 6.91 and 2.35 higher odds of developing hospital-acquired infection, respectively. Health providers and mangers should consider the provision and availability of healthcare materials and facilities in all of the ward rooms, follow appropriate safe medical procedures for use of external devices on patients, and give attention to the immunocompromised patients for the prevention and control of hospital-acquired infections.

  5. Systematically Prioritizing Functional Differentially Methylated Regions (fDMRs) by Integrating Multi-omics Data in Colorectal Cancer

    PubMed Central

    Fan, Huihui; Zhao, Hongying; Pang, Lin; Liu, Ling; Zhang, Guanxiong; Yu, Fulong; Liu, Tingting; Xu, Chaohan; Xiao, Yun; Li, Xia

    2015-01-01

    While genome-wide differential DNA methylation regions (DMRs) have been extensively identified, the comprehensive prioritization of their functional importance is still poorly explored. Here, we aggregated multiple data resources rooted in the genome, epigenome and transcriptome to systematically prioritize functional DMRs (fDMRs) in colorectal cancer (CRC). As demonstrated, the top-ranked fDMRs from all of the data resources showed a strong enrichment for known methylated genes. Additionally, we analyzed those top 5% DMR-coupled coding genes using functional enrichment, which resulted in significant disease-related biological functions in contrast to the tail 5% genes. To further confirm the functional importance of the top-ranked fDMRs, we applied chromatin modification alterations of CRC cell lines to characterize their functional regulation. Specifically, we extended the utility of the top-ranked DMR-coupled genes to serve as classification and survival biomarkers, which showed a robust performance across diverse independent data sets. Collectively, our results established an integrative framework to prioritize fDMRs, which could help characterize aberrant DNA methylation-induced potential mechanisms underlying tumorigenesis and uncover epigenome-based biomarkers for clinical diagnosis and prognosis. PMID:26239918

  6. Quantitative analysis of DNA methylation in the promoter region of the methylguanine-O(6) -DNA-methyltransferase gene by COBRA and subsequent native capillary gel electrophoresis.

    PubMed

    Goedecke, Simon; Mühlisch, Jörg; Hempel, Georg; Frühwald, Michael C; Wünsch, Bernhard

    2015-12-01

    Along with histone modifications, RNA interference and delayed replication timing, DNA methylation belongs to the key processes in epigenetic regulation of gene expression. Therefore, reliable information about the methylation level of particular DNA fragments is of major interest. Herein the methylation level at two positions of the promoter region of the gene methylguanine-O(6) -DNA-Methyltransferase (MGMT) was investigated. Previously, it was demonstrated that the epigenetic status of this DNA region correlates with response to alkylating anticancer agents. An automated CGE method with LIF detection was established to separate the six DNA fragments resulting from combined bisulfite restriction analysis of the methylated and non-methylated MGMT promoter. In COBRA, the DNA was treated with bisulfite converting cytosine into uracil. During PCR uracil pairs with adenine, which changes the original recognition site of the restriction enzyme Taql. Artificial probes generated by mixing appropriate amounts of DNA after bisulfite treatment and PCR amplification were used for validation of the method. The methylation levels of these samples could be determined with high accuracy and precision. DNA samples prepared by mixing the corresponding clones first and then performing PCR amplification led to non-linear correlation between the corrected peak areas and the methylation levels. This effect is explained by slightly different PCR amplification of DNA with different sequences present in the mixture. The superiority of CGE over PAGE was clearly demonstrated. Finally, the established method was used to analyze the methylation levels of human brain tumor tissue samples.

  7. Promoter region methylation and loss of protein expression of PTEN and significance in cervical cancer

    PubMed Central

    QI, QIUFENG; LING, YANG; ZHU, MING; ZHOU, LINYAN; WAN, MEIZHEN; BAO, YANQING; LIU, YONGPING

    2014-01-01

    The genetic basis underlying cervical tumorigenesis and progression are largely unknown. Phosphatase and tensin homologue (PTEN) is a tumor suppressor gene, and genetic changes of PTEN occurs in various types of cancer suggesting that the inactivation of PTEN may play an important role in the pathogenesis of a variety of human malignancies. In the present study, 102 cervical cancer specimens were examined for the expression of the PTEN gene and promoter methylation using methylation-specific-polymerase chain reaction and immunohistochemistry. The PTEN gene mutation was also assessed using PCR single-strand conformational polymorphism. We examined the correlation between PTEN expression and its associated methylation status and the clinical characteristics of cervical cancer. The results showed that there was one case of an A to G point mutation on exon 9 of the PTEN gene in the cervical cancer tissues. This mutation caused the change of aspartic acid to glycine, and the rate of mutation was 1%. The PTEN gene methylation rate of cervical cancer was 62% (63/102) and the rate was associated with the International Federation of Gynecology and Obstetrics stage, cell differentiation, tumor size and lymph node metastasis (P<0.05). The positive rate of PTEN expression was 49% (50/102) in cervical carcinoma and the PTEN expression between stage I–II and III–IV [60 (27/45) vs. 40% (23/57)] was statistically significant (P<0.01). The PTEN gene expression between the metastasis and no lymph node metastasis groups [26 (10/38) vs. 63% (40/64)] was significantly different (P<0.01). The PTEN gene promoter methylation and its protein expression had a significant correlation (P=0.042). These results suggest that hypermethylation can inactivate the transcription of PTEN and reduce its protein expression. Downregulated PTEN expression is involved in the pathogenesis, invasion and metastasis of cervical cancer, possibly by regulating the balance between apoptosis and proliferation

  8. [Relationship between EGFR Promoter Region Methylation and Secondary Resistance Which may be Induced by Gefitinib].

    PubMed

    Wang, Qilong; Li, Min; Hu, Chengping

    2015-04-01

    Nowadays the secondary resistance of gefitinib in the treatment of lung adenocarcinoma is an outstanding problem. This research is to explore whether the gefitinib secondary resistance can be induced by gefitinib, to explore whether epidermal growth factor receptor (EGFR) promotor methylation correlate with the gefitinib-resistance in PC9/GR cell lines and to find a new therapeutic target to overcome the gefitinib secondary resistance in lung adenocarcinoma. In vitro cultivation of lung adenocarcinoma PC9 cell lines, apply gefitinib on lung adenocarcinoma PC9 cell lines, and improve drug concentration. MTT for test of gefitinib resistance index in PC9 cell and PC9/GR cell. Bisulfite sequencing polymerase chain reaction (BSP) and Reverse transcription-polymerase chain reaction (RT-PCR) for detection of EGFR promoter methylation status and mRNA expression. In vitro cultivation of lung adenocarcinoma PC9 cell lines, apply 1 μmol/L 5-Aza-dc on lung adenocarcinoma PC9/GR cell lines for 72 h. MTT method for test of gefitinib resistance index in PC9/GR cell. After improving the gefitinib concentration, MTT results showed that half maximal inhibitory concentration (IC50) of PC9 cell lines increase from (0.01 ± 0.002) μmol/L to (3.95 ± 0.23) μmol/L (P<0.05). BSP results showed that abnormal methylation sites compared the degree of methylation change: PC9: 59%; PC9/GR: 74% (P<0.05). RT-PCR results showed in PC9/GR cell lines, EGFR mRNA expression quantity increased (P<0.05). After applying 5-Aza-dc on PC9 cell lines, IC50 of PC9/GR decrease from (3.87 ± 0.034) μmol/L to (2.55 ± 0.14) μmol/L. The PC9 cell line which is induced by improving gefitinib concentration will be resistant to gefitinib, and the gefitinib-resistant cell line PC9/GR could be built. EGFR gene promoter methylation may be one of the mechanisms for the secondary resistance to gefitinib.

  9. Learning and memory: regional changes in N-methyl-D-aspartate receptors in the chick brain after imprinting.

    PubMed Central

    McCabe, B J; Horn, G

    1988-01-01

    An extensive series of experiments has implicated a restricted region of the chick forebrain in the learning process of imprinting. The region is the intermediate and medial part of the hyperstriatum ventrale (IMHV). Previous studies have shown that training is associated with an increase in the area of the postsynaptic density of axospinous synapses in the left but not the right IMHV. The postsynaptic density is a site of high receptor density, and at least some axospinous synapses are excitatory. We found that imprinting is associated with a 59% increase in N-methyl-D-aspartate-sensitive binding of the excitatory amino acid L-[3H]glutamic acid in the left IMHV. The increase is probably due to an increased number of binding sites. The profile of sensitivity of the sites to a series of amino-, phosphono-substituted carboxylic acids (2-amino-3-phosphonopropionate to 2-amino-8-phosphonooctanoate) is characteristic of N-methyl-D-aspartate-type receptors. There were no significant effects of training on binding in the right IMHV. The effect of training on left IMHV binding could not be attributed to light exposure, arousal, or motor activity per se but was a function of how much the chicks learned. The changes in the left IMHV could increase the effectiveness of synaptic transmission in a region crucial for information storage and so form a neural basis for recognition memory. PMID:2833757

  10. Brain Region-Specific Expression of MeCP2 Isoforms Correlates with DNA Methylation within Mecp2 Regulatory Elements

    PubMed Central

    Liyanage, Vichithra R. B.; Rastegar, Mojgan

    2014-01-01

    MeCP2 is a critical epigenetic regulator in brain and its abnormal expression or compromised function leads to a spectrum of neurological disorders including Rett Syndrome and autism. Altered expression of the two MeCP2 isoforms, MeCP2E1 and MeCP2E2 has been implicated in neurological complications. However, expression, regulation and functions of the two isoforms are largely uncharacterized. Previously, we showed the role of MeCP2E1 in neuronal maturation and reported MeCP2E1 as the major protein isoform in the adult mouse brain, embryonic neurons and astrocytes. Recently, we showed that DNA methylation at the regulatory elements (REs) within the Mecp2 promoter and intron 1 impact the expression of Mecp2 isoforms in differentiating neural stem cells. This current study is aimed for a comparative analysis of temporal, regional and cell type-specific expression of MeCP2 isoforms in the developing and adult mouse brain. MeCP2E2 displayed a later expression onset than MeCP2E1 during mouse brain development. In the adult female and male brain hippocampus, both MeCP2 isoforms were detected in neurons, astrocytes and oligodendrocytes. Furthermore, MeCP2E1 expression was relatively uniform in different brain regions (olfactory bulb, striatum, cortex, hippocampus, thalamus, brainstem and cerebellum), whereas MeCP2E2 showed differential enrichment in these brain regions. Both MeCP2 isoforms showed relatively similar distribution in these brain regions, except for cerebellum. Lastly, a preferential correlation was observed between DNA methylation at specific CpG dinucleotides within the REs and Mecp2 isoform-specific expression in these brain regions. Taken together, we show that MeCP2 isoforms display differential expression patterns during brain development and in adult mouse brain regions. DNA methylation patterns at the Mecp2 REs may impact this differential expression of Mecp2/MeCP2 isoforms in brain regions. Our results significantly contribute towards characterizing

  11. Transcription and chromatin determinants of de novo DNA methylation timing in oocytes.

    PubMed

    Gahurova, Lenka; Tomizawa, Shin-Ichi; Smallwood, Sébastien A; Stewart-Morgan, Kathleen R; Saadeh, Heba; Kim, Jeesun; Andrews, Simon R; Chen, Taiping; Kelsey, Gavin

    2017-01-01

    Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. Molecular and functional studies have shown that imprinted genes become methylated at different times during oocyte growth; however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci. Given the predominant role of transcription, we sought to investigate whether transcription timing is rate limiting for de novo methylation and determines the asynchrony of methylation events. Therefore, we generated genome-wide methylation and transcriptome maps of size-selected, growing oocytes to capture the onset and progression of methylation. We find that most sequence elements, including most classes of transposable elements, acquire methylation at similar rates overall. However, methylation of CpG islands (CGIs) is delayed compared with the genome average and there are reproducible differences amongst CGIs in onset of methylation. Although more highly transcribed genes acquire methylation earlier, the major transitions in the oocyte transcriptome occur well before the de novo methylation phase, indicating that transcription is generally not rate limiting in conferring permissiveness to DNA methylation. Instead, CGI methylation timing negatively correlates with enrichment for histone 3 lysine 4 (H3K4) methylation and dependence on the H3K4 demethylases KDM1A and KDM1B, implicating chromatin remodelling as a major determinant of methylation timing. We also identified differential enrichment of transcription factor binding motifs in CGIs acquiring methylation early or late in oocyte growth. By combining these parameters into multiple regression models, we were able to account for about a fifth of the variation in methylation timing of CGIs. Finally

  12. Tissue-, sex- and age-specific DNA methylation of rat glucocorticoid receptor gene promoter and insulin like growth factor 2 imprinting control region.

    PubMed

    Agba, Ogechukwu Brenda; Lausser, Ludwig; Huse, Klaus; Bergmeier, Christoph; Jahn, Niels; Groth, Marco; Bens, Martin; Sahm, Arne; Gall, Maria; Witte, Otto W; Kestler, Hans A; Schwab, Matthias; Platzer, Matthias

    2017-09-15

    Tissue-, sex- and age-specific epigenetic modifications such as DNA methylation are largely unknown. Changes in DNA methylation of the glucocorticoid receptor gene (NR3C1) and imprinting control region (ICR) of IGF2 and H19 genes during the lifespan are particularly interesting since these genes are susceptible to epigenetic modifications by prenatal stress or malnutrition. They are important regulators of development and aging. Methylation changes of NR3C1 affect glucocorticoid receptor expression, which is associated with stress sensitivity and stress-related diseases predominantly occurring during aging. Methylation changes of IGF2/H19 affect growth trajectory and nutrient use with risk of metabolic syndrome. Using a locus-specific approach, we characterized DNA methylation patterns of different Nr3c1 promoters and Igf2/H19 ICR in seven tissues of rats at 3, 9 and 24 months of age. We found a complex pattern of locus-, tissue-, sex- and age-specific DNA methylation. Tissue-specific methylation was most prominent at the shores of the Nr3c1 CpG island (CGI). Sex-specific differences in methylation peaked at 9 months. During aging, Nr3c1 predominantly displayed hypomethylation mainly in females and at shores, whereas hypermethylation occurred within the CGI. Igf2/H19 ICR exhibited age-related hypomethylation occurring mainly in males. Methylation patterns of Nr3c1 in the skin correlated with those in the cortex, hippocampus and hypothalamus. Skin may serve as proxy for methylation changes in central parts of the hypothalamic-pituitary-adrenal axis and hence for vulnerability to stress- and age-associated diseases. Thus, we provide in-depth insight into the complex DNA methylation changes of rat Nr3c1 and Igf2/H19 during aging that are tissue- and sex-specific. Copyright © 2017, Physiological Genomics.

  13. DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya

    PubMed Central

    Zhang, Wenli; Wang, Xiue; Yu, Qingyi; Ming, Ray; Jiang, Jiming

    2008-01-01

    Sex chromosomes evolved from autosomes. Recombination suppression in the sex-determining region and accumulation of deleterious mutations lead to degeneration of the Y chromosomes in many species with heteromorphic X/Y chromosomes. However, how the recombination suppressed domain expands from the sex-determining locus to the entire Y chromosome remains elusive. The Y chromosome of papaya (Carica papaya) diverged from the X chromosome approximately 2–3 million years ago and represents one of the most recently emerged Y chromosomes. Here, we report that the male-specific region of the Y chromosome (MSY) spans ∼13% of the papaya Y chromosome. Interestingly, the centromere of the Y chromosome is embedded in the MSY. The centromeric domain within the MSY has accumulated significantly more DNA than the corresponding X chromosomal domain, which leads to abnormal chromosome pairing. We observed four knob-like heterochromatin structures specific to the MSY. Fluorescence in situ hybridization and immunofluorescence assay revealed that the DNA sequences associated with the heterochromatic knobs are highly divergent and heavily methylated compared with the sequences in the corresponding X chromosomal domains. These results suggest that DNA methylation and heterochromatinization play an important role in the early stage of sex chromosome evolution. PMID:18593814

  14. Methylation of CpG sites in BCL2 major breakpoint region and the increase of BCL2/JH translocation with aging.

    PubMed

    Martin-Guerrero, Idoia; de Prado, Elena; Ardanaz, Maite; Martin-Arruti, Maialen; Garcia-Orad, Cristina; Guerra, Isabel; Ruiz, Irune; Zabalza, Iñaki; Garcia-Orad, Africa

    2015-10-01

    The BCL2 breakage mechanism has been shown to be highly dependent on DNA methylation at the major breakpoint region (MBR) CpG sites. We recently described an increased frequency of BCL2/ JH translocation with aging. It is known that methylation levels change with aging. The present study aimed to determine whether methylation alterations at CpG sites of BCL2 MBR were the cause of increased breakages with aging. We analyzed the methylation levels of three CpG sites on the region by pyrosequencing and studied if methylation levels and/or polymorphisms affecting CpG sites were associated with an increase of translocations. We observed that although the methylation levels of MBR CpG sites were higher in individuals with BCL2/JH translocation, in contrast to our expectations, these levels decreased with the age. Moreover, we show that polymorphisms at those CpG sites leading to absence of methylation seem to be a protective factor for the apparition of translocations.

  15. Assessment of tropical forest stand characteristics with multipolarization SAR data acquired over a mountainous region in Costa Rica

    NASA Technical Reports Server (NTRS)

    Wu, Shih-Tseng

    1990-01-01

    A digital terrain elevation data set was coregistered with radar data for assessing tropical forest stand characteristics. Both raw and topographically corrected L-band polarimetric radar data acquired over the tropical forests of Costa Rica were analyzed and correlated with field-collected tree parameter data to study the stand characteristics. The results of analyses using 18 out of 81 plots for sites A and B indicated that per-plot bole volume and tree volume are related to SAR data, particularly at site A. The topographically corrected SAR data appear to produce the same findings as those of uncorrected data.

  16. Regions of acquired uniparental disomy at diagnosis of follicular lymphoma are associated with both overall survival and risk of transformation

    PubMed Central

    O'Riain, Ciarán; Gupta, Manu; Waters, Rachel; Yang, Youwen; Wrench, David; Gribben, John; Rosenwald, Andreas; Ott, German; Rimsza, Lisa M.; Holte, Harald; Cazier, Jean-Baptiste; Johnson, Nathalie A.; Campo, Elias; Chan, Wing C.; Gascoyne, Randy D.; Young, Bryan D.; Staudt, Louis M.; Lister, T. Andrew; Fitzgibbon, Jude

    2009-01-01

    Acquired homozygosity in the form of segmental acquired uniparental disomy (aUPD) has been described in follicular lymphoma (FL) and is usually due to mitotic recombination. SNP array analysis was performed with the use of the Affymetrix 10K 2.0 Gene-chip array on DNA from 185 diagnostic FL patients to assess the prognostic relevance of aUPD. Genetic abnormalities were detected in 118 (65%) of 182 patients. Number of abnormalities was predictive of outcome; more than 3 abnormalities was associated with inferior overall survival (OS; P < .03). Sites of recurrent aUPD were detected on 6p (n = 25), 16p (n = 22), 12q (n = 17), 1p36 (n = 14), 10q (n = 8), and 6q (n = 8). On multivariate analysis aUPD on 1p36 correlated with shorter OS (P = .05). aUPD on 16p was predictive of transformation (P = .03) and correlated with poorer progression-free survival (P = .02). aUPD is frequent at diagnosis of FL and affects probability of disease transformation and clinical outcome. PMID:19141865

  17. Regions of acquired uniparental disomy at diagnosis of follicular lymphoma are associated with both overall survival and risk of transformation.

    PubMed

    O'Shea, Derville; O'Riain, Ciarán; Gupta, Manu; Waters, Rachel; Yang, Youwen; Wrench, David; Gribben, John; Rosenwald, Andreas; Ott, German; Rimsza, Lisa M; Holte, Harald; Cazier, Jean-Baptiste; Johnson, Nathalie A; Campo, Elias; Chan, Wing C; Gascoyne, Randy D; Young, Bryan D; Staudt, Louis M; Lister, T Andrew; Fitzgibbon, Jude

    2009-03-05

    Acquired homozygosity in the form of segmental acquired uniparental disomy (aUPD) has been described in follicular lymphoma (FL) and is usually due to mitotic recombination. SNP array analysis was performed with the use of the Affymetrix 10K 2.0 Gene-chip array on DNA from 185 diagnostic FL patients to assess the prognostic relevance of aUPD. Genetic abnormalities were detected in 118 (65%) of 182 patients. Number of abnormalities was predictive of outcome; more than 3 abnormalities was associated with inferior overall survival (OS; P < .03). Sites of recurrent aUPD were detected on 6p (n = 25), 16p (n = 22), 12q (n = 17), 1p36 (n = 14), 10q (n = 8), and 6q (n = 8). On multivariate analysis aUPD on 1p36 correlated with shorter OS (P = .05). aUPD on 16p was predictive of transformation (P = .03) and correlated with poorer progression-free survival (P = .02). aUPD is frequent at diagnosis of FL and affects probability of disease transformation and clinical outcome.

  18. Is the backbone conformation of C(alpha)-methyl proline restricted to a single region?

    PubMed

    De Poli, Matteo; Moretto, Alessandro; Crisma, Marco; Peggion, Cristina; Formaggio, Fernando; Kaptein, Bernard; Broxterman, Quirinus B; Toniolo, Claudio

    2009-08-10

    C(alpha)-methyl-L-proline, or L-(alphaMe)Pro, is probably the most conformationally constrained alpha-amino acid. In particular, its omega and phi torsion angles are restricted to about 180 and -60 degrees, respectively, and only three ranges of values are theoretically available for psi in mono- or longer peptides, namely, about -30 degrees (cis', 3(10)/alpha-helical structure), 60 degrees (inverse gamma turn), or 140 degrees (trans', poly(L-Pro)(n) II structure). In this work, we examined the tendency of a number of N(alpha)-acyl dipeptide N'-alkylamides of the type RCO-(alphaMe)Pro-Xxx-NHR' or RCO-Xxx-(alphaMe)Pro-NHR', in which Xxx is L (or D)-Ala, Aib (alpha-aminoisoburyric acid), or L (or D)-(alphaMe)Pro, long enough to fold into intramolecularly hydrogen-bonded gamma or beta turns. The results are compared with those obtained for the corresponding dipeptides based on Pro, a well-known turn-forming residue. For the crystal-state 3D-structural analysis we used X-ray diffraction, whereas our solution conformational analysis was heavily based on the FTIR absorption and (1)H and (13)C NMR spectroscopy techniques. We conclude that (alphaMe)Pro is able to explore both trans' and cis' psi areas of the conformational space, but in (alphaMe)Pro the latter is overwhelmingly more populated, in marked contrast to the Pro preference. This finding is a clear indication that in (alphaMe)Pro the major 3D-structural determinant is the C(alpha)-methyl group. The circular dichroism (CD) signature of a peptide type III' beta-turn conformation is also proposed.

  19. Mercury Methylation and Environmental Effects of Inactive Mercury Mines in the Circum-Pacific Region

    NASA Astrophysics Data System (ADS)

    Gray, J. E.

    2001-05-01

    Mercury mines worldwide contain of some the highest concentrations of mercury on earth, and as a result of local mercury contamination, these mines represent areas of environmental concern when mine-drainage enters downstream aquatic systems. The most problematic aspect of mine site mercury contamination is the conversion of inorganic mercury to highly toxic organic mercury compounds, such as methylmercury, and their subsequent uptake by aquatic organisms in surrounding ecosystems. Mercury and methylmercury concentrations were measured in sediment and water samples collected from several inactive mercury mines in Nevada, Alaska, and the Philippines, which are part of the circum-Pacific mineral belt. The mines studied represent different mercury deposit types and sizes, and climatic settings. Geochemical data collected from these mines indicate that areas surrounding hot-springs type mercury deposits generally have lower methylmercury concentrations than silica-carbonate mercury deposits. In hot-springs mercury deposits in Nevada and Alaska, ore is dominantly cinnabar with few acid-water generating minerals such as pyrite, and as a result, mine-water drainage has near neutral pH in which there is low solubility of mercury. Conversely, silica-carbonate deposits, such as Palawan, Philippines, contain abundant cinnabar and pyrite, and the resultant acidic-mine drainage generally has higher concentrations of mercury and methylmercury. Additional factors such as the proximity of mercury mines to wetlands, climatic effects, or mine wastes containing highly soluble mercury compounds potentially enhance mercury methylation. The Palawan mercury mine may be a unique example where several adverse environmental factors produced local mercury contamination, high mercury methylation, fish contamination, and mercury poisoning of humans that consumed these contaminated fish.

  20. [Blood Flow and Regional Blood Flow Rate in the Middle Cerebral Artery during Surgical Leg Lengthening in Patients with Congenital and Acquired Limb Shortening].

    PubMed

    Schurov, V A; Popkov, A V

    2015-01-01

    This is a comparative study of changes in blood flow rate in the popliteal artery, the arteries of bone regenerate and cerebral arteries in 45 patients with congenital and acquired diseases of the limbs at different stages of surgical lengthening of 3-15 cm shortened shin by Ilizarov method. We observed an increase in regional blood flow rate in all patients during the periods of distraction and fixation. A 25% increase in blood flow rate in the middle cerebral artery on the contralateral side was found only in patients of the first adult age with acquired limb shortening. Basing on the analysis of the reaction of cerebral arteries during a functional test with additional muscle work, we suggested that the absence of reaction in congenital diseases is caused by relative excess of somatic afferentation which results from morphological and functional immaturity of brain regulatory systems.

  1. Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing

    PubMed Central

    Ross, Jason P.; Shaw, Jan M.; Molloy, Peter L.

    2013-01-01

    We have developed a method that enriches for methylated cytosines by capturing the fraction of bisulfite-treated DNA with unconverted cytosines. The method, called streptavidin bisulfite ligand methylation enrichment (SuBLiME), involves the specific labeling (using a biotin-labeled nucleotide ligand) of methylated cytosines in bisulfite-converted DNA. This step is then followed by affinity capture, using streptavidin-coupled magnetic beads. SuBLiME is highly adaptable and can be combined with deep sequencing library generation and/or genomic complexity-reduction. In this pilot study, we enriched methylated DNA from Csp6I-cut complexity-reduced genomes of colorectal cancer cell lines (HCT-116, HT-29 and SW-480) and normal blood leukocytes with the aim of discovering colorectal cancer biomarkers. Enriched libraries were sequenced with SOLiD-3 technology. In pairwise comparisons, we scored a total of 1,769 gene loci and 33 miRNA loci as differentially methylated between the cell lines and leukocytes. Of these, 516 loci were differently methylated in at least two promoter-proximal CpG sites over two discrete Csp6I fragments. Identified methylated gene loci were associated with anatomical development, differentiation and cell signaling. The data correlated with good agreement to a number of published colorectal cancer DNA methylation biomarkers and genomic data sets. SuBLiME is effective in the enrichment of methylated nucleic acid and in the detection of known and novel biomarkers. PMID:23257838

  2. Development of Biomarkers Based on DNA Methylation in the NCAPH2/LMF2 Promoter Region for Diagnosis of Alzheimer’s Disease and Amnesic Mild Cognitive Impairment

    PubMed Central

    Kobayashi, Nobuyuki; Shinagawa, Shunichiro; Nagata, Tomoyuki; Shimada, Kazuya; Shibata, Nobuto; Ohnuma, Tohru; Kasanuki, Koji; Arai, Heii; Yamada, Hisashi; Nakayama, Kazuhiko; Kondo, Kazuhiro

    2016-01-01

    From the standpoint of early interventions for dementia, a convenient method of diagnosis using biomarkers is required for Alzheimer’s disease (AD) in the early stage as well as amnesic mild cognitive impairment (aMCI). Focusing on differences in DNA methylation due to AD and aMCI, in the present study, we first conducted genome-wide screening, measuring blood DNA methylation levels by the Illumina Infinium HD Methylation Assay in 3 small age-and gender-matched groups consisting of 4 subjects each: normal controls (NC), aMCI and AD. The genome-wide analysis produced 11 DNA methylation loci that distinguished the 3 groups. For confirmation, we increased group sizes and examined samples by pyrosequencing which revealed that DNA methylation in the NCAPH2/LMF2 promoter region was significantly decreased in the AD (n = 30) and aMCI (n = 28) groups as compared to the NC group (n = 30) (P < 0.0001, ANCOVA). No association was found between methylation levels and APOE genotype. NCAPH2/LMF2 methylation levels were considered to potentially be a convenient and useful biomarker for diagnosis of AD and aMCI. PMID:26742120

  3. New constraints on the structure of Hess Deep from regional- and micro-bathymetry data acquired during RRS James Cook in Jan-Feb 2008 (JC021)

    NASA Astrophysics Data System (ADS)

    Shillington, D. J.; Ferrini, V. L.; MacLeod, C. J.; Teagle, D. A.; Gillis, K. M.; Cazenave, P. W.; Hurst, S. D.; Scientific Party, J.

    2008-12-01

    In January-February 2008, new geophysical and geological data were acquired in Hess Deep using the RRS James Cook and the British ROV Isis. Hess Deep provides a tectonic window into oceanic crust emplaced by fast seafloor spreading at the East Pacific Rise, thereby offering the opportunity to test competing hypotheses for oceanic crustal accretion. The goal of this cruise was to collect datasets that can constrain the structure and composition of the lower crustal section exposed in the south-facing slope of the Intrarift Ridge just north of the Deep, and thus provide insights into the emplacement of gabbroic lower crust at fast spreading rates. Additionally, the acquired datasets provide site survey data for IODP Proposal 551-Full. The following datasets were acquired during JC021: 1) regional multibeam bathymetry survey complemented with sub-bottom profiler (SBP) data (in selected areas), 2) two micro-bathymetry surveys, and 3) seafloor rock samples acquired with an ROV. Here we present grids of regional multibeam and microbathymetry data following post-cruise processing. Regional multibeam bathymetry were acquired using the hull-mounted Kongsberg Simrad EM120 system (12 kHz). These data provide new coverage of the northern flank of the rift as far east as 100°W, which show that it comprises of a series of 50- to 100-km-long en echelon segments. Both E-W and NE-SW striking features are observed in the immediate vicinity of the Deep, including in a newly covered region to the SW of the rift tip. Such features might arise due to the rotation of the Galapagos microplate(s), as proposed by other authors. The ROV Isis acquired micro-bathymetry data in two areas using a Simrad SM2000 (200 kHz) multibeam sonar. Data were acquired at a nominal altitude of ~100 m and speed of 0.3 kts to facilitate high-resolution mapping of seabed features and also permit coverage of two relatively large areas. Swath widths were ~200- 350 m depending on noise and seabed characteristics

  4. Methyl mercury concentrations in edible fish and shellfish from Dunedin, and other regions around the South Island, New Zealand.

    PubMed

    Sadhu, Ashish K; Kim, Jonathan P; Furrell, Hamish; Bostock, Ben

    2015-12-15

    Methyl mercury (MeHg) concentrations were determined in edible fish and shellfish available in local markets in Dunedin, New Zealand. While most of the fish species were sourced in Dunedin, some specimens of fish were also collected from waters off Picton, around Stewart Island and also off-shore of the South Island in the Puysegur and Subantarctic regions. The concentrations of MeHg were analysed in 25 different fish species and shellfish (103 muscle tissue samples). Total mercury (HgT) levels were also analysed in a few (n=12) selected fish samples. Most of the Hg was in the form of MeHg (≥ 96%). Higher MeHg concentrations were found in fish at higher trophic levels, particularly in predatory fish species such as ling, school shark, spiny dogfish and albacore tuna. Concentrations of MeHg in all samples ranged from 0.002 to 2.515 μg MeHg/g.

  5. Brain Regional α-[11C]Methyl-L-Tryptophan Trapping in Medication-Free Patients With Obsessive-Compulsive Disorder

    PubMed Central

    Berney, Alexandre; Leyton, Marco; Gravel, Paul; Sibon, Igor; Sookman, Debbie; Neto, Pedro Rosa; Diksic, Mirko; Nakai, Akio; Pinard, Gilbert; Todorov, Christo; Okazawa, Hidehiko; Blier, Pierre; Nordahl, Thomas Edward; Benkelfat, Chawki

    2013-01-01

    Context The hypothesis of a serotonin (5-hydroxytryptamine [5-HT]) dysfunction in obsessive-compulsive disorder (OCD) stems largely from the clinical efficacy of 5-HT reuptake inhibitors. Serotonergic abnormalities in the unmedicated symptomatic state, however, remain to be fully characterized. Objective To investigate brain regional 5-HT synthesis, as indexed by positron emission tomography and the α-[11C]methyl-L-tryptophan trapping constant (K*), in treatment-free adults meeting criteria for OCD. Design Between-group comparison. Setting Department of Psychiatry and Montreal Neurological Institute, McGill University, and Department of Psychology, McGill University Health Centre, Quebec, Canada. Participants Twenty-one medication-free patients with OCD (15 men with a mean [SD] age of 33.2 [9.3] years and 6 women with a mean [SD] age of 35.8 [7.1] years) and 21 healthy controls matched for age and sex (15 men with a mean [SD] age of 32.9 [10.1] years and 6 women with a mean [SD] age of 36.5.5 [8.6] years). Main Outcome Measure The α-[11C]methyl-L-tryptophan brain trapping constant K*, which was analyzed with Statistical Parametric Mapping (SPM8) and with proportional normalization (extent threshold of 100 voxels with a peak threshold of P≤.005). Results Compared with healthy controls, the patients with OCD exhibited significantly greater α-[11C]methyl-L-tryptophan trapping in the right hippocampus and left temporal gyrus (Brodmann area 20). In the larger sub-sample of all men, these same differences were also evident, as well as higher K* values in the caudate nucleus. Individual differences in symptom severity correlated positively with K* values sampled from the caudate and temporal lobe of the patients with OCD, respectively. There were no regions where the patients exhibited abnormally low K* values. Volumetric analyses found no morphometric alterations that would account for the group differences. Conclusion The results support previous reports of greater

  6. DNA methylation patterns in human tissues of uniparental origin using a zinc-Finger gene (ZNF127) from the Angelman/Prader-Willi region

    SciTech Connect

    Mowery-Rushton, P.A.; Surti, U.; Locker, J.

    1996-01-11

    In order to further our understanding of the epigenetic modification of DNA and its role in imprinting, we examined DNA methylation patterns of human tissues of uniparental origin. We used complete hydatidiform moles (CHM), which are totally androgenetic conceptions, to examine the paternal methylation pattern in the absence of a maternal contribution and we used ovarian teratomas to represent the maternal counterpart. We carried out an analysis of DNA methylation of a gene which has been shown to contain sites which are differentially methylated in a parent-specific fashion. The gene, ZNF127, is located on chromosome 15q11-q13 in the region associated with Prader-Willi and Angelman syndromes. The parent-of-origin DNA methylation has been postulated to reflect the presence of an imprint and recent studies have confirmed that ZNF127 is differentially expressed only from the paternal chromosome. We identified a unique pattern of hyper- and hypomethylated sites in androgenetic conceptions which was nearly identical to the paternal pattern found in sperm. This may represent the paternal germ-line methylation imprint. We also studied partial hydatidiform moles, non-molar triploid conceptions, normal chorionic villi, and somatic tissue. These all demonstrated a modified DNA methylation pattern characteristic of normal chorionic villi with only limited findings of the imprint. Our results suggest that human androgenetic conceptions may provide an excellent model to analyze epigenetic DNA modifications, such as methylation, in imprinted genes. The paternal allele-specific methylation imprint will also be useful clinically to confirm the androgenetic nature of suspected molar conceptions in which parental blood samples may not be available. 55 refs., 3 figs.

  7. Aberrant methylation in the promoter region of the reduced folate carrier gene is a potential mechanism of resistance to methotrexate in primary central nervous system lymphomas.

    PubMed

    Ferreri, Andrés J M; Dell'Oro, Stefania; Capello, Daniela; Ponzoni, Maurilio; Iuzzolino, Paolo; Rossi, Davide; Pasini, Felice; Ambrosetti, Achille; Orvieto, Enrico; Ferrarese, Fabio; Arrigoni, Gianluigi; Foppoli, Marco; Reni, Michele; Gaidano, Gianluca

    2004-09-01

    We investigated the prevalence and prognostic role of CpG island methylation of the reduced folate carrier (RFC) gene promoter region in primary central nervous system lymphoma (PCNSL) in immunocompetent patients. Genomic DNA from 40 PCNSL was used for methylation-specific polymerase chain reaction and bisulphite genomic sequencing of the RFC promoter region. Human immunodeficiency virus-negative systemic diffuse large B-cell lymphomas (DLBCL) were used as controls (n = 50). The impact on outcome of RFC promoter methylation was assessed in 37 PCNSL patients treated with high-dose methotrexate (HD-MTX)-based chemotherapy +/- radiotherapy. RFC promoter methylation occurred in 12 of 40 (30%) PCNSL and in four of 50 (8%) DLBCL (P = 0.01). Of 37 PCNSL treated with HD-MTX-based chemotherapy, methylation occurred in nine cases (24%, M-PCNSL), while 28 cases (76%, U-PCNSL) were negative. Three M-PCNSL (33%) and 15 U-PCNSL (54%) achieved complete remission (CR) after primary chemotherapy. Logistic regression confirmed the independent association between CR rate and International Extranodal Lymphoma Study Group score (P = 0.03), RFC promoter methylation (P = 0.07) and use of cytarabine (P = 0.08). The 3-year failure-free survival (FFS) and overall survival for M-PCNSL and U-PCNSL was 0% vs. 31 +/- 9% (P = 0.34) and 0% vs. 31 +/- 9% (P = 0.35) respectively. This is the first study to assess the methylation status of the RFC promoter in human tumour samples. RFC methylation is more common in PCNSL compared with systemic DLBCL, and is associated with a lower CR rate to HD-MTX-based chemotherapy. If confirmed in prospective trials on PCNSL treated with HD-MTX alone, these data may suggest the necessity for alternative strategies in M-PCNSL considering the increased risk of MTX resistance by tumour cells.

  8. DNA methylation of the Fthl17 5’-upstream region regulates differential Fthl17 expression in lung cancer cells and germline stem cells

    PubMed Central

    Aoki, Nana; Matsui, Yasuhisa

    2017-01-01

    The Ferritin heavy polypeptide-like 17 (Fthl17) gene is a member of the cancer/testis antigen gene family, and is preferentially expressed in cancer cells and in testis. Although DNA methylation has been linked to the regulation of human FTHL17 gene expression, detailed epigenetic regulation of its expression has not been investigated. To address this, we assessed the epigenetic regulation of murine Fthl17 gene expression in cancer cells and germ cells. Fthl17 was more highly expressed in testis, a murine lung cancer cell line, KLN205, and in germline stem cells (GSCs) than in normal lung tissues. Furthermore, the Fthl17 expression level in GSCs was significantly higher than in KLN205 cells. We performed bisulfite-sequencing and luciferase (luc) reporter assays to examine the role of DNA methylation of the Fthl17 promoter in the regulation of Fthl17 expression. In KLN205 cells, testis, and GSCs, the Fthl17 5’-upstream region was hypo-methylated compared with normal lung tissues. Luc reporter assays indicated that hypo-methylation of the -0.6 kb to 0 kb region upstream from the transcription start site (TSS) was involved in the up-regulation of Fthl17 expression in KLN205 cells and GSCs. Because the -0.6 kb to -0.3 kb or the -0.3 kb to 0 kb region were relatively more hypo-methylated in KLN205 cells and in GSCs, respectively, compared with other regions between -0.6 kb to 0 kb, those regions may contribute to Fthl17 up-regulation in each cell type. Following treatment with 5-Azacytidine, the -0.3 kb to 0 kb region became hypo-methylated, and Fthl17 expression was up-regulated in KLN205 cells to a level comparable to that in GSCs. Together, the results suggest that hypo-methylation of different but adjacent regions immediately upstream of the Fthl17 gene contribute to differential expression levels in lung cancer cells and GSCs, and hypo-methylation of the TSS-proximal region may be critical for high level expression. PMID:28207785

  9. WHO Collaborating Centre for Acquired Immunodeficiency Syndrome for the Eastern Mediterranean Regional Office, Faculty of Medicine, Kuwait University, Kuwait.

    PubMed

    Altawalah, Haya; Al-Nakib, Widad

    2014-01-01

    In the early 1980s, the World Health Organization (WHO) designated the Virology Unit of the Faculty of Medicine, Health Sciences Centre, Kuwait University, Kuwait, a collaborating centre for AIDS for the Eastern Mediterranean Regional Office (EMRO), recognizing it to be in compliance with WHO guidelines. In this centre, research integral to the efforts of WHO to combat AIDS is conducted. In addition to annual workshops and symposia, the centre is constantly updating and renewing its facilities and capabilities in keeping with current and latest advances in virology. As an example of the activities of the centre, the HIV-1 RNA viral load in plasma samples of HIV-1 patients is determined by real-time PCR using the AmpliPrep TaqMan HIV-1 test v2.0. HIV-1 drug resistance is determined by sequencing the reverse transcriptase and protease regions on the HIV-1 pol gene, using the TRUGENE HIV-1 Genotyping Assay on the OpenGene® DNA Sequencing System. HIV-1 subtypes are determined by sequencing the reverse transcriptase and protease regions on the HIV-1 pol gene using the genotyping assays described above. A fundamental program of Kuwait's WHO AIDS collaboration centre is the national project on the surveillance of drug resistance in human deficiency virus in Kuwait, which illustrates how the centre and its activities in Kuwait can serve the EMRO region of WHO.

  10. [Clinical features of oral lesions in patients with human immunodeficiency virus infection/acquired immunodeficiency syndrome in Guangxi autonomous region].

    PubMed

    Yong, Xiangzhi; Jiang, Lanlan; Lu, Xiangchan; Liu, Wei; Wu, Nianning; Tao, Renchuan

    2014-08-01

    To investigate the features of oral lesions in patients with human immunodeficiency virus infection/acquired immunodeficiency syndrome (HIV/AIDS). A total of 127 HIV-seropositive patients were interviewed for health information and examined for their HIV-related oral lesions according to the EC Clearing House Criteria on Oral Problems related to HIV-Infection (1992). The examinations were conducted by dental specialist and HIV specialist. The CD4 T cell count in peripheral blood of the patients was tested by flow cytometry. The patients were divided into HIV- infected group (42) and AIDS group (85) according to CDC Classification System for HIV- Infected Adults and Adolescents (revised in 1993). Chi-square test was used to test the relationship between systemic disease and oral lesions, and the difference of the prevalence of oral lesions between the two groups. Among the 127 patients, oral candidiasis (51/127), oral hairy leukoplakia (24/127) were common oral manifestation. There was no relationship between the oral manifestation and systemic disease (P = 0.397). The occurrence of oral lesions and oral candidiasis was significantly different between the two groups (χ² = 7.684, P = 0.006; χ² = 14.410, P < 0.001). The CD4 count was related to the prevalence of oral lesions (P = 0.006) and oral candidasis (P = 0.003). Most oral lesions appeared before the appearance of systemic disease. Oral candidiasis and oral hairy leukoplakia were the most common lesions.Oral lesions had no relationship with systemic disease but could be still an indicator for disease progress.

  11. Seasonal patterns of viral and bacterial infections among children hospitalized with community-acquired pneumonia in a tropical region.

    PubMed

    Nascimento-Carvalho, Cristiana M; Cardoso, Maria-Regina A; Barral, Aldina; Araújo-Neto, César A; Oliveira, Juliana R; Sobral, Luciana S; Saukkoriipi, Annika; Paldanius, Mika; Vainionpää, Raija; Leinonen, Maija; Ruuskanen, Olli

    2010-12-01

    Community-acquired pneumonia (CAP) is a common cause of morbidity among children. Evidence on seasonality, especially on the frequency of viral and bacterial causative agents is scarce; such information may be useful in an era of changing climate conditions worldwide. To analyze the frequency of distinct infections, meteorological indicators and seasons in children hospitalized for CAP in Salvador, Brazil, nasopharyngeal aspirate and blood were collected from 184 patients aged < 5 y over a 21-month period. Fourteen microbes were investigated and 144 (78%) cases had the aetiology established. Significant differences were found in air temperature between spring and summer (p = 0.02) or winter (p < 0.001), summer and fall (p = 0.007) or winter (p < 0.001), fall and winter (p = 0.002), and on precipitation between spring and fall (p = 0.01). Correlations were found between: overall viral infections and relative humidity (p = 0.006; r = 0.6) or precipitation (p = 0.03; r = 0.5), parainfluenza and precipitation (p = 0.02; r = -0.5), respiratory syncytial virus (RSV) and air temperature (p = 0.048; r = -0.4) or precipitation (p = 0.045; r = 0.4), adenovirus and precipitation (p = 0.02; r = 0.5), pneumococcus and air temperature (p = 0.04; r = -0.4), and Chlamydia trachomatis and relative humidity (p = 0.02; r = -0.5). The frequency of parainfluenza infection was highest during spring (32.1%; p = 0.005) and that of RSV infection was highest in the fall (36.4%; p < 0.001). Correlations at regular strength were found between several microbes and meteorological indicators. Parainfluenza and RSV presented marked seasonal patterns.

  12. The tRNA methyltransferase NSun2 stabilizes p16INK4 mRNA by methylating the 3′-untranslated region of p16

    PubMed Central

    Zhang, Xiaotian; Liu, Zhenyun; Yi, Jie; Tang, Hao; Xing, Junyue; Yu, Minqwei; Tong, Tanjun; Shang, Yongfeng; Gorospe, Myriam; Wang, Wengong

    2012-01-01

    The impact of methylation of the 3′-untranslated region (UTR) of a messenger RNA (mRNA) remains largely unknown. Here we show that NSun2, a transfer RNA methyltransferase, inhibits the turnover of p16INK4 mRNA. Knockdown of NSun2 reduces p16 expression by shortening the half-life of the p16 mRNA, while overexpression of NSun2 stabilizes the p16 mRNA. In vitro methylation assays show that NSun2 methylates the p16 3′UTR at A988. Knockdown of NSun2 reduces the stability of the EGFP-p16 chimeric reporter transcripts bearing wild-type p16 3′UTR, but not p16 3′UTR with a mutant methylation site. Methylation by NSun2 prevents the association of p16 3′UTR with HuR, AUF1 and Ago2/RISC, and prevents the recruitment of EGFP-p16 3′UTR chimeric transcripts to processing bodies. In response to oxidative stress, NSun2 is essential for elevating p16 expression levels. We conclude that NSun2-mediated methylation of the p16 3′UTR is a novel mechanism to stabilize p16 mRNA. PMID:22395603

  13. The tRNA methyltransferase NSun2 stabilizes p16INK⁴ mRNA by methylating the 3'-untranslated region of p16.

    PubMed

    Zhang, Xiaotian; Liu, Zhenyun; Yi, Jie; Tang, Hao; Xing, Junyue; Yu, Minqwei; Tong, Tanjun; Shang, Yongfeng; Gorospe, Myriam; Wang, Wengong

    2012-03-06

    The impact of methylation of the 3'-untranslated region (UTR) of a messenger RNA (mRNA) remains largely unknown. Here we show that NSun2, a transfer RNA methyltransferase, inhibits the turnover of p16(INK4) mRNA. Knockdown of NSun2 reduces p16 expression by shortening the half-life of the p16 mRNA, while overexpression of NSun2 stabilizes the p16 mRNA. In vitro methylation assays show that NSun2 methylates the p16 3'UTR at A988. Knockdown of NSun2 reduces the stability of the EGFP-p16 chimeric reporter transcripts bearing wild-type p16 3'UTR, but not p16 3'UTR with a mutant methylation site. Methylation by NSun2 prevents the association of p16 3'UTR with HuR, AUF1 and Ago2/RISC, and prevents the recruitment of EGFP-p16 3'UTR chimeric transcripts to processing bodies. In response to oxidative stress, NSun2 is essential for elevating p16 expression levels. We conclude that NSun2-mediated methylation of the p16 3'UTR is a novel mechanism to stabilize p16 mRNA.

  14. Generation of Five Human Lactoferrin Transgenic Cloned Goats Using Fibroblast Cells and Their Methylation Status of Putative Differential Methylation Regions of IGF2R and H19 Imprinted Genes

    PubMed Central

    Sun, Yanyan; Zhang, Yanli; Wang, Ziyu; Song, Yang; Wang, Feng

    2013-01-01

    Background Somatic cell nuclear transfer (SCNT) is a promising technique to produce transgenic cloned mammalian, including transgenic goats which may produce Human Lactoferrin (hLF). However, success percentage of SCNT is low, because of gestational and neonatal failure of transgenic embryos. According to the studies on cattle and mice, DNA methylation of some imprinted genes, which plays a vital role in the reprogramming of embryo in NT maybe an underlying mechanism. Methodology/Principal Findings Fibroblast cells were derived from the ear of a two-month-old goat. The vector expressing hLF was constructed and transfected into fibroblasts. G418 selection, EGFP expression, PCR, and cell cycle distribution were applied sequentially to select transgenic cells clones. After NT and embryo transfer, five transgenic cloned goats were obtained from 240 cloned transgenic embryos. These transgenic goats were identified by 8 microsatellites genotyping and southern blot. Of the five transgenic goats, 3 were lived after birth, while 2 were dead during gestation. We compared differential methylation regions (DMR) pattern of two paternally imprinted genes (H19 and IGF2R) of the ear tissues from the lived transgenic goats, dead transgenic goats, and control goats from natural reproduction. Hyper-methylation pattern appeared in cloned aborted goats, while methylation status was relatively normal in cloned lived goats compared with normal goats. Conclusions/Significance In this study, we generated five hLF transgenic cloned goats by SCNT. This is the first time the DNA methylation of lived and dead transgenic cloned goats was compared. The results demonstrated that the methylation status of DMRs of H19 and IGF2R were different in lived and dead transgenic goats and therefore this may be potentially used to assess the reprogramming status of transgenic cloned goats. Understanding the pattern of gene imprinting may be useful to improve cloning techniques in future. PMID:24204972

  15. DNA methylation aberrations rather than polymorphisms of FZD3 gene increase the risk of spina bifida in a high-risk region for neural tube defects.

    PubMed

    Shangguan, Shaofang; Wang, Li; Chang, Shaoyan; Lu, Xiaoling; Wang, Zhen; Wu, Lihua; Wang, Jianhua; Wang, Xiuwei; Guan, Zhen; Bao, Yihua; Zhao, Huizhi; Zou, Jizhen; Niu, Bo; Zhang, Ting

    2015-01-01

    Animal models of neural tube defects (NTDs) have indicated roles for the Fzd3 gene and the planar cell polarity signaling pathway in convergent extension. We investigated the involvement of FZD3 in genetic and epigenetic mechanisms associated with human NTDs, especially spina bifida. We explored the effects of variants spanning the FZD3 gene in NTDs and examined the role of aberrant methylation of the FZD3 promoter on gene expression in brain tissue in spina bifida. Six FZD3 single nucleotide polymorphisms were genotyped using a MassARRAY system in tissue from 165 NTD fetuses and 152 controls. DNA methylation aberrations in the FZD3 promoter region were detected using a MassARRAY EpiTYPER (17 CpG units from -500 to -2400 bp from the transcription start site) in brain tissue from 77 spina bifida and 74 control fetuses. None of the six single nucleotide polymorphisms evaluated were significantly associated with spina bifida, but the mean methylation level was significantly higher in spina bifida samples (13.70%) compared with control samples (10.91%) (p = 0.001). In terms of specific sites, DNA methylation levels were significantly higher in the spina bifida samples at 14 of the 17 CpG units, which mostly included in R2 region. FZD3 mRNA expression was negatively correlated with methylation of the FZD3 promoter region, especially the R2 region (R = 0.970; p = 0.001) in HeLa cells. The results of this study suggest that DNA methylation plays an important role in FZD3 gene expression regulation and may be associated with an increased risk of spina bifida. © 2014 Wiley Periodicals, Inc.

  16. Pneumococcal Conjugated Vaccine Reduces the High Mortality for Community-Acquired Pneumonia in the Elderly: an Italian Regional Experience

    PubMed Central

    Gallo, Tolinda; Furlan, Patrizia; Romor, Pierantonio; Bertoncello, Chiara; Buja, Alessandra; Baldovin, Tatjana

    2016-01-01

    Background Community-acquired pneumonia (CAP) is an important cause of illness and death worldwide, particularly among the elderly. Previous studies on the factors associated with mortality in patients hospitalized for CAP revealed a direct association between the type of microorganism involved, the characteristics of the patient and mortality. Vaccination status against pneumococcal disease was not considered. We conducted a retrospective analysis on the mortality rates after a first hospitalization for CAP in north-east Italy with a view to examining especially the role of anti-pneumococcal vaccination as a factor associated with pneumonia-related mortality at one year. Method Between 2012–2013, patients aged 65+ hospitalized with a primary diagnosis of CAP, identified based on International Classification of Diseases, Ninth Revision, Clinical Modification codes 481–486, were enrolled in the study only once. Patients were divided into three groups by pneumococcal vaccination status: 1) 13-valent pneumococcal conjugate vaccine (PCV13) prior to their hospitalization; 2) 23-valent pneumococcal polysaccharide vaccine (PPV23) within 5 years before hospitalization and 3) unvaccinated or PPV23 more than 5 years prior to admission. Gender, age, length of hospital stay and influenza vaccination were considered. Comorbidities were ascertained by means of a properly coded diagnosis. Every patient was followed up for 1 year and the outcome investigated was mortality for any cause and for pneumonia. Results A total of 4,030 patient were included in the study; mean age at the time of admission to hospital was 84.3±7.7; 50.9% were female. 74.2% of subjects had at least one comorbidity; 73.7% has been vaccinated against influenza. Regard to pneumococcal vaccine, 80.4% of patients were not vaccinated, 14.5% vaccinated with PPV23 and 5.1% with PCV13. The 1-year survival rates after hospitalization for pneumonia were 83.6%, 85.9% and 89.3% in the unvaccinated, PPV23 and PCV13

  17. Effects of pentadecapeptide BPC157 on regional serotonin synthesis in the rat brain: alpha-methyl-L-tryptophan autoradiographic measurements.

    PubMed

    Tohyama, Y; Sikirić, P; Diksic, M

    2004-12-03

    A novel pentadecapeptide, BPC157, was recently reported to have a large spectrum of in vivo activities, from anti-ulcer to central action on the brain dopaminergic system. The mechanisms of these actions are not well understood. In this study, the evaluation of the effects of acute and repeated administration of BPC157 on serotonin (5-HT) synthesis in the rat brain is reported. The alpha-[14C]methyl-L-tryptophan (alpha-MTrp) autoradiographic method was used to measure regional 5-HT synthesis rates. In the first series of experiments, a single dose treatment of BPC157 (10 microg/kg) administered intraperitoneally 40 min before the alpha-MTrp tracer injection significantly reduced the regional rate of 5-HT synthesis in the dorsal thalamus, hippocampus, lateral geniculate body and hypothalamus. 5-HT synthesis rates in the substantia nigra reticulate and medial anterior olfactory nucleus in BPC157 treated rats were significantly higher than in the control rats. No significant change in the synthesis rate was observed in the raphe nuclei. In the second series of experiments, following a 7-day treatment with BPC157 (10 microg/kg; s.c.), a significant reduction in the 5-HT synthesis rate was observed in the dorsal raphe nucleus, and significant increases were observed in the substantia nigra, lateral caudate, accumbens nucleus and superior olive. This data suggests that BPC157, a gut peptide, influences brain 5-HT synthesis in rats, but we cannot determine, from this data, the mechanism of this action.

  18. Fully automated rodent brain MR image processing pipeline on a Midas server: from acquired images to region-based statistics

    PubMed Central

    Budin, Francois; Hoogstoel, Marion; Reynolds, Patrick; Grauer, Michael; O'Leary-Moore, Shonagh K.; Oguz, Ipek

    2013-01-01

    Magnetic resonance imaging (MRI) of rodent brains enables study of the development and the integrity of the brain under certain conditions (alcohol, drugs etc.). However, these images are difficult to analyze for biomedical researchers with limited image processing experience. In this paper we present an image processing pipeline running on a Midas server, a web-based data storage system. It is composed of the following steps: rigid registration, skull-stripping, average computation, average parcellation, parcellation propagation to individual subjects, and computation of region-based statistics on each image. The pipeline is easy to configure and requires very little image processing knowledge. We present results obtained by processing a data set using this pipeline and demonstrate how this pipeline can be used to find differences between populations. PMID:23964234

  19. Fully automated rodent brain MR image processing pipeline on a Midas server: from acquired images to region-based statistics.

    PubMed

    Budin, Francois; Hoogstoel, Marion; Reynolds, Patrick; Grauer, Michael; O'Leary-Moore, Shonagh K; Oguz, Ipek

    2013-01-01

    Magnetic resonance imaging (MRI) of rodent brains enables study of the development and the integrity of the brain under certain conditions (alcohol, drugs etc.). However, these images are difficult to analyze for biomedical researchers with limited image processing experience. In this paper we present an image processing pipeline running on a Midas server, a web-based data storage system. It is composed of the following steps: rigid registration, skull-stripping, average computation, average parcellation, parcellation propagation to individual subjects, and computation of region-based statistics on each image. The pipeline is easy to configure and requires very little image processing knowledge. We present results obtained by processing a data set using this pipeline and demonstrate how this pipeline can be used to find differences between populations.

  20. Region-Based 3d Surface Reconstruction Using Images Acquired by Low-Cost Unmanned Aerial Systems

    NASA Astrophysics Data System (ADS)

    Lari, Z.; Al-Rawabdeh, A.; He, F.; Habib, A.; El-Sheimy, N.

    2015-08-01

    Accurate 3D surface reconstruction of our environment has become essential for an unlimited number of emerging applications. In the past few years, Unmanned Aerial Systems (UAS) are evolving as low-cost and flexible platforms for geospatial data collection that could meet the needs of aforementioned application and overcome limitations of traditional airborne and terrestrial mobile mapping systems. Due to their payload restrictions, these systems usually include consumer-grade imaging and positioning sensor which will negatively impact the quality of the collected geospatial data and reconstructed surfaces. Therefore, new surface reconstruction surfaces are needed to mitigate the impact of using low-cost sensors on the final products. To date, different approaches have been proposed to for 3D surface construction using overlapping images collected by imaging sensor mounted on moving platforms. In these approaches, 3D surfaces are mainly reconstructed based on dense matching techniques. However, generated 3D point clouds might not accurately represent the scanned surfaces due to point density variations and edge preservation problems. In order to resolve these problems, a new region-based 3D surface renostruction trchnique is introduced in this paper. This approach aims to generate a 3D photo-realistic model of individually scanned surfaces within the captured images. This approach is initiated by a Semi-Global dense Matching procedure is carried out to generate a 3D point cloud from the scanned area within the collected images. The generated point cloud is then segmented to extract individual planar surfaces. Finally, a novel region-based texturing technique is implemented for photorealistic reconstruction of the extracted planar surfaces. Experimental results using images collected by a camera mounted on a low-cost UAS demonstrate the feasibility of the proposed approach for photorealistic 3D surface reconstruction.

  1. Specific association between the methyl-CpG-binding domain protein 2 and the hypermethylated region of the human telomerase reverse transcriptase promoter in cancer cells.

    PubMed

    Chatagnon, Amandine; Bougel, Stéphanie; Perriaud, Laury; Lachuer, Joël; Benhattar, Jean; Dante, Robert

    2009-01-01

    Human telomerase reverse transcriptase (hTERT) is expressed in most cancer cells. Paradoxically, its promoter is embedded in a hypermethylated CpG island. A short region escapes to this alteration, allowing a basal level of transcription. However, the methylation of adjacent regions may play a role in the maintenance of low hTERT expression. It is now well established that methyl-CpG binding domain proteins mediate the transcriptional silencing of hypermethylated genes. The potential involvement of these proteins in the control of hTERT expression was firstly investigated in HeLa cells. Chromatin immunoprecipitation assays showed that only methyl-CpG-binding domain protein 2 (MBD2) associated the hypermethylated hTERT promoter. In MBD2 knockdown HeLa cells, constitutively depleted in MBD2, neither methyl CpG binding protein 2 (MeCP2) nor MBD1 acted as substitutes for MBD2. MBD2 depletion by transient or constitutive RNA interference led to an upregulation of hTERT transcription that can be downregulated by expressing mouse Mbd2 protein. Our results indicate that MBD2 is specifically and directly involved in the transcriptional repression of hTERT in HeLa cells. This specific transcriptional repression was also observed in breast, liver and neuroblastoma cancer cell lines. Thus, MBD2 seems to be a general repressor of hTERT in hTERT-methylated telomerase-positive cells.

  2. Acquired hyperpigmentations*

    PubMed Central

    Cestari, Tania Ferreira; Dantas, Lia Pinheiro; Boza, Juliana Catucci

    2014-01-01

    Cutaneous hyperpigmentations are frequent complaints, motivating around 8.5% of all dermatological consultations in our country. They can be congenital, with different patterns of inheritance, or acquired in consequence of skin problems, systemic diseases or secondary to environmental factors. The vast majority of them are linked to alterations on the pigment melanin, induced by different mechanisms. This review will focus on the major acquired hyperpigmentations associated with increased melanin, reviewing their mechanisms of action and possible preventive measures. Particularly prominent aspects of diagnosis and therapy will be emphasized, with focus on melasma, post-inflammatory hyperpigmentation, periorbital pigmentation, dermatosis papulosa nigra, phytophotodermatoses, flagellate dermatosis, erythema dyschromicum perstans, cervical poikiloderma (Poikiloderma of Civatte), acanthosis nigricans, cutaneous amyloidosis and reticulated confluent dermatitis PMID:24626644

  3. The methylation of the C-terminal region of hnRNPQ (NSAP1) is important for its nuclear localization

    SciTech Connect

    Passos, Dario O.; Quaresma, Alexandre J.C.; Kobarg, Joerg . E-mail: jkobarg@lnls.br

    2006-07-28

    Protein arginine methylation is an irreversible post-translational protein modification catalyzed by a family of at least nine different enzymes entitled PRMTs (protein arginine methyl transferases). Although PRMT1 is responsible for 85% of the protein methylation in human cells, its substrate spectrum has not yet been fully characterized nor are the functional consequences of methylation for the protein substrates well understood. Therefore, we set out to employ the yeast two-hybrid system in order to identify new substrate proteins for human PRMT1. We were able to identify nine different PRMT1 interacting proteins involved in different aspects of RNA metabolism, five of which had been previously described either as substrates for PRMT1 or as functionally associated with PRMT1. Among the four new identified possible protein substrates was hnRNPQ3 (NSAP1), a protein whose function has been implicated in diverse steps of mRNA maturation, including splicing, editing, and degradation. By in vitro methylation assays we were able to show that hnRNPQ3 is a substrate for PRMT1 and that its C-terminal RGG box domain is the sole target for methylation. By further studies with the inhibitor of methylation Adox we provide evidence that hnRNPQ1-3 are methylated in vivo. Finally, we demonstrate by immunofluorescence analysis of HeLa cells that the methylation of hnRNPQ is important for its nuclear localization, since Adox treatment causes its re-distribution from the nucleus to the cytoplasm.

  4. DNA methylation within the I.4 promoter region correlates with CYPl19A1 gene expression in human ex vivo mature omental and subcutaneous adipocytes

    PubMed Central

    2013-01-01

    Background DNA methylation at specific CpG sites within gene promoter regions is known to regulate transcriptional activity in vitro. In human adipose tissue, basal transcription of the aromatase (CYP19A1) gene is driven primarily by the I.4 promoter however the role of DNA methylation in regulating expression in ex vivo mature adipocytes is unknown. This observational study reports the correlation of DNA methylation within the I.4 promoter region of human mature subcutaneous and omental adipocytes with aromatase expression and body composition measures. Methods Omental and subcutaneous adipose tissue were collected from 25 obese subjects undergoing bariatric surgery and the mature adipocyte fraction purified. DNA methylation status of 5 CpG sites within a 550 base pair region encompassing the transcription start site (TSS) of promoter I.4 was determined using pyrosequencing. Relative aromatase and I.4 promoter specific mRNA expression was determined by qRT-PCR and whole body DXA performed in 25 participants. Results Site-specific DNA methylation varied from 21 ± 10% to 81 ± 11%. In omental adipocytes percentage methylation at the I.4.1 and I.4.2 CpG sites, but not other nearby sites, was negatively correlated with relative aromatase mRNA expression (R = - 0.52, P = 0.017 and R = - 0.52, P = 0.015). In contrast subcutaneous adipocytes percentage DNA methylation at the I.4.3 and I.4.5 sites were positively correlated with relative aromatase mRNA expression (R = 0.47, P = 0.022 and R = 0.55, P = 0.004). In a small subset of patients DNA methylation at the I.4.5 site was also positively correlated with whole body lean mass, bone mineral content and density. Conclusions In conclusion in mature adipocytes, the primary source of estradiol after menopause, increasing DNA methylation was correlated with aromatase mRNA expression and thus estradiol biosynthesis. These findings support a tissue-specific epigenetic regulation of the

  5. Lectins from opportunistic bacteria interact with acquired variable-region glycans of surface immunoglobulin in follicular lymphoma

    PubMed Central

    Schneider, Dunja; Dühren-von Minden, Marcus; Alkhatib, Alabbas; Setz, Corinna; van Bergen, Cornelis A. M.; Benkißer-Petersen, Marco; Wilhelm, Isabel; Villringer, Sarah; Krysov, Sergey; Packham, Graham; Zirlik, Katja; Römer, Winfried; Buske, Christian; Stevenson, Freda K.; Veelken, Hendrik

    2015-01-01

    B-cell antigen receptor (BCR) expression is a key feature of most B-cell lymphomas, but the mechanisms of BCR signal induction and the involvement of autoantigen recognition remain unclear. In follicular lymphoma (FL) B cells, BCR expression is retained despite a chromosomal translocation that links the antiapoptotic gene BCL2 to the regulatory elements of immunoglobulin genes, thereby disrupting 1 heavy-chain allele. A remarkable feature of FL-BCRs is the acquisition of potential N-glycosylation sites during somatic hypermutation. The introduced glycans carry mannose termini, which create potential novel binding sites for mannose-specific lectins. Here, we investigated the effect of N-linked variable-region glycosylation for BCR interaction with cognate antigen and with lectins of different origins. N-glycans were found to severely impair BCR specificity and affinity to the initial cognate antigen. In addition, we found that lectins from Pseudomonas aeruginosa and Burkholderia cenocepacia bind and stimulate FL cells. Human exposure to these bacteria can occur by contact with soil and water. In addition, they represent opportunistic pathogens in susceptible hosts. Understanding the role of bacterial lectins might elucidate the pathogenesis of FL and establish novel therapeutic approaches. PMID:25784678

  6. Lectins from opportunistic bacteria interact with acquired variable-region glycans of surface immunoglobulin in follicular lymphoma.

    PubMed

    Schneider, Dunja; Dühren-von Minden, Marcus; Alkhatib, Alabbas; Setz, Corinna; van Bergen, Cornelis A M; Benkißer-Petersen, Marco; Wilhelm, Isabel; Villringer, Sarah; Krysov, Sergey; Packham, Graham; Zirlik, Katja; Römer, Winfried; Buske, Christian; Stevenson, Freda K; Veelken, Hendrik; Jumaa, Hassan

    2015-05-21

    B-cell antigen receptor (BCR) expression is a key feature of most B-cell lymphomas, but the mechanisms of BCR signal induction and the involvement of autoantigen recognition remain unclear. In follicular lymphoma (FL) B cells, BCR expression is retained despite a chromosomal translocation that links the antiapoptotic gene BCL2 to the regulatory elements of immunoglobulin genes, thereby disrupting 1 heavy-chain allele. A remarkable feature of FL-BCRs is the acquisition of potential N-glycosylation sites during somatic hypermutation. The introduced glycans carry mannose termini, which create potential novel binding sites for mannose-specific lectins. Here, we investigated the effect of N-linked variable-region glycosylation for BCR interaction with cognate antigen and with lectins of different origins. N-glycans were found to severely impair BCR specificity and affinity to the initial cognate antigen. In addition, we found that lectins from Pseudomonas aeruginosa and Burkholderia cenocepacia bind and stimulate FL cells. Human exposure to these bacteria can occur by contact with soil and water. In addition, they represent opportunistic pathogens in susceptible hosts. Understanding the role of bacterial lectins might elucidate the pathogenesis of FL and establish novel therapeutic approaches.

  7. DNMT3B interacts with constitutive centromere protein CENP-C to modulate DNA methylation and the histone code at centromeric regions.

    PubMed

    Gopalakrishnan, Suhasni; Sullivan, Beth A; Trazzi, Stefania; Della Valle, Giuliano; Robertson, Keith D

    2009-09-01

    DNA methylation is an epigenetically imposed mark of transcriptional repression that is essential for maintenance of chromatin structure and genomic stability. Genome-wide methylation patterns are mediated by the combined action of three DNA methyltransferases: DNMT1, DNMT3A and DNMT3B. Compelling links exist between DNMT3B and chromosome stability as emphasized by the mitotic defects that are a hallmark of ICF syndrome, a disease arising from germline mutations in DNMT3B. Centromeric and pericentromeric regions are essential for chromosome condensation and the fidelity of segregation. Centromere regions contain distinct epigenetic marks, including dense DNA hypermethylation, yet the mechanisms by which DNA methylation is targeted to these regions remains largely unknown. In the present study, we used a yeast two-hybrid screen and identified a novel interaction between DNMT3B and constitutive centromere protein CENP-C. CENP-C is itself essential for mitosis. We confirm this interaction in mammalian cells and map the domains responsible. Using siRNA knock downs, bisulfite genomic sequencing and ChIP, we demonstrate for the first time that CENP-C recruits DNA methylation and DNMT3B to both centromeric and pericentromeric satellite repeats and that CENP-C and DNMT3B regulate the histone code in these regions, including marks characteristic of centromeric chromatin. Finally, we demonstrate that loss of CENP-C or DNMT3B leads to elevated chromosome misalignment and segregation defects during mitosis and increased transcription of centromeric repeats. Taken together, our data reveal a novel mechanism by which DNA methylation is targeted to discrete regions of the genome and contributes to chromosomal stability.

  8. Mitigation of Variability among 3D Echocardiography-Derived Regional Strain Values Acquired by Multiple Ultrasound Systems by Vendor Independent Analysis

    PubMed Central

    Streiff, Cole; Zhu, Meihua; Shimada, Eriko; Sahn, David J.; Ashraf, Muhammad

    2016-01-01

    Introduction This study compared the variability of 3D echo derived circumferential and longitudinal strain values computed from vendor-specific and vendor-independent analyses of images acquired using ultrasound systems from different vendors. Methods Ten freshly harvested porcine hearts were studied. Each heart was mounted on a custom designed phantom and driven to simulate normal cardiac motion. Cardiac rotation was digitally controlled and held constant at 5°, while pumped stroke volume (SV) ranged from 30-70ml. Full-volume image data was acquired using three different ultrasound systems from different vendors. The image data was analyzed for longitudinal and circumferential strains (LS, CS) using both vendor-specific and vendor-independent analysis packages. Results Good linear relationships were observed for each vendor-specific analysis package for both CS and LS at the mid-anterior segment, with correlation coefficients ranging from 0.82–0.91 (CS) and 0.86–0.89 (LS). Comparable linear regressions were observed for results determined by a vendor independent program (CS: R = 0.82–0.89; LS: R = 0.86–0.89). Variability between analysis packages was examined via a series of ANOVA tests. A statistical difference was found between vendor-specific analysis packages (p<0.001), while no such difference was observed between ultrasound systems when using the vendor-independent program (p>0.05). Conclusions Circumferential and longitudinal regional strain values differ when quantified by vendor-specific analysis packages; however, this variability is mitigated by use of a vendor-independent quantification method. These results suggest that echocardiograms acquired using different ultrasound systems could be meaningfully compared using vendor-independent software. PMID:27149685

  9. Improved spectroscopic line list of methyl chloride in the 1900-2600 cm-1 spectral region

    NASA Astrophysics Data System (ADS)

    Nikitin, A. V.; Dmitrieva, T. A.; Gordon, I. E.

    2016-07-01

    Parameters of line positions and line intensities up to 2×10-25 cm-1/(molecule cm-2) for 12CH335Cl and 12CH337Cl were retrieved from the Fourier transform spectra in the range of 1900-2600 cm-1. Line intensities were scaled with measurements from literature. Measured line positions and intensities were treated using global effective Hamiltonian and dipole moment model. The RMS of intensity fitting was 7.4% for 12CH335Cl and 6.6% for 12CH337Cl. List of positions and intensities were calculated for 22,098 and 21,014 lines between 1900 and 2600 cm-1 for 12CH335Cl and 12CH337Cl, respectively. Updated intensities allow extending assignments. The new line list of positions and intensities for both isotopologues in this spectral region was calculated. The calculations from the line list of this work have been compared with values from the HITRAN2012 database and PNNL spectra.

  10. Sterically hindered complexes of platinum(II) with planar heterocyclic nitrogen donors. A novel complex with 1-methyl-cytosine has a spectrum of activity different from cisplatin and is able of overcoming acquired cisplatin resistance.

    PubMed

    Margiotta, Nicola; Natile, Giovanni; Capitelli, Francesco; Fanizzi, Francesco P; Boccarelli, Angelina; De Rinaldis, Pietro; Giordano, Domenico; Coluccia, Mauro

    2006-11-01

    A very interesting series of water soluble platinum compounds violating some of the classical structure-activity relationships, but still showing antitumor activity, was reported by Hollis and collaborators some 25 years ago [L.S. Hollis, A.R. Amundsenm, E.W. Stern. J. Med. Chem. 32 (1989) 128-136]. The compounds, having formula [PtClA(2)L](+) (A(2)=two monodentate or a bidentate amine, L=a secondary or tertiary amine or a N-donor heterocycle), were characterized by a positive charge and three non-labile N-donor ligands. We have extended the investigation to analogous compounds in which 2,9-dimethyl-1,10-phenanthroline has taken the place of the A(2) ligand(s) and L is 2-picoline (1), 6-amino-2-picoline (2), or 1-methyl-cytosine (3). The X-ray analysis of 2 has revealed a bow-like distortion of the phenanthroline plane, a sloping of the phenanthroline plane with respect to the coordination plane, and an overall shielding of the metallic core by the ortho substituents of the phenanthroline and pyridine ligands. In vitro grow inhibition assays have been performed on the most water soluble complex 3. The results indicate that this complex is characterized by a potent growth inhibitory activity with mean IC(50) value (in a panel of 11 human tumor cell lines) of 1.1 microM to be compared with a mean value of 3.8 microM for cisplatin. The same compound also appears to completely overcome the acquired cisplatin resistance stemming from reduced uptake or a multifocal mechanism, thus pointing to a mechanism of action distinctly different from that of cisplatin.

  11. Methyl and total mercury in precipitation in the Great Lakes region

    NASA Astrophysics Data System (ADS)

    Hall, B. D.; Manolopoulos, H.; Hurley, J. P.; Schauer, J. J.; St. Louis, V. L.; Kenski, D.; Graydon, J.; Babiarz, C. L.; Cleckner, L. B.; Keeler, G. J.

    Methylmercury (MeHg) and total mercury (THg) concentrations were measured in precipitation collected from five US sites in the Great Lakes region: three sites on the southern shore of Lake Superior (Brule River, WI, Eagle Harbor, MI, and Tahquamenon Falls, MI), one at Isle Royale National Park (MI), and one in southern Wisconsin (Devil's Lake), between May 1997 and December 2003. MeHg and THg concentrations at these sites were compared to MeHg and THg concentrations in precipitation collected at the Experimental Lakes Area (ELA) in north-western Ontario, Canada. Detectable MeHg concentrations (>0.01 ng L -1) were found in the majority of rain and snow samples collected from all sites (range=0.01-0.85 ng L -1). In general, the lowest MeHg concentrations were observed in samples taken at Tahquamenon Falls and the ELA, and the highest MeHg concentrations in precipitation were observed in samples collected from Brule River and Eagle Harbor. Total Hg concentrations in precipitation were generally between 10 and 60 ng L -1, exceeding 60 ng L -1 in one precipitation event sampled from each of Brule River, Isle Royale, Tahquamenon Falls, and Devil's Lake. The proportion of THg that was MeHg (%MeHg), was less than 6% at all sites, with the exception of seven events at Tahquamenon Falls and two events at the ELA that were between 6% and 18% MeHg. Generally, the highest MeHg concentrations were found in low-volume precipitation events (<100 mL). At Tahquamenon Falls, meteorological analysis indicated that events with higher MeHg concentrations and %MeHg exceeding 6% were generally associated with lake effect precipitation and weak local winds.

  12. Sevoflurane attenuate hypoxia-induced VEGF level in tongue squamous cell carcinoma cell by upregulating the DNA methylation states of the promoter region.

    PubMed

    Lu, Yi; Wang, Jing; Yan, Jia; Yang, Yaqiong; Sun, Yu; Huang, Yan; Hu, Rong; Zhang, Ying; Jiang, Hong

    2015-04-01

    Anaesthetic agents were confirmed to play a role on the tumor angiogenesis. The effect of sevoflurane on tongue squamous cell carcinoma (TSCC) cell has not been investigated. SCC-4 cells were exposed to sevoflurane after simulating hypoxia. Then, both the mRNA and protein level of hypoxia-inducible factor (HIF)-1α and VEGF were detected. The methylation states of the VEGF promoter region were also assessed to reveal the underlying mechanism. Finally, the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-Aza) was administrated to reveal the relationship of DNA methylation on the regulation of the VEGF level. Results showed that sevoflurane attenuated the hypoxia-induced VEGF level without altering the HIF-1α after exposure for 24 and 72 h. Sevoflurane increased the DNA methylation of the VEGF promoter region. The attenuation effect of sevoflurane on hypoxia-induced VEGF level could be blocked by 5-Aza. We concluded that sevoflurane attenuates hypoxia-induced VEGF level via DNA methylation of the promoter region in TSCC cell.

  13. IIP Tropospheric Infrared Mapping Spectrometers (TIMS) demonstration of CO retrieval, including multi-layer, from atmospheric data acquired simultaneously in the solar reflective region near 2.3 um and the thermal emissive region near 4.7 um

    NASA Astrophysics Data System (ADS)

    Mergenthaler, J. L.; Kumer, J.; Roche, A. E.; Rairden, R. L.; Blatherwick, R.; Hawat, T.; Desouza-Machado, S.; Hannon, S.; Chatfield, R. B.

    2008-12-01

    The NASA Earth Science Technology Office (ESTO) Instrument Incubator Program (IIP) Tropospheric Infrared Mapping Spectrometers (TIMS) have been developed to demonstrate measurement capability, when deployed in space, for multi-layer retrieval of CO from spectral measurements acquired in the solar reflective (SR) region ~ 4281 to 4301 cm-1 and in the thermal InfraRed (TIR) region ~ 2110 to 2165 cm-1. We describe joint deployment at Denver University (DU) with co-investigators there of the TIMS, and of the DU colleagues FTS, to acquire simultaneous measurements of atmospheric spectra in the SR and the TIR. The FTS provided validation radiance data for the TIMS. The TIMS retrievals of CO, H2O and CH4 agreed well with validation vs these as retrieved from the DU data, AIRS retrieval, standard models and ECMWF. The TIMS CO retrievals included column retrieved from the just the SR data, column retrieved from just the TIR data, and a simple two-layer retrieval from the combined data sets. The data were acquired in an operational mode that mimicked the operations in a conceptual application that would provide footprints, coverage, refresh time as in the Decadal Survey GEO-CAPE mission statement. Very encouraging CO precisions were achieved, e.g., the TIMS CO column retrieval from the SR data demonstrated better than the 10% precision requirement as listed on slide 32 of the GEO-CAPE Reference document http://geo- cape.larc.nasa.gov/docs/GEOMAC_FinalReport_no_costs.ppt

  14. DNA methylation dynamics of a maternally methylated DMR in the mouse Dlk1-Dio3 domain.

    PubMed

    Zeng, Tie-Bo; He, Hong-Juan; Han, Zheng-Bin; Zhang, Feng-Wei; Huang, Zhi-Jun; Liu, Qi; Cui, Wei; Wu, Qiong

    2014-12-20

    The mouse delta-like homolog 1 and type III iodothyronine deiodinase (Dlk1-Dio3) imprinted domain contains three known paternally methylated differentially methylated regions (DMRs): intergenic DMR (IG-DMR), maternally expressed 3-DMR (Gtl2-DMR), and Dlk1-DMR. Here, we report the first maternally methylated DMR, CpG island 2 (CGI-2), is located approximately 800 bp downstream of miR-1188. CGI-2 is highly methylated in sperm and oocytes, de-methylated in pre-implantation embryos, and differentially re-methylated during post-implantation development. CGI-2, similarly to Gtl2-DMR and Dlk1-DMR, acquires differential methylation prior to embryonic day 7.5 (E7.5). Both H3K4me3 and H3K9me3 histone modifications are enriched at CGI-2. Furthermore, CCCTC-binding factor (CTCF) binds to both alleles of CGI-2 in vivo. These results contribute to the investigation of imprinting regulation in this domain.

  15. Depression in systemic lupus erythematosus patients is associated with link-polymorphism but not methylation status of the 5HTT promoter region.

    PubMed

    Xu, J; Cheng, Y Q; Chen, B; Bai, R; Li, S; Xu, X F; Xu, L; Wen, J F; Lu, Z P; Zeng, X F

    2013-09-01

    A higher prevalence of depression in systemic lupus erythematosus (SLE) patients has been reported, though the mechanism underlying this phenomenon remains unclear. The present study was conducted to explore whether the polymorphism and methylation status of the serotonin transporter gene (5HTT) promoter region (PR-5HTT) contribute to depression in SLE patients from both genetic and epigenetic perspectives. In this study, 96 SLE patients and 96 healthy controls (HCs) were recruited. Depression levels of all subjects were evaluated using the Hamilton Depression Rating Scale (HDRS). The serotonin transporter-linked polymorphism (5HTTLPR) and the DNA methylation status of PR-5HTT were detected in peripheral lymphocytes of SLE patients and HCs. The differences in 5HTTLPR and DNA methylation of PR-5HTT between SLEs and HCs were compared. In SLE patients, the frequencies of short allele (S) and SS genotype of 5HTTLPR were higher in depressive SLE (SLE-D) patients than in non-depressive SLE (SLE-ND) patients. The mean HDRS score of SS homozygote patients was higher than that of patients with SL/LL genotypes. Conversely, PR-5HTT was hypomethylated in HCs as well as SLE patients. There was no difference in the methylation status between HCs and SLEs. Thus, the functional expression of PR-5HTT may be primarily regulated by gene polymorphism and not by DNA methylation. The risk allele of 5HTTLPR appears to be a major contributor to depression in SLE patients.

  16. Use of Combined MSAP and NGS Techniques to Identify Differentially Methylated Regions in Somaclones: A Case Study of Two Stable Somatic Wheat Mutants

    PubMed Central

    Baránek, Miroslav; Čechová, Jana; Kovacs, Tamas; Eichmeier, Aleš; Wang, Shunli; Raddová, Jana; Nečas, Tomáš; Ye, Xingguo

    2016-01-01

    The appearance of somaclonal variability induced by in vitro cultivation is relatively frequent and can, in some cases, provide a valuable source of new genetic variation for crop improvement. The cause of this phenomenon remains unknown; however, there are a number of reports suggesting that epigenetics, including DNA methylations, are an important factor. In addition to the non-heritable DNA methylation changes caused by transient and reversible stress-responsive gene regulation, recent evidence supports the existence of mitotically and meiotically inherited changes. The induction of phenotypes via stable DNA methylation changes has occasionally great economical value; however, very little is known about the genetic or molecular basis of these phenotypes. We used a novel approach consisting of a standard MSAP analysis followed by deep amplicon sequencing to better understand this phenomenon. Our models included two wheat genotypes, and their somaclones induced using in vitro cultivation with a changed heritable phenotype (shortened stem height and silenced high molecular weight glutenin). Using this novel procedure, we obtained information on the dissimilarity of DNA methylation landscapes between the standard cultivar and its respective somaclones, and we extracted the sequences and genome regions that were differentially methylated between subjects. Transposable elements were identified as the most likely factor for producing changes in somaclone properties. In summary, the novel approach of combining MSAP and NGS is relatively easy and widely applicable, which is a rather unique feature compared with the currently available techniques in the epigenetics field. PMID:27792769

  17. Characterization of differentially methylated regions in 3 bovine imprinted genes: a model for studying human germ-cell and embryo development.

    PubMed

    Hansmann, T; Heinzmann, J; Wrenzycki, C; Zechner, U; Niemann, H; Haaf, T

    2011-01-01

    Correct imprinting is crucial for normal fetal and placental development in mammals. Experimental evidence in animal models and epidemiological studies in humans suggest that assisted reproductive technologies (ARTs) can interfere with imprinted gene regulation in gametogenesis and early embryogenesis. Bos taurus is an agriculturally important species in which ARTs are commonly employed. Because this species exhibits a similar preimplantation development and gestation length as humans, it is increasingly being used as a model for human germ-cell and embryo development. However, in contrast to humans and mice, there is relatively little information on bovine imprinted genes. Here, we characterized the bovine intergenic IGF2-H19 imprinting control region (ICR) spanning approximately 3 kb. We identified a 300-bp differentially methylated region (DMR) approximately 6 kb upstream of the H19 promoter, containing a CpG island with CTCF-binding site and high sequence similarity with the human intergenic ICR. Additional differentially methylated CpG islands lie -6 kb to -3 kb upstream of the promoter, however these are less conserved. Both classical bisulfite sequencing and bisulfite pyrosequencing demonstrated complete methylation of the IGF2-H19 ICR in sperm, complete demethylation in parthenogenetic embryos having only the female genome, and differential methylation in placental and somatic tissues. In addition, we established pyrosequencing assays for the previously reported bovine SNRPN and PEG3 DMRs. The observed methylation patterns were consistent with genomic imprinting in all analyzed tissues/cell types. The identified IGF2-H19 ICR and the developed quantitative methylation assays may prove useful for further studies on the relationship between ARTs and imprinting defects in the bovine model. Copyright © 2010 S. Karger AG, Basel.

  18. Functional mapping of community-acquired respiratory distress syndrome (CARDS) toxin of Mycoplasma pneumoniae defines regions with ADP-ribosyltransferase, vacuolating and receptor-binding activities.

    PubMed

    Kannan, Thirumalai R; Krishnan, Manickam; Ramasamy, Kumaraguruparan; Becker, Argentina; Pakhomova, Olga N; Hart, P John; Baseman, Joel B

    2014-08-01

    Community-acquired respiratory distress syndrome (CARDS) toxin from Mycoplasma pneumoniae is a 591-amino-acid virulence factor with ADP-ribosyltransferase (ADPRT) and vacuolating activities. It is expressed at low levels during in vitro growth and at high levels during colonization of the lung. Exposure of experimental animals to purified recombinant CARDS toxin alone is sufficient to recapitulate the cytopathology and inflammatory responses associated with M. pneumoniae infection in humans and animals. Here, by molecular modelling, serial truncations and site-directed mutagenesis, we show that the N-terminal region is essential for ADP-ribosylating activity. Also, by systematic truncation and limited proteolysis experiments we identified a portion of the C-terminal region that mediates toxin binding to mammalian cell surfaces and subsequent internalization. In addition, the C-terminal region alone induces vacuolization in a manner similar to full-length toxin. Together, these data suggest that CARDS toxin has a unique architecture with functionally separable N-terminal and C-terminal domains. © 2014 John Wiley & Sons Ltd.

  19. Functional Mapping of Community Acquired Respiratory Distress Syndrome (CARDS) Toxin of Mycoplasma pneumoniae Defines Regions with ADP-ribosyltransferase, Vacuolating, and Receptor-Binding Activities

    PubMed Central

    Kannan, T. R.; Krishnan, Manickam; Ramasamy, Kumaraguruparan; Becker, Argentina; Pakhomova, Olga N.; Hart, P. John; Baseman, Joel B.

    2014-01-01

    SUMMARY Community-acquired respiratory distress syndrome (CARDS) toxin from Mycoplasma pneumoniae is a 591 amino acid virulence factor with ADP-ribosyltransferase (ADPRT) and vacuolating activities. It is expressed at low levels during in vitro growth and at high levels during colonization of the lung. Exposure of experimental animals to purified recombinant CARDS toxin alone is sufficient to recapitulate the cytopathology and inflammatory responses associated with M. pneumoniae infection in humans and animals. Here, by molecular modeling, serial truncations and site-directed mutagenesis, we show that the N-terminal region is essential for ADP-ribosylating activity. Also, by systematic truncation and limited proteolysis experiments we identified a portion of the C-terminal region that mediates toxin binding to mammalian cell surfaces and subsequent internalization. In addition, the C-terminal region alone induces vacuolization in a manner similar to full-length toxin. Together, these data suggest that CARDS toxin has a unique architecture with functionally separable N-terminal and C-terminal domains. PMID:24948331

  20. Nuclear translocation of Acinetobacter baumannii transposase induces DNA methylation of CpG regions in the promoters of E-cadherin gene.

    PubMed

    Moon, Dong Chan; Choi, Chul Hee; Lee, Su Man; Lee, Jung Hwa; Kim, Seung Il; Kim, Dong Sun; Lee, Je Chul

    2012-01-01

    Nuclear targeting of bacterial proteins has emerged as a pathogenic mechanism whereby bacterial proteins induce host cell pathology. In this study, we examined nuclear targeting of Acinetobacter baumannii transposase (Tnp) and subsequent epigenetic changes in host cells. Tnp of A. baumannii ATCC 17978 possesses nuclear localization signals (NLSs), (225)RKRKRK(230). Transient expression of A. baumannii Tnp fused with green fluorescent protein (GFP) resulted in the nuclear localization of these proteins in COS-7 cells, whereas the truncated Tnp without NLSs fused with GFP were exclusively localized in the cytoplasm. A. baumannii Tnp was found in outer membrane vesicles, which delivered this protein to the nucleus of host cells. Nuclear expression of A. baumannii Tnp fused with GFP in A549 cells induced DNA methylation of CpG regions in the promoters of E-cadherin (CDH1) gene, whereas the cytoplasmic localization of the truncated Tnp without NLSs fused with GFP did not induce DNA methylation. DNA methylation in the promoters of E-cadherin gene induced by nuclear targeting of A. baumannii Tnp resulted in down-regulation of gene expression. In conclusion, our data show that nuclear traffic of A. baumannii Tnp induces DNA methylation of CpG regions in the promoters of E-cadherin gene, which subsequently down-regulates gene expression. This study provides a new insight into the epigenetic control of host genes by bacterial proteins.

  1. Cell-specific transcriptional regulation and reactivation of galectin-1 gene expression are controlled by DNA methylation of the promoter region.

    PubMed Central

    Benvenuto, G; Carpentieri, M L; Salvatore, P; Cindolo, L; Bruni, C B; Chiariotti, L

    1996-01-01

    The galectin-1 gene is developmentally regulated gene whose activity is strongly modulated during cell differentiation and transformation. We have previously shown that galectin-1 promoter constructs are highly active when transiently transfected in cells both expressing and not expressing the endogenous gene and that the basal activity is determined by a small region encompassing the transcription start site (from positions -50 to +50). We have now investigated the role of DNA methylation in galectin-1 gene expression. Southern blot analysis with HpaII and MspI endonucleases and sodium bisulfite analysis of genomic DNA from expressing and nonexpressing cell lines and cell hybrids showed a close correlation between gene activity and demethylation of the 5' region of the galectin-1 gene. We found that the galectin-1 promoter region is fully methylated, at every CpG site on both strands, in nonexpressing differentiated rat liver (FAO) and thyroid (PC C13) cells and unmethylated in the expressing undifferentiated liver (BRL3A) and thyroid transformed (PC myc/raf) cell lines. In addition, reactivation of the silent FAO alleles in FAO-human osteosarcoma (143tk-) hybrid cells is accompanied by a complete demethylation of the promoter region. Finally, when galectin-1 chloramphenicol acetyltransferase (CAT) promoter constructs were methylated in vitro by SssI methylase at every cytosine residue of the CpG doublets and transfected into mouse fibroblasts, the transcription of the CAT reporter gene was strongly inhibited. PMID:8649381

  2. Genome-wide blood DNA methylation alterations at regulatory elements and heterochromatic regions in monozygotic twins discordant for obesity and liver fat.

    PubMed

    Ollikainen, Miina; Ismail, Khadeeja; Gervin, Kristina; Kyllönen, Anjuska; Hakkarainen, Antti; Lundbom, Jesper; Järvinen, Elina A; Harris, Jennifer R; Lundbom, Nina; Rissanen, Aila; Lyle, Robert; Pietiläinen, Kirsi H; Kaprio, Jaakko

    2015-01-01

    The current epidemic of obesity and associated diseases calls for swift actions to better understand the mechanisms by which genetics and environmental factors affect metabolic health in humans. Monozygotic (MZ) twin pairs showing discordance for obesity suggest that epigenetic influences represent one such mechanism. We studied genome-wide leukocyte DNA methylation variation in 30 clinically healthy young adult MZ twin pairs discordant for body mass index (BMI; average within-pair BMI difference: 5.4 ± 2.0 kg/m(2)). There were no differentially methylated cytosine-guanine (CpG) sites between the co-twins discordant for BMI. However, stratification of the twin pairs based on the level of liver fat accumulation revealed two epigenetically highly different groups. Significant DNA methylation differences (n = 1,236 CpG sites (CpGs)) between the co-twins were only observed if the heavier co-twins had excessive liver fat (n = 13 twin pairs). This unhealthy pattern of obesity was coupled with insulin resistance and low-grade inflammation. The differentially methylated CpGs included 23 genes known to be associated with obesity, liver fat, type 2 diabetes mellitus (T2DM) and metabolic syndrome, and potential novel metabolic genes. Differentially methylated CpG sites were overrepresented at promoters, insulators, and heterochromatic and repressed regions. Based on predictions by overlapping histone marks, repressed and weakly transcribed sites were significantly more often hypomethylated, whereas sites with strong enhancers and active promoters were hypermethylated. Further, significant clustering of differentially methylated genes in vitamin, amino acid, fatty acid, sulfur, and renin-angiotensin metabolism pathways was observed. The methylome in leukocytes is altered in obesity associated with metabolic disturbances, and our findings indicate several novel candidate genes and pathways in obesity and obesity-related complications.

  3. [DNA methylation in the promoter regions of the laminin family genes in normal and breast carcinoma tissues].

    PubMed

    Simonova, O A; Kuznetsova, E B; Poddubskaya, E V; Kekeeva, T V; Kerimov, R A; Trotsenko, I D; Tanas, A S; Rudenko, V V; Alekseeva, E A; Zaletayev, D V; Strelnikov, V V

    2015-01-01

    Extracellular glycoproteins of the laminin family are essential components of basement membranes involved in a number of biological processes, including tissue differentiation, wound healing, and tumorigenesis. We present the first comprehensive study of promoter methylation status of the genes encoding laminin chains in normal tissues (peripheral blood leucocytes, buccal epithelial cells, autopsy breast tissue samples) and in breast carcinoma samples. Based on the results of this study, we divide laminin genes into three categories. Genes, constitutively methylated in breast tissues include LAMA3A, LAMB2, LAMB3, and LAMC2. Genes prone to abnormal methylation in breast carcinoma include LAMA1, LAMA2, LAMA3B, LAMA4, LAMB1, and LAMC3. Genes that are rarely if ever methylated in breast carcinoma include LAMA5 and LAMC1. The constitutively methylated group includes all of the genes that encode subunits of laminin-5 (the historical name of laminin 332), the promoters of which were previously considered unmethylated in normal tissues and prone to abnormal methylation in breast cancer.

  4. Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

    PubMed Central

    Taberlay, Phillippa C.; Statham, Aaron L.; Kelly, Theresa K.

    2014-01-01

    It is well established that cancer-associated epigenetic repression occurs concomitant with CpG island hypermethylation and loss of nucleosomes at promoters, but the role of nucleosome occupancy and epigenetic reprogramming at distal regulatory elements in cancer is still poorly understood. Here, we evaluate the scope of global epigenetic alterations at enhancers and insulator elements in prostate and breast cancer cells using simultaneous genome-wide mapping of DNA methylation and nucleosome occupancy (NOMe-seq). We find that the genomic location of nucleosome-depleted regions (NDRs) is mostly cell type specific and preferentially found at enhancers in normal cells. In cancer cells, however, we observe a global reconfiguration of NDRs at distal regulatory elements coupled with a substantial reorganization of the cancer methylome. Aberrant acquisition of nucleosomes at enhancer-associated NDRs is associated with hypermethylation and epigenetic silencing marks, and conversely, loss of nucleosomes with demethylation and epigenetic activation. Remarkably, we show that nucleosomes remain strongly organized and phased at many facultative distal regulatory elements, even in the absence of a NDR as an anchor. Finally, we find that key transcription factor (TF) binding sites also show extensive peripheral nucleosome phasing, suggesting the potential for TFs to organize NDRs genome-wide and contribute to deregulation of cancer epigenomes. Together, our findings suggest that “decommissioning” of NDRs and TFs at distal regulatory elements in cancer cells is accompanied by DNA hypermethylation susceptibility of enhancers and insulator elements, which in turn may contribute to an altered genome-wide architecture and epigenetic deregulation in malignancy. PMID:24916973

  5. Differential Methylation of Genomic Regions Associated with Heteroblasty Detected by M&M Algorithm in the Nonmodel Species Eucalyptus globulus Labill.

    PubMed Central

    Hasbún, Rodrigo; Iturra, Carolina; Bravo, Soraya; Rebolledo-Jaramillo, Boris; Valledor, Luis

    2016-01-01

    Epigenetic regulation plays important biological roles in plants, including timing of flowering and endosperm development. Little is known about the mechanisms controlling heterochrony (the change in the timing or rate of developmental events during ontogeny) in Eucalyptus globulus. DNA methylation has been proposed as a potential heterochrony regulatory mechanism in model species, but its role during the vegetative phase in E. globulus has not been explored. In order to investigate the molecular mechanisms governing heterochrony in E. globulus, we have developed a workflow aimed at generating high-resolution hypermethylome and hypomethylome maps that have been tested in two stages of vegetative growth phase: juvenile (6-month leaves) and adult (30-month leaves). We used the M&M algorithm, a computational approach that integrates MeDIP-seq and MRE-seq data, to identify differentially methylated regions (DMRs). Thousands of DMRs between juvenile and adult leaves of E. globulus were found. Although further investigations are required to define the loci associated with heterochrony/heteroblasty that are regulated by DNA methylation, these results suggest that locus-specific methylation could be major regulators of vegetative phase change. This information can support future conservation programs, for example, selecting the best methylomes for a determinate environment in a restoration project. PMID:27123440

  6. Early life adversity and serotonin transporter gene variation interact to affect DNA methylation of the corticotropin-releasing factor gene promoter region in the adult rat brain.

    PubMed

    van der Doelen, Rick H A; Arnoldussen, Ilse A; Ghareh, Hussein; van Och, Liselot; Homberg, Judith R; Kozicz, Tamás

    2015-02-01

    The interaction between childhood maltreatment and the serotonin transporter (5-HTT) gene linked polymorphic region has been associated with increased risk to develop major depression. This Gene × Environment interaction has furthermore been linked with increased levels of anxiety and glucocorticoid release upon exposure to stress. Both endophenotypes are regulated by the neuropeptide corticotropin-releasing factor (CRF) or hormone, which is expressed by the paraventricular nucleus of the hypothalamus, the bed nucleus of the stria terminalis, and the central amygdala (CeA). Therefore, we hypothesized that altered regulation of the expression of CRF in these areas represents a major neurobiological mechanism underlying the interaction of early life stress and 5-HTT gene variation. The programming of gene transcription by Gene × Environment interactions has been proposed to involve epigenetic mechanisms such as DNA methylation. In this study, we report that early life stress and 5-HTT genotype interact to affect DNA methylation of the Crf gene promoter in the CeA of adult male rats. Furthermore, we found that DNA methylation of a specific site in the Crf promoter significantly correlated with CRF mRNA levels in the CeA. Moreover, CeA CRF mRNA levels correlated with stress coping behavior in a learned helplessness paradigm. Together, our findings warrant further investigation of the link of Crf promoter methylation and CRF expression in the CeA with behavioral changes that are relevant for psychopathology.

  7. DNA Methylation and Transcription in a Distal Region Upstream from the Bovine AlphaS1 Casein Gene after Once or Twice Daily Milking

    PubMed Central

    Nguyen, Minh; Boutinaud, Marion; Pétridou, Barbara; Gabory, Anne; Pannetier, Maëlle; Chat, Sophie; Bouet, Stephan; Jouneau, Luc; Jaffrezic, Florence; Laloë, Denis; Klopp, Christophe; Brun, Nicolas; Kress, Clémence; Jammes, Hélène; Charlier, Madia; Devinoy, Eve

    2014-01-01

    Once daily milking (ODM) induces a reduction in milk production when compared to twice daily milking (TDM). Unilateral ODM of one udder half and TDM of the other half, enables the study of underlying mechanisms independently of inter-individual variability (same genetic background) and of environmental factors. Our results show that in first-calf heifers three CpG, located 10 kb upstream from the CSN1S1 gene were methylated to 33, 34 and 28%, respectively, after TDM but these levels were higher after ODM, 38, 38 and 33%, respectively. These methylation levels were much lower than those observed in the mammary gland during pregnancy (57, 59 and 50%, respectively) or in the liver (74, 78 and 61%, respectively). The methylation level of a fourth CpG (CpG4), located close by (29% during TDM) was not altered after ODM. CpG4 methylation reached 39.7% and 59.5%, during pregnancy or in the liver, respectively. CpG4 is located within a weak STAT5 binding element, arranged in tandem with a second high affinity STAT5 element. STAT5 binding is only marginally modulated by CpG4 methylation, but it may be altered by the methylation levels of the three other CpG nearby. Our results therefore shed light on mechanisms that help to explain how milk production is almost, but not fully, restored when TDM is resumed (15.1±0.2 kg/day instead of 16.2±0.2 kg/day, p<0.01). The STAT5 elements are 100 bp away from a region transcribed in the antisense orientation, in the mammary gland during lactation, but not during pregnancy or in other reproductive organs (ovary or testes). We now need to clarify whether the transcription of this novel RNA is a consequence of STAT5 interacting with the CSN1S1 distal region, or whether it plays a role in the chromatin structure of this region. PMID:25369064

  8. DNA methylation and transcription in a distal region upstream from the bovine AlphaS1 casein gene after once or twice daily milking.

    PubMed

    Nguyen, Minh; Boutinaud, Marion; Pétridou, Barbara; Gabory, Anne; Pannetier, Maëlle; Chat, Sophie; Bouet, Stephan; Jouneau, Luc; Jaffrezic, Florence; Laloë, Denis; Klopp, Christophe; Brun, Nicolas; Kress, Clémence; Jammes, Hélène; Charlier, Madia; Devinoy, Eve

    2014-01-01

    Once daily milking (ODM) induces a reduction in milk production when compared to twice daily milking (TDM). Unilateral ODM of one udder half and TDM of the other half, enables the study of underlying mechanisms independently of inter-individual variability (same genetic background) and of environmental factors. Our results show that in first-calf heifers three CpG, located 10 kb upstream from the CSN1S1 gene were methylated to 33, 34 and 28%, respectively, after TDM but these levels were higher after ODM, 38, 38 and 33%, respectively. These methylation levels were much lower than those observed in the mammary gland during pregnancy (57, 59 and 50%, respectively) or in the liver (74, 78 and 61%, respectively). The methylation level of a fourth CpG (CpG4), located close by (29% during TDM) was not altered after ODM. CpG4 methylation reached 39.7% and 59.5%, during pregnancy or in the liver, respectively. CpG4 is located within a weak STAT5 binding element, arranged in tandem with a second high affinity STAT5 element. STAT5 binding is only marginally modulated by CpG4 methylation, but it may be altered by the methylation levels of the three other CpG nearby. Our results therefore shed light on mechanisms that help to explain how milk production is almost, but not fully, restored when TDM is resumed (15.1 ± 0.2 kg/day instead of 16.2 ± 0.2 kg/day, p<0.01). The STAT5 elements are 100 bp away from a region transcribed in the antisense orientation, in the mammary gland during lactation, but not during pregnancy or in other reproductive organs (ovary or testes). We now need to clarify whether the transcription of this novel RNA is a consequence of STAT5 interacting with the CSN1S1 distal region, or whether it plays a role in the chromatin structure of this region.

  9. Body Mass Index in Pregnancy Does Not Affect Peroxisome Proliferator-activated Receptor Gamma Promoter Region (−359 to −260) Methylation in the Neonate

    PubMed Central

    Casamadrid, VRE; Amaya, CA; Mendieta, ZH

    2016-01-01

    Background: Obesity in pregnancy can contribute to epigenetic changes. Aim: To assess whether body mass index (BMI) in pregnancy is associated with changes in the methylation of the peroxisome proliferator-activated receptor γ (PPAR) promoter region (-359 to - 260) in maternal and neonatal leukocytes. Subjects and Methods: In this matched, cohort study 41 pregnant women were allocated into two groups: (a) Normal weight (n = 21) and (b) overweight (n = 20). DNA was extracted from maternal and neonatal leukocytes (4000-10,000 cells) in MagNA Pure (Roche) using MagNA Pure LC DNA Isolation Kit 1 (Roche, Germany). Treatment of DNA (2 μg) was performed with sodium bisulfite (EZ DNA Methylation-Direct™ Kit; Zymo Research). Real-time quantitative polymerase chain reaction (qPCR) was performed in a LightCycler 2.0 (Roche) using the SYBR® Advantage® qPCR Premix Kit (Clontech). The primers used for PPARγ coactivator (PPARG) M3 were 5’- aagacggtttggtcgatc-3’ (forward), and5’- cgaaaaaaaatccgaaatttaa-3’ (reverse) and those for PPARG unmethylated were: 5’-gggaagatggtttggttgatt-3’ (forward) and 5’- ttccaaaaaaaaatccaaaatttaa-3’ (reverse). Intergroup differences were calculated using the Mann-Whitney U-test, and intragroup differences, with the Wilcoxon test (IBM SPSS Statistics for Windows, Version 19.0. Armonk, NY: IBM Corp.). Results: Significant differences were found in BMI, pregestational weight, and postdelivery weight between groups but not in the methylation status of the PPARγ promoter region (-359 to - 260). Conclusion: The PPARγ promoter region (-359 to - 260) in peripheral leukocytes is unlikely to get an obesity-induced methylation in pregnancy. PMID:27144075

  10. Methylation of MYLK3 gene promoter region: a biomarker to stratify surgical care in ovarian cancer in a multicentre study.

    PubMed

    Phelps, David L; Borley, Jane V; Flower, Kirsty J; Dina, Roberto; Darb-Esfahani, Silvia; Braicu, Ioana; Sehouli, Jalid; Fotopoulou, Christina; Wilhelm-Benartzi, Charlotte S; Gabra, Hani; Yazbek, Joseph; Chatterjee, Jayanta; Ip, Jacey; Khan, Harun; Likos-Corbett, Marina-Therese; Brown, Robert; Ghaem-Maghami, Sadaf

    2017-05-09

    Survival benefit from surgical debulking of ovarian cancer (OC) is well established, but some women, despite total macroscopic clearance of disease, still have poor prognosis. We aimed to identify biomarkers to predict benefit from conventional surgery. Clinical data from women debulked for high-stage OC were analysed (Hammersmith Hospital, London, UK; 2001-2014). Infinium's HumanMethylation27 array interrogated tumour DNA for differentially methylated CpG sites, correlated to survival, in patients with the least residual disease (RD; Hammersmith Array). Validation was performed using bisulphite pyrosequencing (Charité Hospital, Berlin, Germany cohort) and The Cancer Genome Atlas' (TCGA) methylation data set. Kaplan-Meier curves and Cox models tested survival. Altogether 803 women with serous OC were studied. No RD was associated with significantly improved overall survival (OS; hazard ratio (HR) 1.25, 95% CI 1.06-1.47; P=0.0076) and progression-free survival (PFS; HR 1.23, 95% CI 1.05-1.43; P=0.012; Hammersmith database n=430). Differentially methylated loci within FGF4, FGF21, MYLK2, MYLK3, MYL7, and ITGAE associated with survival. Patients with the least RD had significantly better OS with higher methylation of MYLK3 (Hammersmith (HR 0.51, 95% CI 0.31-0.84; P=0.01), Charité (HR 0.46, 95% CI 0.21-1.01; P=0.05), and TCGA (HR 0.64, 95% CI 0.44-0.93; P=0.02)). MYLK3 methylation is associated with improved OS in patients with the least RD, which could potentially be used to determine response to surgery.

  11. Lower total and regional grey matter brain volumes in youth with perinatally-acquired HIV infection: Associations with HIV disease severity, substance use, and cognition.

    PubMed

    Lewis-de Los Angeles, C Paula; Williams, Paige L; Huo, Yanling; Wang, Shirlene D; Uban, Kristina A; Herting, Megan M; Malee, Kathleen; Yogev, Ram; Csernansky, John G; Nichols, Sharon; Van Dyke, Russell B; Sowell, Elizabeth R; Wang, Lei

    2017-05-01

    Despite improved survival due to combination antiretroviral therapy (cART), youth with perinatally-acquired HIV (PHIV) show cognitive deficits and developmental delay at increased rates. HIV affects the brain during critical periods of development, and the brain may be a persistent reservoir for HIV due to suboptimal blood brain barrier penetration of cART. We conducted structural magnetic resonance imaging (sMRI) and cognitive testing in 40 PHIV youth (mean age=16.7years) recruited from the NIH Pediatric HIV/AIDS Cohort Study (PHACS) who are part of the first generation of PHIV youth surviving into adulthood. Historical and current HIV disease severity and substance use measures were also collected. Total and regional cortical grey matter brain volumes were compared to a group of 334 typically-developing, HIV-unexposed and uninfected youth (frequency-matched for age and sex) from the Pediatric Imaging, Neurocognition, and Genetics (PING) study (mean age=16.1years). PHIV youth had smaller (2.8-5.1%) total and regional grey matter volumes than HIV-unexposed and uninfected youth, with smallest volumes seen among PHIV youth with higher past peak viral load (VL) and recent unsuppressed VL. In PHIV youth, worse cognitive performance correlated with smaller volumes. This pattern of smaller grey matter volumes suggests that PHIV infection may influence brain development and underlie cognitive dysfunction seen in this population. Among PHIV youth, smaller volumes were also linked to substance use (alcohol use: 9.0-13.4%; marijuana use: 10.1-16.0%). In this study, collection of substance use information was limited to the PHIV cohort; future studies should also collect substance use information in controls to further address interactions between HIV and substance use on brain volume.

  12. Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes

    PubMed Central

    Qu, Ying; Lennartsson, Andreas; Gaidzik, Verena I; Deneberg, Stefan; Karimi, Mohsen; Bengtzén, Sofia; Höglund, Martin; Bullinger, Lars; Döhner, Konstanze; Lehmann, Sören

    2014-01-01

    The extent and role of aberrant DNA methylation in promoter CpG islands (CGIs) have been extensively studied in leukemia and other malignancies. Still, CGIs represent only a small fraction of the methylome. We aimed to characterize genome-wide differential methylation of cytogenetically normal AML (CN-AML) cells compared with normal CD34+ bone marrow cells using the Illumina® 450K methylation array. Differential methylation in CN-AML was most prominent in genomic areas far from CGIs, in so called open sea regions. Furthermore, differential methylation was specifically found in genes encoding transcription factors (TFs), with WT1 being the most differentially methylated TF. Among genetic mutations in AML, DNMT3A mutations showed the most prominent association with the DNA methylation pattern, characterized by hypomethylation of CGIs (as compared with DNMT3A wild type cases). The differential methylation in DNMT3A mutant cells vs. wild type cells was predominantly found in HOX genes, which were hypomethylated. These results were confirmed and validated in an independent CN-AML cohort. In conclusion, we show that, in CN-AML, the most pronounced changes in DNA methylation occur in non-CGI regions and that DNMT3A mutations confer a pattern of global hypomethylation that specifically targets HOX genes. PMID:24866170

  13. Real life management of community-acquired Pneumonia in adults in the Gulf region and comparison with practice guidelines: a prospective study.

    PubMed

    Mahboub, Bassam; Al Zaabi, Ashraf; Al Ali, Ola Mohamed; Ahmed, Raees; Niederman, Michael S; El-Bishbishi, Rania

    2015-09-30

    Very few data exist on the management of community-acquired pneumonia (CAP) in patients admitted to hospitals in the Gulf region. The objectives of this study were to describe treatment patterns for CAP in 38 hospitals in five Gulf countries (United Arab Emirates, Kuwait, Bahrain, Oman, and Qatar) and to compare the findings to the most recent Infectious Diseases Society of America (IDSA)/American Thoracic Society (ATS) guidelines. This was a prospective, observational study conducted between January 2009 and February 2011. Adult patients hospitalised (excluding intensive care units) for CAP and subsequently discharged were included. Data were collected retrospectively at hospital discharge, and prospectively during two follow-up visits. Data on medical history, mortality-risk scores, diagnostic criteria, antibiotic treatment, isolated pathogens and clinical and radiographic outcomes were collected. Care practices were compared to the IDSA/ATS guidelines. A total of 684 patients were included. The majority (82.9 %) of patients were classified as low risk for mortality (pneumonia severity index II and III). The majority of patients fulfilled criteria for treatment success at discharge, although only 77.6 % presented a normalised leukocyte count. Overall, the management of CAP in Gulf countries is in line with the IDSA/ATS guidelines. This applied to the diagnosis of CAP, to the identification of high-risk CAP patients, to the identification of etiologic agent responsible for CAP and to the type of treatment despite the fact that combinations of antimicrobial agents were not consistent with the guidelines in 10 % of patients. In all patients, information about Gram's staining was not captured as recommended by the IDSA/ATS and in the majority of patients (>85 %) chest radiography was not systematically performed at the post-discharge follow-up visits. The management of CAP in the Gulf region is globally in line with current IDSA/ATS guidelines, although rates of

  14. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes.

    PubMed

    Tran, Robert K; Henikoff, Jorja G; Zilberman, Daniel; Ditt, Renata F; Jacobsen, Steven E; Henikoff, Steven

    2005-01-26

    Cytosine DNA methylation in vertebrates is widespread, but methylation in plants is found almost exclusively at transposable elements and repetitive DNA. Within regions of methylation, methylcytosines are typically found in CG, CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and asymmetric sites appears to be maintained at each cell cycle by other mechanisms. We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters found at scattered sites throughout the genome. These clusters lack non-CG methylation and are preferentially found in genes, although they are relatively deficient toward the 5' end. CG methylation clusters are present in lines derived from different accessions and in mutants that eliminate de novo methylation, indicating that CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine is mutagenic, the appearance of CG methylation clusters over evolutionary time predicts a genome-wide deficiency of CG dinucleotides and an excess of C(A/T)G trinucleotides within transcribed regions. This is exactly what we find, implying that CG methylation clusters have contributed profoundly to plant gene evolution. We suggest that CG methylation clusters silence cryptic promoters that arise sporadically within transcription units.

  15. Maternal separation alters nerve growth factor and corticosterone levels but not the DNA methylation status of the exon 17 glucocorticoid receptor promoter region

    PubMed Central

    Daniels, WMU; Fairbairn, LR; van Tilburg, G; McEvoy, CRE; Zigmond, MJ; Russell, VA; Stein, DJ

    2010-01-01

    Separating rat pups from their mothers during the early stages of life is an animal model commonly used to study the development of psychiatric disorders such as anxiety and depression. The present study investigated how soon after the termination of the maternal separation period behavioural and neuroendocrine abnormalities relevant to above-mentioned illnesses would manifest. Sprague Dawley rat pups were subjected to maternal separation (3 hours per day from postnatal day 2 through 14) and their behaviour and HPA axis activity determined 7 days later. We also measured nerve growth factor levels in their hippocampi and assessed the DNA methylation status of the promoter region of exon 17 of the glucocorticoid receptor in this brain region. As early as 7 days after the termination of the adverse event, a change in behaviour was observed that was associated with increased plasma corticosterone release and elevated nerve growth factor levels in the hippocampus. No alteration in the methylation status of the exon 17 glucocorticoid receptor promoter region was observed. Our data indicate that early life adversity may lead to the rapid development of abnormal behaviours and HPA axis dysregulation though no epigenetic changes to the exon 17 glucocorticoid receptor promoter region occurred. We further propose that the observed increased neurotrophin levels reflect compensatory mechanisms that attempt to combat the long-term deleterious effects of maternal separation. PMID:19816761

  16. Clinical Characteristics of Q Fever and Etiology of Community-Acquired Pneumonia in a Tropical Region of Southern Taiwan: A Prospective Observational Study

    PubMed Central

    Lai, Chung-Hsu; Chang, Lin-Li; Lin, Jiun-Nong; Chen, Wei-Fang; Wei, Yu-Feng; Chiu, Chien-Tung; Wu, Jiun-Ting; Hsu, Chi-Kuei; Chen, Jung-Yueh; Lee, Ho-Sheng; Lin, Hsi-Hsun; Chen, Yen-Hsu

    2014-01-01

    Background The clinical characteristics of Q fever are poorly identified in the tropics. Fever with pneumonia or hepatitis are the dominant presentations of acute Q fever, which exhibits geographic variability. In southern Taiwan, which is located in a tropical region, the role of Q fever in community-acquired pneumonia (CAP) has never been investigated. Methodology/Principal Findings During the study period, May 2012 to April 2013, 166 cases of adult CAP and 15 cases of acute Q fever were prospectively investigated. Cultures of clinical specimens, urine antigen tests for Streptococcus pneumoniae and Legionella pneumophila, and paired serologic assessments for Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Q fever (Coxiella burnetii) were used for identifying pathogens associated with CAP. From April 2004 to April 2013 (the pre-study period), 122 cases of acute Q fever were also included retrospectively for analysis. The geographic distribution of Q fever and CAP cases was similar. Q fever cases were identified in warmer seasons and younger ages than CAP. Based on multivariate analysis, male gender, chills, thrombocytopenia, and elevated liver enzymes were independent characteristics associated with Q fever. In patients with Q fever, 95% and 13.5% of cases presented with hepatitis and pneumonia, respectively. Twelve (7.2%) cases of CAP were seropositive for C. burnetii antibodies, but none of them had acute Q fever. Among CAP cases, 22.9% had a CURB-65 score ≧2, and 45.8% had identifiable pathogens. Haemophilus parainfluenzae (14.5%), S. pneumoniae (6.6%), Pseudomonas aeruginosa (4.8%), and Klebsiella pneumoniae (3.0%) were the most common pathogens identified by cultures or urine antigen tests. Moreover, M. pneumoniae, C. pneumoniae, and co-infection with 2 pathogens accounted for 9.0%, 7.8%, and 1.8%, respectively. Conclusions In southern Taiwan, Q fever is an endemic disease with hepatitis as the major presentation and is not a common etiology of CAP

  17. Report for borehole explosion data acquired in the 1999 Los Angeles Region Seismic Experiment (LARSE II), Southern California: Part I, description of the survey

    USGS Publications Warehouse

    Fuis, Gary S.; Murphy, Janice M.; Okaya, David A.; Clayton, Robert W.; Davis, Paul M.; Thygesen, Kristina; Baher, Shirley A.; Ryberg, Trond; Benthien, Mark L.; Simila, Gerry; Perron, J. Taylor; Yong, Alan K.; Reusser, Luke; Lutter, William J.; Kaip, Galen; Fort, Michael D.; Asudeh, Isa; Sell, Russell; Van Schaack, John R.; Criley, Edward E.; Kaderabek, Ronald; Kohler, Will M.; Magnuski, Nickolas H.

    2001-01-01

    The Los Angeles Region Seismic Experiment (LARSE) is a joint project of the U.S. Geological Survey (USGS) and the Southern California Earthquake Center (SCEC). The purpose of this project is to produce seismic images of the subsurface of the Los Angeles region down to the depths at which earthquakes occur, and deeper, in order to remedy a deficit in our knowledge of the deep structure of this region. This deficit in knowledge has persisted despite over a century of oil exploration and nearly 70 years of recording earthquakes in southern California. Understanding the deep crustal structure and tectonics of southern California is important to earthquake hazard assessment. Specific imaging targets of LARSE include (a) faults, especially blind thrust faults, which cannot be reliably detected any other way; and (b) the depths and configurations of sedimentary basins. Imaging of faults is important in both earthquake hazard assessment but also in modeling earthquake occurrence. Earthquake occurrence cannot be understood unless the earthquake-producing "machinery" (tectonics) is known (Fuis and others, 2001). Imaging the depths and configurations of sedimentary basins is important because earthquake shaking at the surface is enhanced by basin depth and by the presence of sharp basin edges (Wald and Graves, 1998, Working Group on California Earthquake Probabilities, 1995; Field and others, 2001). (Sedimentary basins are large former valleys now filled with sediment eroded from nearby mountains.) Sedimentary basins in the Los Angeles region that have been investigated by LARSE include the Los Angeles, San Gabriel Valley, San Fernando Valley, and Santa Clarita Valley basins. The seismic imaging surveys of LARSE include recording of earthquakes (both local and distant earthquakes) along several corridors (or transects) through the Los Angeles region and also recording of man-made sources along these same corridors. Man-made sources have included airguns offshore and borehole

  18. Severe psychosocial deprivation in early childhood is associated with increased DNA methylation across a region spanning the transcription start site of CYP2E1

    PubMed Central

    Kumsta, R; Marzi, S J; Viana, J; Dempster, E L; Crawford, B; Rutter, M; Mill, J; Sonuga-Barke, E J S

    2016-01-01

    Exposure to adverse rearing environments including institutional deprivation and severe childhood abuse is associated with an increased risk for mental and physical health problems across the lifespan. Although the mechanisms mediating these effects are not known, recent work in rodent models suggests that epigenetic processes may be involved. We studied the impact of severe early-life adversity on epigenetic variation in a sample of adolescents adopted from the severely depriving orphanages of the Romanian communist era in the 1980s. We quantified buccal cell DNA methylation at ~400 000 sites across the genome in Romanian adoptees exposed to either extended (6–43 months; n=16) or limited duration (<6 months; n=17) of severe early-life deprivation, in addition to a matched sample of UK adoptees (n=16) not exposed to severe deprivation. Although no probe-wise differences remained significant after controlling for the number of probes tested, we identified an exposure-associated differentially methylated region (DMR) spanning nine sequential CpG sites in the promoter-regulatory region of the cytochrome P450 2E1 gene (CYP2E1) on chromosome 10 (corrected P=2.98 × 10−5). Elevated DNA methylation across this region was also associated with deprivation-related clinical markers of impaired social cognition. Our data suggest that environmental insults of sufficient biological impact during early development are associated with long-lasting epigenetic changes, potentially reflecting a biological mechanism linking the effects of early-life adversity to cognitive and neurobiological phenotypes. PMID:27271856

  19. Variation in whole DNA methylation in red maple (Acer rubrum) populations from a mining region: association with metal contamination and cation exchange capacity (CEC) in podzolic soils.

    PubMed

    Kalubi, K N; Mehes-Smith, M; Spiers, G; Omri, A

    2017-02-15

    Although a number of publications have provided convincing evidence that abiotic stresses such as drought and high salinity are involved in DNA methylation reports on the effects of metal contamination, pH, and cation exchange on DNA modifications are limited. The main objective of the present study is to determine the relationship between metal contamination and Cation exchange capacity (CEC) on whole DNA modifications. Metal analysis confirms that nickel and copper are the main contaminants in sampled sites within the Greater Sudbury Region (Ontario, Canada) and liming has increased soil pH significantly even after 30 years following dolomitic limestone applications. The estimated CEC values varied significantly among sites, ranging between 1.8 and 10.5 cmol(+) kg(-1), with a strong relationship being observed between CEC and pH (r = 0.96**). Cation exchange capacity, significantly lower in highly metal contaminated sites compared to both reference and less contaminated sites, was higher in the higher organic matter limed compared to unlimed sites. There was a significant variation in the level of cytosine methylation among the metal-contaminated sites. Significant and strong negative correlations between [5mdC]/[dG] and bioavailable nickel (r = -0.71**) or copper (r = -0.72**) contents were observed. The analysis of genomic DNA for adenine methylation in this study showed a very low level of [6N-mdA]/dT] in Acer rubrum plants analyzed ranging from 0 to 0.08%. Significant and very strong positive correlation was observed between [6N-mdA]/dT] and soil bioavailable nickel (r = 0.78**) and copper (r = 0.88**) content. This suggests that the increased bioavailable metal levels associated with contamination by nickel and copper particulates are associated with cytosine and adenine methylation.

  20. {sup 13}C-METHYL FORMATE: OBSERVATIONS OF A SAMPLE OF HIGH-MASS STAR-FORMING REGIONS INCLUDING ORION-KL AND SPECTROSCOPIC CHARACTERIZATION

    SciTech Connect

    Favre, Cécile; Bergin, Edwin A.; Crockett, Nathan R.; Neill, Justin L.; Carvajal, Miguel; Field, David; Jørgensen, Jes K.; Bisschop, Suzanne E.; Brouillet, Nathalie; Despois, Didier; Baudry, Alain; Kleiner, Isabelle; Margulès, Laurent; Huet, Thérèse R.; Demaison, Jean E-mail: miguel.carvajal@dfa.uhu.es

    2015-01-01

    We have surveyed a sample of massive star-forming regions located over a range of distances from the Galactic center for methyl formate, HCOOCH{sub 3}, and its isotopologues H{sup 13}COOCH{sub 3} and HCOO{sup 13}CH{sub 3}. The observations were carried out with the APEX telescope in the frequency range 283.4-287.4 GHz. Based on the APEX observations, we report tentative detections of the {sup 13}C-methyl formate isotopologue HCOO{sup 13}CH{sub 3} toward the following four massive star-forming regions: Sgr B2(N-LMH), NGC 6334 IRS 1, W51 e2, and G19.61-0.23. In addition, we have used the 1 mm ALMA science verification observations of Orion-KL and confirm the detection of the {sup 13}C-methyl formate species in Orion-KL and image its spatial distribution. Our analysis shows that the {sup 12}C/{sup 13}C isotope ratio in methyl formate toward the Orion-KL Compact Ridge and Hot Core-SW components (68.4 ± 10.1 and 71.4 ± 7.8, respectively) are, for both the {sup 13}C-methyl formate isotopologues, commensurate with the average {sup 12}C/{sup 13}C ratio of CO derived toward Orion-KL. Likewise, regarding the other sources, our results are consistent with the {sup 12}C/{sup 13}C in CO. We also report the spectroscopic characterization, which includes a complete partition function, of the complex H{sup 13}COOCH{sub 3} and HCOO{sup 13}CH{sub 3} species. New spectroscopic data for both isotopomers H{sup 13}COOCH{sub 3} and HCOO{sup 13}CH{sub 3}, presented in this study, have made it possible to measure this fundamentally important isotope ratio in a large organic molecule for the first time.

  1. Success of the PCR-based replication assay depends on the number of methylation sensitive restriction sites in the PCR amplifying region.

    PubMed

    Metta, M K; Tantravahi, S; Kunaparaju, R

    2015-06-02

    The PCR—based replication assay is one of the most simple, quick and economical methods for the analysis of episomal replication. However, in spite of its advantages the method has not been able to replace the southern—based replication assay, the latter of which is a tedious and time—consuming process. This is due to the generation of spurious amplification products in the PCR—based replication assay. The replication assay is based on the use of methylation—sensitive restriction endonucleases (eg. DpnI, MboI) to distinguish bacterial replicated (adenosine methylated) and mammalian replicated plasmids (adenosine non—methylated). In this work we addressed the problem by evaluating (a) restriction enzyme digestion and (b) the minimum number of restriction sites that are required in the amplifying region. The efficiency of restriction digestion was tested by subjecting the plasmid to one and two rounds of digestion. Multiple rounds of digestions were found to be inefficient in preventing false positives when the number of DpnI sites in the amplifying region is less than 8. However, use of a minimum of 15 DpnI sites in the amplifying region was found to overcome the false positives.

  2. Regional-scale geometry of the central Skellefte district, northern Sweden—results from 2.5D potential field modeling along three previously acquired seismic profiles

    NASA Astrophysics Data System (ADS)

    Tavakoli, Saman; Bauer, Tobias E.; Elming, Sten-Åke; Thunehed, Hans; Weihed, Pär

    2012-10-01

    The Skellefte district in northern Sweden is one of the most important mining districts in Europe hosting approximately 80 volcanic massive sulfide (VMS) deposits. Due to its economical importance, geological and geophysical studies were carried out in order to create an image of the geometry of the upper crustal structure and integral geological elements and to evaluate their relationship to mineral deposits. Consequently, seismic reflection data along three sub-parallel profiles were acquired during 2009-2010 to map the spatial relationships between the geological structures down to a depth of ~ 4.5 km. Although these seismic studies helped researchers understand the regional relationship between geologic units in the central Skellefte district (CSD), the seismic reflection data did not succeed entirely in mapping the lithological contacts in the area. In this study, the model derived from the seismic reflection data was examined by using 2.5D modeling of potential field data (down to a 5 km depth) constrained by physical properties of the rocks and surface geology. Moreover, we modeled gravity and magnetic data along the non-reflective or poorly reflective parts of the seismic profiles to identify major lithological contacts and shear zones in the CSD, which could not be modeled on the basis of the seismic reflection data. Gravity and magnetic data helped reveal the spatial relationship between the Skellefte volcanic rocks, Vargfors group meta-sedimentary rocks and two meta­intrusive complexes. Results suggest a maximum depth extent of 2.1 km for the tectonic contact at the southern border of the Jörn granitoid. Furthermore, this north-dipping Skellefte-Jörn contact coincides closely with magnetic lows and gravity highs, which implies that the Jörn intrusive rocks have a greater thickness than the underlying basalt. Further to the NW, gravity and magnetic data suggest a depth extent of 2 km for the Gallejaur complex, which coincides with a set of gently

  3. COLD-PCR amplification of bisulfite-converted DNA allows the enrichment and sequencing of rare un-methylated genomic regions.

    PubMed

    Castellanos-Rizaldos, Elena; Milbury, Coren A; Karatza, Elli; Chen, Clark C; Makrigiorgos, G Mike; Merewood, Anne

    2014-01-01

    Aberrant hypo-methylation of DNA is evident in a range of human diseases including cancer and diabetes. Development of sensitive assays capable of detecting traces of un-methylated DNA within methylated samples can be useful in several situations. Here we describe a new approach, fast-COLD-MS-PCR, which amplifies preferentially un-methylated DNA sequences. By employing an appropriate denaturation temperature during PCR of bi-sulfite converted DNA, fast-COLD-MS-PCR enriches un-methylated DNA and enables differential melting analysis or bisulfite sequencing. Using methylation on the MGMT gene promoter as a model, it is shown that serial dilutions of controlled methylation samples lead to the reliable sequencing of un-methylated sequences down to 0.05% un-methylated-to-methylated DNA. Screening of clinical glioma tumor and infant blood samples demonstrated that the degree of enrichment of un-methylated over methylated DNA can be modulated by the choice of denaturation temperature, providing a convenient method for analysis of partially methylated DNA or for revealing and sequencing traces of un-methylated DNA. Fast-COLD-MS-PCR can be useful for the detection of loss of methylation/imprinting in cancer, diabetes or diet-related methylation changes.

  4. Domain regulation of imprinting cluster in Kip2/Lit1 subdomain on mouse chromosome 7F4/F5: large-scale DNA methylation analysis reveals that DMR-Lit1 is a putative imprinting control region.

    PubMed

    Yatsuki, Hitomi; Joh, Keiichiro; Higashimoto, Ken; Soejima, Hidenobu; Arai, Yuji; Wang, Youdong; Hatada, Izuho; Obata, Yayoi; Morisaki, Hiroko; Zhang, Zhongming; Nakagawachi, Tetsuji; Satoh, Yuji; Mukai, Tsunehiro

    2002-12-01

    Mouse chromosome 7F4/F5, where the imprinting domain is located, is syntenic to human 11p15.5, the locus for Beckwith-Wiedemann syndrome. The domain is thought to consist of the two subdomains Kip2 (p57(kip2))/Lit1 and Igf2/H19. Because DNA methylation is believed to be a key factor in genomic imprinting, we performed large-scale DNA methylation analysis to identify the cis-element crucial for the regulation of the Kip2/Lit1 subdomain. Ten CpG islands (CGIs) were found, and these were located at the promoter sites, upstream of genes, and within intergenic regions. Bisulphite sequencing revealed that CGIs 4, 5, 8, and 10 were differentially methylated regions (DMRs). CGIs 4, 5, and 10 were methylated paternally in somatic tissues but not in germ cells. CGI8 was methylated in oocyte and maternally in somatic tissues during development. Parental-specific DNase I hypersensitive sites (HSSs) were found near CGI8. These data indicate that CGI8, called DMR-Lit1, is not only the region for gametic methylation but might also be the imprinting control region (ICR) of the subdomain.

  5. MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain.

    PubMed

    Thambirajah, Anita A; Ng, Marlee K; Frehlick, Lindsay J; Li, Andra; Serpa, Jason J; Petrotchenko, Evgeniy V; Silva-Moreno, Begonia; Missiaen, Kristal K; Borchers, Christoph H; Adam Hall, J; Mackie, Ryan; Lutz, Frank; Gowen, Brent E; Hendzel, Michael; Georgel, Philippe T; Ausió, Juan

    2012-04-01

    Methyl-CpG-binding protein 2 (MeCP2) is a chromatin-binding protein that mediates transcriptional regulation, and is highly abundant in brain. The nature of its binding to reconstituted templates has been well characterized in vitro. However, its interactions with native chromatin are less understood. Here we show that MeCP2 displays a distinct distribution within fractionated chromatin from various tissues and cell types. Artificially induced global changes in DNA methylation by 3-aminobenzamide or 5-aza-2'-deoxycytidine, do not significantly affect the distribution or amount of MeCP2 in HeLa S3 or 3T3 cells. Most MeCP2 in brain is chromatin-bound and localized within highly nuclease-accessible regions. We also show that, while in most tissues and cell lines, MeCP2 forms stable complexes with nucleosome, in brain, a fraction of it is loosely bound to chromatin, likely to nucleosome-depleted regions. Finally, we provide evidence for novel associations of MeCP2 with mononucleosomes containing histone H2A.X, H3K9me(2) and H3K27me(3) in different chromatin fractions from brain cortex and in vitro. We postulate that the functional compartmentalization and tissue-specific distribution of MeCP2 within different chromatin types may be directed by its association with nucleosomes containing specific histone variants, and post-translational modifications.

  6. Tumour specific promoter region methylation of the human homologue of the Drosophila Roundabout gene DUTT1 (ROBO1) in human cancers.

    PubMed

    Dallol, Ashraf; Forgacs, Eva; Martinez, Alonso; Sekido, Yoshitaka; Walker, Rosemary; Kishida, Takeshi; Rabbitts, Pamela; Maher, Eamonn R; Minna, John D; Latif, Farida

    2002-05-02

    The human homologue of the Drosophila Roundabout gene DUTT1 (Deleted in U Twenty Twenty) or ROBO1 (Locus Link ID 6091), a member of the NCAM family of receptors, was recently cloned from the lung cancer tumour suppressor gene region 2 (LCTSGR2 or U2020 region) at 3p12. DUTT1 maps within a region of overlapping homozygous deletions characterized in both small cell lung cancer lines (SCLC) and in a breast cancer line. In this report we (a) defined the genomic organization of the DUTT1 gene, (b) performed mutation and expression analysis of DUTT1 in lung, breast and kidney cancers, (c) identified tumour specific promoter region methylation of DUTT1 in human cancers. The gene was found to contain 29 exons and spans at least 240 kb of genomic sequence. The 5' region contains a CpG island, and the poly(A)(+) tail has an atypical 5'-GATAAA-3' signal. We analysed DUTT1 for mutations in lung, breast and kidney cancers, no inactivating mutations were detected by PCR-SSCP. However, seven germline missense changes were found and characterized. DUTT1 expression was not detectable in one out of 18 breast tumour lines analysed by RT-PCR. Bisulfite sequencing of the promoter region of DUTT1 gene in the HTB-19 breast tumour cell line (not expressing DUTT1) showed complete hypermethylation of CpG sites within the promoter region of the DUTT1 gene (-244 to +27 relative to the translation start site). The expression of DUTT1 gene was reactivated in HTB-19 after treatment with the demethylating agent 5-aza-2'-deoxycytidine. The same region was also found to be hypermethylated in six out of 32 (19%) primary invasive breast carcinomas and eight out of 44 (18%) primary clear cell renal cell carcinomas (CC-RCC) and in one out of 26 (4%) primary NSCLC tumours. Furthermore 80% of breast and 75% of CC-RCC tumours showing DUTT1 methylation had allelic losses for 3p12 markers hence obeying Knudson's two hit hypothesis. Our findings suggest that DUTT1 warrants further analysis as a candidate for

  7. Epigenome-wide association study suggests that SNPs in the promoter region of RETN influence plasma resistin level via effects on DNA methylation at neighbouring sites.

    PubMed

    Nakatochi, Masahiro; Ichihara, Sahoko; Yamamoto, Ken; Ohnaka, Keizo; Kato, Yosuke; Yokota, Shigeki; Hirashiki, Akihiro; Naruse, Keiko; Asano, Hiroyuki; Izawa, Hideo; Matsubara, Tatsuaki; Yokota, Mitsuhiro

    2015-12-01

    To investigate epigenetic regulation of the plasma concentration of resistin, we performed an epigenome-wide association study for this variable and DNA methylation (DNAm) in an elderly Japanese cohort and then assessed the relation of single nucleotide polymorphisms (SNPs) associated with the plasma resistin concentration to DNAm level at identified sites. The association of plasma resistin level with DNAm status was examined in 191 nondiabetic elderly men with the Illumina Infinium HumanMethylation450 BeadChip array. The association between DNAm status at specific sites in the flanking region of the resistin gene (RETN) and RETN mRNA abundance was then evaluated with a public data set for 1202 monocyte samples from a multi-ethnic cohort. Finally, the association of DNAm status and SNPs in the promoter region of RETN was assessed in two cohorts comprising a total of 478 Japanese individuals. DNAm status at cg02346997 located in the RETN promoter region showed a negative genome-wide significant association with the plasma resistin level (p = 6.02 × 10(-10)). Four DNAm sites in the RETN promoter region including cg02346997 (p = 4.23 × 10(-70)) showed a negative genome-wide significant association with RETN mRNA abundance in monocytes. Furthermore, the number of minor alleles of the RETN promoter SNPs rs34861192 and rs3219175 was negatively associated with DNAm level at cg02346997 (p = 4.43 × 10(-17)). Our results suggest that RETN promoter SNPs might influence the circulating resistin level through an effect on DNAm at cg02346997 and on RETN mRNA abundance in monocytes.

  8. PTSD and DNA Methylation in Select Immune Function Gene Promoter Regions: A Repeated Measures Case-Control Study of U.S. Military Service Members

    PubMed Central

    Rusiecki, Jennifer A.; Byrne, Celia; Galdzicki, Zygmunt; Srikantan, Vasantha; Chen, Ligong; Poulin, Matthew; Yan, Liying; Baccarelli, Andrea

    2013-01-01

    Background: The underlying molecular mechanisms of PTSD are largely unknown. Distinct expression signatures for PTSD have been found, in particular for immune activation transcripts. DNA methylation may be significant in the pathophysiology of PTSD, since the process is intrinsically linked to gene expression. We evaluated temporal changes in DNA methylation in select promoter regions of immune system-related genes in U.S. military service members with a PTSD diagnosis, pre- and post-diagnosis, and in controls. Methods: Cases (n = 75) had a post-deployment diagnosis of PTSD in their medical record. Controls (n = 75) were randomly selected service members with no PTSD diagnosis. DNA was extracted from pre- and post-deployment sera. DNA methylation (%5-mC) was quantified at specific CpG sites in promoter regions of insulin-like growth factor 2 (IGF2), long non-coding RNA transcript H19, interleukin-8 (IL8), IL16, and IL18 via pyrosequencing. We used multivariate analysis of variance and generalized linear models to calculate adjusted means (adjusted for age, gender, and race) to make temporal comparisons of %5-mC for cases (pre- to post-deployment) versus controls (pre- to post-deployment). Results: There were significant differences in the change of %5-mC pre- to post-deployment between cases and controls for H19 (cases: +0.57%, controls: −1.97%; p = 0.04) and IL18 (cases: +1.39%, controls: −3.83%; p = 0.01). For H19 the difference was driven by a significant reduction in %5-mC among controls; for IL18 the difference was driven by both a reduction in %5-mC among controls and an increase in %5-mC among cases. Stratified analyses revealed more pronounced differences in the adjusted means of pre-post H19 and IL18 methylation differences for cases versus controls among older service members, males, service members of white race, and those with shorter deployments (6–12 months). Conclusion: In the study of deployed personnel, those who did not

  9. Methylation matters

    PubMed Central

    Costello, J.; Plass, C.

    2001-01-01

    DNA methylation is not just for basic scientists any more. There is a growing awareness in the medical field that having the correct pattern of genomic methylation is essential for healthy cells and organs. If methylation patterns are not properly established or maintained, disorders as diverse as mental retardation, immune deficiency, and sporadic or inherited cancers may follow. Through inappropriate silencing of growth regulating genes and simultaneous destabilisation of whole chromosomes, methylation defects help create a chaotic state from which cancer cells evolve. Methylation defects are present in cells before the onset of obvious malignancy and therefore cannot be explained simply as a consequence of a deregulated cancer cell. Researchers are now able to detect with exquisite sensitivity the cells harbouring methylation defects, sometimes months or years before the time when cancer is clinically detectable. Furthermore, aberrant methylation of specific genes has been directly linked with the tumour response to chemotherapy and patient survival. Advances in our ability to observe the methylation status of the entire cancer cell genome have led us to the unmistakable conclusion that methylation abnormalities are far more prevalent than expected. This methylomics approach permits the integration of an ever growing repertoire of methylation defects with the genetic alterations catalogued from tumours over the past two decades. Here we discuss the current knowledge of DNA methylation in normal cells and disease states, and how this relates directly to our current understanding of the mechanisms by which tumours arise.


Keywords: methylation; cancer PMID:11333864

  10. Occupationally Acquired American Cutaneous Leishmaniasis

    PubMed Central

    Felinto de Brito, Maria Edileuza; Andrade, Maria Sandra; de Almeida, Éricka Lima; Medeiros, Ângela Cristina Rapela; Werkhäuser, Roberto Pereira; de Araújo, Ana Isabele Freitas; Brandão-Filho, Sinval Pinto; Paiva de Almeida, Alzira Maria; Gomes Rodrigues, Eduardo Henrique

    2012-01-01

    We report two occupationally acquired cases of American cutaneous leishmaniasis (ACL): one accidental laboratory autoinoculation by contaminated needlestick while handling an ACL lesion sample, and one acquired during field studies on bird biology. Polymerase chain reaction (PCR) assays of patient lesions were positive for Leishmania, subgenus Viannia. One isolate was obtained by culture (from patient 2 biopsy samples) and characterized as Leishmania (Viannia) naiffi through an indirect immunofluorescence assay (IFA) with species-specific monoclonal antibodies (mAbs) and by multilocus enzyme electrophoresis (MLEE). Patients were successfully treated with N-methyl-glucamine. These two cases highlight the potential risks of laboratory and field work and the need to comply with strict biosafety procedures in daily routines. The swab collection method, coupled with PCR detection, has greatly improved ACL laboratory diagnosis. PMID:23227369

  11. A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies.

    PubMed

    Shames, David S; Girard, Luc; Gao, Boning; Sato, Mitsuo; Lewis, Cheryl M; Shivapurkar, Narayan; Jiang, Aixiang; Perou, Charles M; Kim, Young H; Pollack, Jonathan R; Fong, Kwun M; Lam, Chi-Leung; Wong, Maria; Shyr, Yu; Nanda, Rita; Olopade, Olufunmilayo I; Gerald, William; Euhus, David M; Shay, Jerry W; Gazdar, Adi F; Minna, John D

    2006-12-01

    Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The "rules" governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor type-specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype would identify pathways important as therapeutic targets. In an effort to identify new cancer-specific methylation markers, we employed a high-throughput global expression profiling approach in lung cancer cells. We identified 132 genes that have 5' CpG islands, are induced from undetectable levels by 5-aza-2'-deoxycytidine in multiple non-small cell lung cancer cell lines, and are expressed in immortalized human bronchial epithelial cells. As expected, these genes were also expressed in normal lung, but often not in companion primary lung cancers. Methylation analysis of a subset (45/132) of these promoter regions in primary lung cancer (n = 20) and adjacent nonmalignant tissue (n = 20) showed that 31 genes had acquired methylation in the tumors, but did not show methylation in normal lung or peripheral blood cells. We studied the eight most frequently and specifically methylated genes from our lung cancer dataset in breast cancer (n = 37), colon cancer (n = 24), and prostate cancer (n = 24) along with counterpart nonmalignant tissues. We found that seven loci were frequently methylated in both breast and lung cancers, with four showing extensive methylation in all four epithelial tumors. By using a systematic biological screen we identified multiple genes that are methylated with high penetrance in primary lung, breast, colon, and prostate cancers. The cross-tumor methylation pattern we observed for these novel markers suggests

  12. A Genome-Wide Screen for Promoter Methylation in Lung Cancer Identifies Novel Methylation Markers for Multiple Malignancies

    PubMed Central

    Shames, David S; Girard, Luc; Gao, Boning; Sato, Mitsuo; Lewis, Cheryl M; Shivapurkar, Narayan; Jiang, Aixiang; Perou, Charles M; Kim, Young H; Pollack, Jonathan R; Fong, Kwun M; Lam, Chi-Leung; Wong, Maria; Shyr, Yu; Nanda, Rita; Olopade, Olufunmilayo I; Gerald, William; Euhus, David M; Shay, Jerry W; Gazdar, Adi F; Minna, John D

    2006-01-01

    Background Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The “rules” governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor type-specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype would identify pathways important as therapeutic targets. Methods and Findings In an effort to identify new cancer-specific methylation markers, we employed a high-throughput global expression profiling approach in lung cancer cells. We identified 132 genes that have 5′ CpG islands, are induced from undetectable levels by 5-aza-2′-deoxycytidine in multiple non-small cell lung cancer cell lines, and are expressed in immortalized human bronchial epithelial cells. As expected, these genes were also expressed in normal lung, but often not in companion primary lung cancers. Methylation analysis of a subset (45/132) of these promoter regions in primary lung cancer (n = 20) and adjacent nonmalignant tissue (n = 20) showed that 31 genes had acquired methylation in the tumors, but did not show methylation in normal lung or peripheral blood cells. We studied the eight most frequently and specifically methylated genes from our lung cancer dataset in breast cancer (n = 37), colon cancer (n = 24), and prostate cancer (n = 24) along with counterpart nonmalignant tissues. We found that seven loci were frequently methylated in both breast and lung cancers, with four showing extensive methylation in all four epithelial tumors. Conclusions By using a systematic biological screen we identified multiple genes that are methylated with high penetrance in primary lung, breast, colon, and prostate cancers. The cross-tumor methylation

  13. Factors Affecting Elevated Arsenic and Methyl Mercury Concentrations in Small Shield Lakes Surrounding Gold Mines near the Yellowknife, NT, (Canada) Region.

    PubMed

    Houben, Adam James; D'Onofrio, Rebecca; Kokelj, Steven V; Blais, Jules M

    2016-01-01

    Gold mines in the Yellowknife, NT, region--in particular, the Giant Mine--operated from 1949-99, releasing 237,000 tonnes of waste arsenic trioxide (As2O3) dust, among other compounds, from gold ore extraction and roasting processes. For the first time, we show the geospatial distribution of roaster-derived emissions of several chemical species beyond the mine property on otherwise undisturbed taiga shield lakes within a 25 km radius of the mine, 11 years after its closing. Additionally, we demonstrate that underlying bedrock is not a significant source for the elevated concentrations in overlying surface waters. Aquatic arsenic (As) concentrations are well above guidelines for drinking water (10 μg/L) and protection for aquatic life (5 μg/L), ranging up to 136 μg/L in lakes within 4 km from the mine, to 2.0 μg/L in lakes 24 km away. High conversion ratios of methyl mercury were shown in lakes near the roaster stack as well, with MeHg concentrations reaching 44% of total mercury. The risk of elevated exposures by these metals is significant, as many lakes used for recreation and fishing near the City of Yellowknife are within this radius of elevated As and methyl Hg concentrations.

  14. Inheritance of acquired traits in plants

    PubMed Central

    2010-01-01

    Since Lamarck proposed the idea of inheritance of acquired traits 200 years ago, much has been said for and against it, but the theory was finally declined after the 1930s. Despite of the negative opinions of the majority of geneticists, botanists and plant breeders have long recognized that altered properties during the growth were occasionally transmitted to the offspring. This was also the case with artificially altered properties such as dwarfism, flowering timing and plant stature, which were induced by a non-mutagenic chemical, 5-azacytidine and its derivatives. As these drugs are powerful inhibitors of DNA methylation in vivo, a close correlation between methylation and phenotypic expression was suggested. Subsequent studies showed that rice plants acquired disease resistance upon demethylation of the corresponding resistant gene, and that both resistant trait and hypomethylated status were inherited by the progeny up to nine generations. Whether or not the methylation pattern changes under natural condition was then questioned, and recent studies have indicated that it indeed naturally changes in response to environmental stresses. Whether or not the altered methylation pattern during the vegetative growth is heritable was also questioned, and studies on toadflax and rice affirmed the question, showing stable maintenance of hypermethylation in the former and hypomethylation in the latter for 250 and 10 years, respectively. The observation strongly suggested that acquired traits can be heritable as far as the acquired methylation pattern is stably transmitted. This concept is consistent with the Lamarck's theory of the inheritance of acquired traits, which therefore should be carefully reevaluated to reestablish his impaired reputation. PMID:20118668

  15. Mercury methylation in high and low-sulphate impacted wetland ponds within the prairie pothole region of North America.

    PubMed

    Hoggarth, Cameron G J; Hall, Britt D; Mitchell, Carl P J

    2015-10-01

    Using enriched stable (201)Hg injections into intact sediment cores, we provide the first reported Hg methylation potential rate constants (km) in prairie wetland ponds (0.016-0.17 d(-1)). Our km values were similar to other freshwater wetlands and did not differ in ponds categorized with high compared to low surface water concentrations of sulphate. Sites with high sulphate had higher proportions of methylmercury (MeHg) in sediment (2.9 ± 1.6% vs. 1.0 ± 0.3%) and higher surface water MeHg concentrations (1.96 ± 1.90 ng L(-1)vs. 0.56 ± 0.55 ng L(-1)). Sediment-porewater partitioning coefficients were small, and likely due to high ionic activity. Our work suggests while km measurements are useful for understanding mercury cycling processes, they are less important than surface water MeHg concentrations for assessing MeHg risks to biota. Significant differences in MeHg concentrations between sites with high and low sulphate concentrations may also inform management decisions concerning wetland remediation and creation.

  16. DNA methylation dynamics at imprinted genes during bovine pre-implantation embryo development.

    PubMed

    O'Doherty, Alan M; Magee, David A; O'Shea, Lynee C; Forde, Niamh; Beltman, Marijke E; Mamo, Solomon; Fair, Trudee

    2015-03-10

    In mammals, maternal differentially methylated regions (DMRs) acquire DNA methylation during the postnatal growth stage of oogenesis, with paternal DMRs acquiring DNA methylation in the perinatal prospermatagonia. Following fusion of the male and female gametes, it is widely accepted that murine DNA methylation marks at the DMRs of imprinted genes are stable through embryogenesis and early development, until they are reprogrammed in primordial germ cells. However, the DNA methylation dynamics at DMRs of bovine imprinted genes during early stages of development remains largely unknown. The objective of this investigation was to analyse the methylation dynamics at imprinted gene DMRs during bovine embryo development, from blastocyst stage until implantation. To this end, pyrosequencing technology was used to quantify DNA methylation at DMR-associated CpG dinucleotides of six imprinted bovine genes (SNRPN, MEST, IGF2R, PLAGL1, PEG10 and H19) using bisulfite-modified genomic DNA isolated from individual blastocysts (Day 7); ovoid embryos (Day 14); filamentous embryos (Day 17) and implanting conceptuses (Day 25). For all genes, the degree of DNA methylation was most variable in Day 7 blastocysts compared to later developmental stages (P < 0.05). Furthermore, mining of RNA-seq transcriptomic data and western blot analysis revealed a specific window of expression of DNA methylation machinery genes (including DNMT3A, DNMT3B, TRIM28/KAP1 and DNMT1) and proteins (DNMT3A, DNMT3A2 and DNMT3B) by bovine embryos coincident with imprint stabilization. The findings of this study suggest that the DNA methylation status of bovine DMRs might be variable during the early stages of embryonic development, possibly requiring an active period of imprint stabilization.

  17. The genetics of dopa decarboxylase in Drosophila melanogaster. I. Isolation and characterization of deficiencies that delete the dopa-decarboxylase-dosage-sensitive region and the alpha-methyl-dopa-hypersensitive locus.

    PubMed

    Wright, T R; Hodgetts, R B; Sherald, A F

    1976-10-01

    A detailed cytogenetic investigation of 16 overlapping deficiencies in the 36C-40A region on the left arm of the second chromosome (2L) in Drosophila melanogaster is reported. These deficiencies permit a localization of both the dopa-decarboxylase-dosage-sensitive region and the alpha-methyl-dopa-hypersensitive locus, l(2) amd, to the same region, 37B10-37C7.

  18. In Vitro Methylation of the BsuRI (5′-GGCC-3′) Sites in the E2a Region of Adenovirus Type 2 DNA Does Not Affect Expression in Xenopus laevis Oocytes

    PubMed Central

    Vardimon, Lily; Günthert, Ursula; Doerfler, Walter

    1982-01-01

    The early region 2a (E2a) of adenovirus type 2 (Ad2) DNA codes for a 72,000-dalton DNA-binding protein and is expressed in the Ad2-transformed hamster cell line HE1 but not in cell lines HE2 and HE3 (H. Esche, J. Virol. 41:1076-1082, 1982; K. Johansson et al., J. Virol. 27:628-639, 1978). An inverse correlation between DNA methylation at the 5′-CCGG-3′ sites of the E2a region and of gene expression in these cell lines has been observed (L. Vardimon et al., Nucleic Acids Res. 8:2461-2473, 1980). When the cloned E2a region of Ad2 DNA is methylated in vitro at the 5′-CCGG-3′ sites, the gene is not transcribed after being injected into the nuclei of Xenopus laevis oocytes, whereas unmethylated DNA is expressed (L. Vardimon et al., Eur. J. Cell Biol. 25:13-15, 1981; L. Vardimon et al., Proc. Natl. Acad. Sci. U.S.A. 79:1073-1077, 1982). These data demonstrate that DNA methylation is directly involved in the shut-off of transcription. In the present communication we investigated in detail the control region of the gene for the DNA-binding protein in Ad2-transformed cell lines and showed that the first late control region (map coordinate 72 on the viral DNA) of the E2a region is present in its entirety in cell lines HE1, HE2, and HE3. The HaeIII sites (5′-GGCC-3′) in the E2a region in all three cell lines were not methylated. When the DNA methyltransferase BsuRI was used, all 5′-GGCC-3′ sites in the cloned E2a region of Ad2 DNA were methylated in vitro. It was shown that methylation of these sites did not inhibit the expression of this viral gene in X. laevis oocytes. Thus, for methylation to affect gene expression in the E2a region it has to occur at specific sites (e.g., 5′-CCGG-3′) which may be different for other genes. Images PMID:14582198

  19. Characterisation of DNA methylation status using spectroscopy (mid-IR versus Raman) with multivariate analysis.

    PubMed

    Kelly, Jemma G; Najand, Ghazal M; Martin, Francis L

    2011-05-01

    Methylation status plays important roles in the regulation of gene expression and significantly influences the dynamics, bending and flexibility of DNA. The aim of this study was to determine whether attenuated total reflection Fourier-transform infrared (ATR-FTIR) or Raman spectroscopy with subsequent multivariate analysis could determine methylation patterning in oligonucleotides variously containing 5-methylcytosine, cytosine and guanine bases. Applied to Low-E reflective glass slides, 10 independent spectral acquisitions were acquired per oligonucleotide sample. Resultant spectra were baseline-corrected and vector normalised over the 1750 cm(-1) -760 cm(-1) (for ATR-FTIR spectroscopy) or the 1750 cm(-1) -600 cm(-1) (for Raman spectroscopy) regions. Data were then analysed using principal component analysis (PCA) coupled with linear discriminant analysis (LDA). Exploiting this approach, biomolecular signatures enabling sensitive and specific discrimination of methylation patterning were derived. For DNA sequence and methylation analysis, this approach has the potential to be an important tool, especially when material is scarce.

  20. Methylation levels of the SCD1 gene promoter and LINE-1 repeat region are associated with weight change: an intervention study.

    PubMed

    Martín-Núñez, Gracia María; Cabrera-Mulero, Rebeca; Rubio-Martín, Elehazara; Rojo-Martínez, Gemma; Olveira, Gabriel; Valdés, Sergio; Soriguer, Federico; Castaño, Luis; Morcillo, Sonsoles

    2014-07-01

    Epigenetic processes may be affected by environmental factors. DNA methylation measured in LINE-1 elements (LINE-1, long interspersed nucleotide element-1) correlates with LINE-1 DNA methylation. Variations in stearoyl CoA desaturase (SCD) activity (a key enzyme in the fatty acid metabolism) may be involved in various processes that can lead to diseases such as obesity. We evaluated whether changes in diet after a nutritional intervention would be associated with changes in LINE-1 DNA methylation and/or specific methylation of SCD1 gene promoter. Prospective cohort intervention study with a control group. We recorded phenotypic, anthropometric, biochemical, and nutritional information at baseline and 1 year later. DNA methylation was quantified by pyrosequencing. LINE-1 DNA methylation and SCD1 gene promoter methylation levels were similar at the beginning of the study in both populations, whereas after a year these levels were higher in the control group (p < 0.001). In the intervention group, those subjects who lost weight showed higher levels of SCD1 gene promoter methylation after the intervention. Subjects with lower adherence to a Mediterranean diet experienced larger changes in LINE-1 methylation. DNA methylation levels were associated with weight change and with adherence to a Mediterranean diet. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Does parent of origin matter? Methylation studies should be performed on patients with multiple copies of the Prader-Willi/Angelman syndrome critical region.

    PubMed

    Aypar, Umut; Brodersen, Pamela R; Lundquist, Patrick A; Dawson, D Brian; Thorland, Erik C; Hoppman, Nicole

    2014-10-01

    Deletion of 15q11.2-q13 results in either Prader-Willi syndrome (PWS) or Angelman syndrome (AS) depending on the parent of origin. Duplication of the PWS/AS critical region (PWASCR) has also been reported in association with developmental delay and autism, and it has been shown that they also show a parent-of-origin effect. It is generally accepted that maternal duplications are pathogenic. However, there is conflicting evidence as to the pathogenicity of paternal duplications. We have identified 35 patients with gain of the PWASCR using array comparative genomic hybridization. Methylation testing was performed to determine parent of origin of the extra copies. Of the 35 cases, 22 had a supernumerary marker chromosome 15 (SMC15), 12 had a tandem duplication, and 1 had a tandem triplication. Only one patient had a paternal duplication; this patient does not have features typical of patients with maternal duplication of the PWASCR. Three of the mothers had a tandem duplication (two were paternal and one was maternal origin). While one of the two mothers with paternal duplication was noted not to have autism, the other was noted to have learning disability and depression. Based on our data, we conclude that SMC15 are almost exclusively maternal in origin and result in an abnormal phenotype. Tandem duplications/triplications are generally of maternal origin when ascertained on the basis of abnormal phenotype; however, tandem duplications of paternal origin have also been identified. Therefore, we suggest that methylation testing be performed for cases of tandem duplications/triplications since the pathogenicity of paternal gains is uncertain. © 2014 Wiley Periodicals, Inc.

  2. Methyl chloroform

    SciTech Connect

    Wray, T.K.

    1994-04-01

    Methyl chloroform is identified as a Class 1 ozone-depleting substance under Title VI of the CAA Amendments. On Nov. 30, 1993, EPA ordered the phaseout of Class 1 ozone-depleting substances -- chlorofluorocarbons (CFCs), halons, carbon tetrachloride and methyl chloroform -- by Jan. 1, 1996. Methyl chloroform and other Class 1 substances may be used after the dead-line if sources can be found through recycling or existing inventories. Methyl chloroform is listed as a hazardous air pollutant under CAA. It also is a SARA Title III, Sec. 313 compound with a reportable quantity of 1,000 pounds. OSHA and the American Conference of Government Industrial Hygienists have set 350 ppm as the time-weighted average airborne exposure level for methyl chloroform. NIOSH lists its immediately dangerous to life or health'' concentration as 1,000 parts per million. DOT identifies the substance as a hazardous material, Class 6.1 (poison).

  3. DNA methylation is critical for tooth agenesis: implications for sporadic non-syndromic anodontia and hypodontia

    PubMed Central

    Wang, Jing; Sun, Ke; Shen, Yun; Xu, Yuanzhi; Xie, Jing; Huang, Renhuan; Zhang, Yiming; Xu, Chenyuan; Zhang, Xu; Wang, Raorao; Lin, Yunfeng

    2016-01-01

    Hypodontia is caused by interactions among genetic, epigenetic, and environmental factors during tooth development, but the actual mechanism is unknown. DNA methylation now appears to play a significant role in abnormal developments, flawed phenotypes, and acquired diseases. Methylated DNA immunoprecipitation (MeDIP) has been developed as a new method of scanning large-scale DNA-methylation profiles within particular regions or in the entire genome. Here, we performed a genome-wide scan of paired DNA samples obtained from 4 patients lacking two mandibular incisors and 4 healthy controls with normal dentition. We scanned another female with non-syndromic anodontia and her younger brother with the same gene mutations of the PAX9,MSX1,AXIN2 and EDA, but without developmental abnormalities in the dentition. Results showed significant differences in the methylation level of the whole genome between the hypodontia and the normal groups. Nine genes were spotted, some of which have not been associated with dental development; these genes were related mainly to the development of cartilage, bone, teeth, and neural transduction, which implied a potential gene cascade network in hypodontia at the methylation level. This pilot study reveals the critical role of DNA methylation in hypodontia and might provide insights into developmental biology and the pathobiology of acquired diseases. PMID:26759063

  4. DNA methylation is critical for tooth agenesis: implications for sporadic non-syndromic anodontia and hypodontia.

    PubMed

    Wang, Jing; Sun, Ke; Shen, Yun; Xu, Yuanzhi; Xie, Jing; Huang, Renhuan; Zhang, Yiming; Xu, Chenyuan; Zhang, Xu; Wang, Raorao; Lin, Yunfeng

    2016-01-13

    Hypodontia is caused by interactions among genetic, epigenetic, and environmental factors during tooth development, but the actual mechanism is unknown. DNA methylation now appears to play a significant role in abnormal developments, flawed phenotypes, and acquired diseases. Methylated DNA immunoprecipitation (MeDIP) has been developed as a new method of scanning large-scale DNA-methylation profiles within particular regions or in the entire genome. Here, we performed a genome-wide scan of paired DNA samples obtained from 4 patients lacking two mandibular incisors and 4 healthy controls with normal dentition. We scanned another female with non-syndromic anodontia and her younger brother with the same gene mutations of the PAX9,MSX1,AXIN2 and EDA, but without developmental abnormalities in the dentition. Results showed significant differences in the methylation level of the whole genome between the hypodontia and the normal groups. Nine genes were spotted, some of which have not been associated with dental development; these genes were related mainly to the development of cartilage, bone, teeth, and neural transduction, which implied a potential gene cascade network in hypodontia at the methylation level. This pilot study reveals the critical role of DNA methylation in hypodontia and might provide insights into developmental biology and the pathobiology of acquired diseases.

  5. Methylation at the CpG island shore region upregulates Nr3c1 promoter activity after early-life stress.

    PubMed

    Bockmühl, Yvonne; Patchev, Alexandre V; Madejska, Arleta; Hoffmann, Anke; Sousa, Joao C; Sousa, Nuno; Holsboer, Florian; Almeida, Osborne F X; Spengler, Dietmar

    2015-01-01

    Early-life stress (ELS) induces long-lasting changes in gene expression conferring an increased risk for the development of stress-related mental disorders. Glucocorticoid receptors (GR) mediate the negative feedback actions of glucocorticoids (GC) in the paraventricular nucleus (PVN) of the hypothalamus and anterior pituitary and therefore play a key role in the regulation of the hypothalamic-pituitary-adrenal (HPA) axis and the endocrine response to stress. We here show that ELS programs the expression of the GR gene (Nr3c1) by site-specific hypermethylation at the CpG island (CGI) shore in hypothalamic neurons that produce corticotropin-releasing hormone (Crh), thus preventing Crh upregulation under conditions of chronic stress. CpGs mapping to the Nr3c1 CGI shore region are dynamically regulated by ELS and underpin methylation-sensitive control of this region's insulation-like function via Ying Yang 1 (YY1) binding. Our results provide new insight into how a genomic element integrates experience-dependent epigenetic programming of the composite proximal Nr3c1 promoter, and assigns an insulating role to the CGI shore.

  6. Characterization of the IGF2 Imprinted Gene Methylation Status in Bovine Oocytes during Folliculogenesis.

    PubMed

    Mendonça, Anelise dos Santos; Guimarães, Ana Luíza Silva; da Silva, Naiara Milagres Augusto; Caetano, Alexandre Rodrigues; Dode, Margot Alves Nunes; Franco, Maurício Machaim

    2015-01-01

    DNA methylation reprogramming occurs during mammalian gametogenesis and embryogenesis. Sex-specific DNA methylation patterns at specific CpG islands controlling imprinted genes are acquired during this window of development. Characterization of the DNA methylation dynamics of imprinted genes acquired by oocytes during folliculogenesis is essential for understanding the physiological and genetic aspects of female gametogenesis and to determine the parameters for oocyte competence. This knowledge can be used to improve in vitro embryo production (IVP), specifically because oocyte competence is one of the most important aspects determining the success of IVP. Imprinted genes, such as IGF2, play important roles in embryo development, placentation and fetal growth. The aim of this study was to characterize the DNA methylation profile of the CpG island located in IGF2 exon 10 in oocytes during bovine folliculogenesis. The methylation percentages in oocytes from primordial follicles, final secondary follicles, small antral follicles, large antral follicles, MII oocytes and spermatozoa were 73.74 ± 2.88%, 58.70 ± 7.46%, 56.00 ± 5.58%, 65.77 ± 5.10%, 56.35 ± 7.45% and 96.04 ± 0.78%, respectively. Oocytes from primordial follicles showed fewer hypomethylated alleles (15.5%) than MII oocytes (34.6%) (p = 0.039); spermatozoa showed only hypermethylated alleles. Moreover, MII oocytes were less methylated than spermatozoa (p<0.001). Our results showed that the methylation pattern of this region behaves differently between mature oocytes and spermatozoa. However, while this region has a classical imprinted pattern in spermatozoa that is fully methylated, it was variable in mature oocytes, showing hypermethylated and hypomethylated alleles. Furthermore, our results suggest that this CpG island may have received precocious reprogramming, considering that the hypermethylated pattern was already found in growing oocytes from primordial follicles. These results may contribute to

  7. Methylation profiling using methylated DNA immunoprecipitation and tiling array hybridization.

    PubMed

    Cheung, Hoi-Hung; Lee, Tin-Lap; Rennert, Owen M; Chan, Wai-Yee

    2012-01-01

    DNA methylation is an important epigenetic modification that regulates development and plays a role in the pathophysiology of many diseases. It is dynamically changed during germline development. Methylated DNA immunoprecipitation (MeDIP) is an efficient, cost-effective method for locus-specific and genome-wide analysis. Methylated DNA fragments are enriched by a 5-methylcytidine-recognizing antibody, therefore allowing the analysis of both CpG and non-CpG methylation. The enriched DNA fragments can be amplified and hybridized to tiling arrays covering CpG islands, promoters, or the entire genome. Comparison of different methylomes permits the discovery of differentially methylated regions that might be important in disease- or tissue-specific expression. Here, we describe an established MeDIP protocol and tiling array hybridization method for profiling methylation of testicular germ cells.

  8. Report for borehole explosion data acquired in the 1999 Los Angeles Region Seismic Experiment (LARSE II), Southern California; Part II, Data tables and plots

    USGS Publications Warehouse

    Murphy, Janice M.; Fuis, Gary S.; Okaya, D.A.; Thygesen, Kristina; Baher, Shirley A.; Rybert, Trond; Kaip, Galen; Fort, Michael D.; Asudeh, Isa; Sell, Russell

    2002-01-01

    The Los Angeles Region Seismic Experiment (LARSE), a joint project of the U.S. Geological Survey (USGS) and the Southern California Earthquake Center (SCEC), was conducted to produce seismic images of the subsurface in the Los Angeles region. Primary targets were major fault systems and sedimentary basins; the goal of the project was to address the earthquake hazard posed by these geologic features. The first phase of data collection (LARSE 1) was completed in 1994; the second phase (LARSE 2) was completed in 1999. A description of the 1999 survey and an overview of both phase I and II is given in Fuis and others (2001). In this report, we present the technical details for the explosion data collected in 1999.

  9. Methyl methacrylate

    Integrated Risk Information System (IRIS)

    TOXICOLOGICAL REVIEW of METHYL METHACRYLATE ( CAS No . 80 - 62 - 6 ) In Support of Summary Information on the Integrated Risk Information System ( IRIS ) January 1998 U.S . Environmental Protection Agency Washington , DC TABLE OF CONTENTS DISCLAIMER . . . . . . . . . . . . . . . . . . . . . . . . .

  10. Exposure to 3,3',5-triiodothyronine affects histone and RNA polymerase II modifications, but not DNA methylation status, in the regulatory region of the Xenopus laevis thyroid hormone receptor βΑ gene.

    PubMed

    Kasai, Kentaro; Nishiyama, Norihito; Izumi, Yushi; Otsuka, Shunsuke; Ishihara, Akinori; Yamauchi, Kiyoshi

    2015-11-06

    Thyroid hormones (THs) play a critical role in amphibian metamorphosis, during which the TH receptor (TR) gene, thrb, is upregulated in a tissue-specific manner. The Xenopus laevis thrb gene has 3 TH response elements (TREs) in the 5' flanking regulatory region and 1 TRE in the exon b region, around which CpG sites are highly distributed. To clarify whether exposure to 3,3',5-triiodothyronine (T3) affects histone and RNA polymerase II (RNAPII) modifications and the level of DNA methylation in the 5' regulatory region, we conducted reverse transcription-quantitative polymerase chain reaction, bisulfite sequencing and chromatin immunoprecipitation assay using X. laevis cultured cells and premetamorphic tadpoles treated with or without 2 nM T3. Exposure to T3 increased the amount of the thrb transcript, in parallel with enhanced histone H4 acetylation and RNAPII recruitment, and probably phosphorylation of RNAPII at serine 5, in the 5' regulatory and exon b regions. However, the 5' regulatory region remained hypermethylated even with exposure to T3, and there was no significant difference in the methylation status between DNAs from T3-untreated and -treated cultured cells or tadpole tissues. Our results demonstrate that exposure to T3 induced euchromatin-associated epigenetic marks by enhancing histone acetylation and RNAPII recruitment, but not by decreasing the level of DNA methylation, in the 5' regulatory region of the X. laevis thrb gene.

  11. The clinical characteristics of 80 cases of acquired immunodeficiency syndrome-associated Kaposi's sarcoma in Xinjiang Autonomous Region and the effect of different treatments on the prognosis.

    PubMed

    Yang, Tongtong; He, Li; Wan, Xuefeng; Maimaitiaili, Wubuli; Song, Yuxia; Zhang, Yuexin; Lu, Xiaobo

    2015-01-01

    To analyze the clinical features of AIDS-related Kaposi's sarcoma (AIDS-KS) patients in Xinjiang Autonomous Region and the impact of CD4 (+)T lymphocyte count, highly active antiretroviral therapy (HAART) and systemic chemotherapy on the prognosis. The clinical information of 80 AIDS-KS patients admitted in Sixth People's Hospital of Xinjiang Autonomous Region from January 2008 to August 2014 was retrospectively reviewed. Population characteristics, extent of lesions, KS progress, CD4 (+)T lymphocyte count, combined opportunistic infections, treatment and prognosis of these patients were analyzed. The 80 patients were divided into five groups according to treatment methods, including HAART, HAART + chemotherapy, chemotherapy + HAART, chemotherapy, and untreated groups. The efficacy and prognosis of the five groups were compared. Among the 80 patients, 74 (92.50%) patients were Uygur. The average age was 39.5±9.9 years and male-to-female ratio was 3:1. The median of baseline CD4 (+)T lymphocyte count was 152.5 cells/μL and the interquartile was 233.25 cells/μL. CD4 (+)T lymphocyte counts were significantly increased after treatment in HAART, HAART + chemotherapy, and chemotherapy + HAART groups (P < 0.05). CD4 (+)T lymphocyte count in chemotherapy groups was significantly reduced after treatment (P < 0.05). The untreated group had the highest mortality rate (33.3%). In HAART group, KS-associated immune reconstitution inflammatory response syndrome (KS-IRIS) appeared in 45.5% cases and 2 death cases were caused by KS-IRIS. In Xinjiang Autonomous Region, the incidence of AIDS-KS is high in young Uygur male people. HAART followed by chemotherapy has ideal efficacy, reduces the incidence of KS-IRIS and improves the prognosis.

  12. Restoration of Dlk1 and Rtl1 is necessary but insufficient to rescue lethality in intergenic differentially methylated region (IG-DMR)-deficient mice.

    PubMed

    Takahashi, Nozomi; Kobayashi, Ryota; Kono, Tomohiro

    2010-08-20

    In the Dlk1-Dio3 imprinted domain, an intergenic differentially methylated region (IG-DMR) regulates the parental allele-specific expression of imprinted genes. The maternally inherited deletion of IG-DMR (IG-DMR((-/+))) results in perinatal lethality because of the overexpression of paternally expressed genes and repression of maternally expressed noncoding RNAs (ncRNAs), including Gtl2. To better understand the possible contribution of paternally expressed genes to the lethality, we attempted to rescue the lethality of IG-DMR((-/+)) mutants by restoring the paternally expressed genes. Because the paternally inherited Gtl2 deletion (Gtl2((+/-))) induced a decrease in the expression of paternally expressed genes, we crossed female IG-DMR heterozygous mice and male Gtl2 heterozygous mutant mice. The resultant IG-DMR((-/+))/Gtl2((+/-)) double mutant mice had normal expression levels of paternally expressed genes, and none of them showed perinatal lethality; however, most mice showed postnatal lethality with decreased expression of the maternally expressed ncRNAs. Thus, we inferred that paternally expressed genes are necessary for perinatal survivability and that maternally expressed ncRNAs are involved in postnatal lethality.

  13. Magnetic resonance anatomy of the proximal metacarpal region of the horse described from images acquired from low- and high-field magnets.

    PubMed

    Nagy, Annamaria; Dyson, Sue

    2009-01-01

    While low-field magnetic resonance (MR) images can provide useful information in the investigation of proximal metacarpal region pain, an in-depth knowledge of anatomy and comparison with more detailed high-field images are essential to understand the meaning of different signal intensities within tissues. This anatomic description is based on low-field and high-field MR examination of 30 cadaver metacarpal regions of mature horses with no history of carpal or proximal metacarpal pain. Normal MR anatomy is described and is illustrated by high-field and low-field MR images in transverse, sagittal and dorsal planes. Normal anatomic variations of soft tissue and osseous structures are discussed. Differences between the signal intensity and definition of tissues on high-field and low-field MR images and in different pulse sequences are highlighted. Several structures could be evaluated in both high-field and low-field images that cannot easily be imaged using radiography and ultrasonography, including the abaxial margins of the suspensory ligament, the interosseous ligaments between the metacarpal bones and the carpometacarpal ligaments. Structures that have previously not been described in detail were also identified.

  14. Gene methylation profile of gastric cancerous tissue according to tumor site in the stomach.

    PubMed

    Kupcinskaite-Noreikiene, Rita; Ugenskiene, Rasa; Noreika, Alius; Rudzianskas, Viktoras; Gedminaite, Jurgita; Skieceviciene, Jurgita; Juozaityte, Elona

    2016-01-26

    There is considerable information on the methylation of the promoter regions of different genes involved in gastric carcinogenesis. However, there is a lack of information on how this epigenetic process differs in tumors originating at different sites in the stomach. The aim of this study is to assess the methylation profiles of the MLH1, MGMT, and DAPK-1 genes in cancerous tissues from different stomach sites. Samples were acquired from 81 patients suffering stomach adenocarcinoma who underwent surgery for gastric cancer in the Lithuanian University of Health Sciences Hospital Kaunas Clinics in 2009-2012. Gene methylation was investigated with methylation-specific PCR. The study was approved by the Lithuanian Biomedical Research Ethics Committee. The frequencies of methylation in cancerous tissues from the upper, middle, and lower thirds of the stomach were 11.1, 23.1, and 45.4%, respectively, for MLH1; 22.2, 30.8, and 57.6%, respectively, for MGMT; and 44.4, 48.7, and 51.5%, respectively, for DAPK-1. MLH1 and MGMT methylation was observed more often in the lower third of the stomach than in the upper third (p < 0.05). In the middle third, DAPK-1 promoter methylation was related to more-advanced disease in the lymph nodes (N2-3 compared with N0-1 [p = 0.02]) and advanced tumor stage (stage III rather than stages I-II [p = 0.05]). MLH1 and MGMT methylation correlated inversely when the tumor was located in the lower third of the stomach (coefficient, -0.48; p = 0.01). DAPK-1 and MLH1 methylation correlated inversely in tumors in the middle-third of the stomach (coefficient, -0.41; p = 0.01). Gene promoter methylation depends on the gastric tumor location.

  15. DNA Methylation

    PubMed Central

    Marinus, M.G.; Løbner-Olesen, A.

    2014-01-01

    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholerae, Caulobacter crescentus) adenine methylation is essential and in C. crescentus, it is important for temporal gene expression which, in turn, is required for coordinating chromosome initiation, replication and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage; decrease transformation frequency in certain bacteria; decrease the stability of short direct repeats; are necessary for site-directed mutagenesis; and to probe eukaryotic structure and function. PMID:26442938

  16. LABORATORY-ACQUIRED MYCOSES

    DTIC Science & Technology

    laboratory- acquired mycoses . Insofar as possible, the etiological fungus, type of laboratory, classification of personnel, type of work conducted, and other...pertinent data have been listed in this study. More than 288 laboratory- acquired mycoses are described here, including 108 cases of

  17. Acquired Idiopathic Generalized Anhidrosis.

    PubMed

    Gangadharan, Geethu; Criton, Sebastian; Surendran, Divya

    2015-01-01

    Acquired idiopathic generalized anhidrosis is a rare condition, where the exact pathomechanism is unknown. We report a case of acquired idiopathic generalized anhidrosis in a patient who later developed lichen planus. Here an autoimmune-mediated destruction of sweat glands may be the probable pathomechanism.

  18. P35 and P22 Toxoplasma gondii antigens abbreviate regions to diagnose acquired toxoplasmosis during pregnancy: toward single-sample assays.

    PubMed

    Costa, Juan G; Peretti, Leandro E; García, Valeria S; Peverengo, Luz; González, Verónica D G; Gugliotta, Luis M; Dalla Fontana, Maria L; Lagier, Claudia M; Marcipar, Iván S

    2017-03-01

    P35 and P22 Toxoplasma gondii proteins are recognized by specific IgG at the early infection stage, making them ideal for acute toxoplasmosis pregnancy control. Both proteins have been studied to discriminate between acute and chronic toxoplasmosis. However, results were hardly comparable because different protein obtainment procedures led to different antigens, the reference panels used were not optimally typified, and avidity tests were either not performed or narrowly examined. We bioinformatically predicted P35 and P22 regions with the highest density of epitopes, and expressed them in pET32/BL21DE3 alternative expression system, obtaining the soluble proteins rP35a and rP22a. We assessed their diagnostic performance using pregnant woman serum samples typified as: not infected, NI (IgG-, IgM-), typical-chronic, TC (IgM-, IgG+), presumably acute, A (IgG+, IgM+, low-avidity IgG), and recently chronic, RC (IgG+, IgM+, high-avidity IgG). rP35a performed better than rP22a to differentiate A from RC, the areas under the curve (AUC) being 0.911 and 0.818, respectively. They, however, performed similarly to differentiate A from TC+RC (AUC: 0.915 and 0.907, respectively). rP35a and rP22a evaluation by avidity ELISA to discriminate A from RC rendered AUC values of 0.974 and 0.921, respectively. The indirect ELISA and avidity ELISA results analyzed in tandem were consistent with those obtained using commercial kits. rP35a and rP22a features suggest that, with complementary use, they could replace parasite lysate for toxoplasmosis infection screening and for acute toxoplasmosis diagnosis. Our proposal should be validated by a longitudinal study and may lead to a reliable toxoplasmosis pregnancy control, performing tests in only one serum sample.

  19. Methyl Chloride V5 Region Line Shape Parameters and Rotational Constants for the V2, V5 and 2V3 Vibrational Band

    NASA Technical Reports Server (NTRS)

    Chackerian, C., Jr.; Brown, L. R.; Lacome, N.; Tarrago, G.

    1998-01-01

    Methyl chloride (CH3Cl) is relatively abundant in the Earth's atmosphere, and because it is easily photodissociated is an important source of the chlorine atoms which are involved in the destruction of atmospheric ozone.

  20. Loss of estrogen receptor beta isoform expression and its correlation with aberrant DNA methylation of the 5'-untranslated region in human epithelial ovarian carcinoma.

    PubMed

    Suzuki, Fumihiko; Akahira, Jun-Ichi; Miura, Ikumi; Suzuki, Takashi; Ito, Kiyoshi; Hayashi, Shin-Ichi; Sasano, Hironobu; Yaegashi, Nobuo

    2008-12-01

    Evidence exists that sex steroids such as estrogens affect epithelial ovarian cancer. The expression profiles of the estrogen receptors (ER) and ERbeta in particular have not been fully described. Therefore, in our present study, we examined the methylation status of the promoters 0K and 0N, and the expression of ERbeta isoforms in human epithelial ovarian carcinoma. We then correlated methylation status with ER expression status. Twelve ovarian carcinoma cell lines, six primary cultures of ovarian surface epithelial cells (OSE), and 64 cases of ovarian carcinoma tissues were examined. Bisulfite sequencing and quantitative reverse transcription-polymerase chain reaction were used to evaluate methylation status and expression of ERbeta isoforms. The relative abundance of exon 0N, ERbeta1, ERbeta2, and ERbeta4 mRNA was significantly lower in ovarian cancer cell lines and tissues than in their corresponding normal counterparts. However, ERbeta5 mRNA level was relatively higher in the cancers, in clear cell adenocarcinoma in particular, than in the normal ovary. Bisulfite sequencing analysis demonstrated that the two promoters of the ERbeta gene exhibited distinct methylation patterns. Promoter 0N was unmethylated in OSE, rarely methylated in normal ovarian tissues, and extensively methylated in ovarian cancer cell lines and tissues (11/15 cell lines and 18/32 cancer tissues were extensively methylated). The promoter 0K was, however, unmethylated in both normal and malignant ovarian cells and tissues. A significant correlation between promoter 0N hypermethylation and the loss of exon 0N, ERbeta1, ERbeta2, and ERbeta4 mRNA expression was detected in ovarian carcinoma cells and tissues. Treatment of ovarian carcinoma cells with 5-aza-2' deoxycytidine resulted in reexpression of the ERbeta gene. The results of our present study suggest that ERbeta is inactivated mainly through aberrant DNA methylation. This process may play an important role in the pathogenesis of

  1. Mercury methylation, export and bioaccumulation in rice agriculture - model results from comparative and experimental studies in 3 regions of the California Delta, USA

    NASA Astrophysics Data System (ADS)

    Windham-Myers, L.; Fleck, J.; Eagles-Smith, C.; Ackerman, J.

    2013-12-01

    Seasonally flooded wetland ecosystems are often poised for mercury (Hg) methylation, thus becoming sources of methylmercury (MeHg) to in situ and downstream biota. The seasonal flooding associated with cultivation of rice (Oryza sativa) also generates MeHg, which may be stored in sediment or plants, bioaccumulated into fauna, degraded or exported, depending on hydrologic and seasonal conditions. While many U.S. waters are regulated for total Hg concentrations based on fish targets, California's Sacramento-San Joaquin Delta (Delta) will soon implement the first MeHg total maximum daily load (TMDL) control program. Since 2007, a conceptual model (DRERIP-MCM) and several ecosystem-level studies have been advanced to better understand the mechanisms behind Hg methylation, export and bioaccumulation within Delta wetlands, including rice agriculture. Three Delta rice-growing regions (Yolo Bypass, Cosumnes River, Central Delta) of varied soil characteristics, mining influences and hydrology, were monitored over full crop years to evaluate annual MeHg dynamics. In addition to fish tissue Hg accumulation, a broad suite of biogeochemical and hydrologic indices were assessed and compared between wetland types, seasons, and regions. In general, Delta rice fields were found to export MeHg during the post-harvest winter season, and promote MeHg uptake in fish and rice grain during the summer growing season. As described in a companion presentation (Eagles-Smith et al., this session), the experimental Cosumnes River study suggests that rice-derived dissolved organic carbon (DOC) fuels MeHg production and uptake into aquatic foodwebs. Explicit DRERIP-MCM linkages for the role of rice-DOC in MeHg production, export and bioaccumulation were verified across two summers (2011, 2012): rice biomass and root productivity influenced porewater DOC availability and microbial processes, which drove sediment MeHg production and flux to surface water, promoting MeHg bioaccumulation in fish

  2. Identification of endometrial cancer methylation features using combined methylation analysis methods

    PubMed Central

    Trimarchi, Michael P.; Yan, Pearlly; Groden, Joanna; Bundschuh, Ralf; Goodfellow, Paul J.

    2017-01-01

    Background DNA methylation is a stable epigenetic mark that is frequently altered in tumors. DNA methylation features are attractive biomarkers for disease states given the stability of DNA methylation in living cells and in biologic specimens typically available for analysis. Widespread accumulation of methylation in regulatory elements in some cancers (specifically the CpG island methylator phenotype, CIMP) can play an important role in tumorigenesis. High resolution assessment of CIMP for the entire genome, however, remains cost prohibitive and requires quantities of DNA not available for many tissue samples of interest. Genome-wide scans of methylation have been undertaken for large numbers of tumors, and higher resolution analyses for a limited number of cancer specimens. Methods for analyzing such large datasets and integrating findings from different studies continue to evolve. An approach for comparison of findings from a genome-wide assessment of the methylated component of tumor DNA and more widely applied methylation scans was developed. Methods Methylomes for 76 primary endometrial cancer and 12 normal endometrial samples were generated using methylated fragment capture and second generation sequencing, MethylCap-seq. Publically available Infinium HumanMethylation 450 data from The Cancer Genome Atlas (TCGA) were compared to MethylCap-seq data. Results Analysis of methylation in promoter CpG islands (CGIs) identified a subset of tumors with a methylator phenotype. We used a two-stage approach to develop a 13-region methylation signature associated with a “hypermethylator state.” High level methylation for the 13-region methylation signatures was associated with mismatch repair deficiency, high mutation rate, and low somatic copy number alteration in the TCGA test set. In addition, the signature devised showed good agreement with previously described methylation clusters devised by TCGA. Conclusion We identified a methylation signature for a

  3. The methyl- and aza-substituent effects on nonradiative decay mechanisms of uracil in water: a transient absorption study in the UV region.

    PubMed

    Hua, XinZhong; Hua, LinQiang; Liu, XiaoJun

    2016-05-18

    The nonradiative decay dynamics of photo-excited uracil (Ura) and its derivatives, i.e., thymine (5-methyluracil, Thy), 6-methyluracil (6-MU) and 6-azauracil (6-AU) in water, has been studied using a femtosecond transient absorption method. The molecules are populated in the lowest (1)ππ* state by a pump pulse at 266 nm, and a broadband continuum in the deep UV region is then employed as the probe. The extension of the continuous UV probe down to 250 nm enables us to investigate comprehensively the population dynamics of the ground states for those molecules and to uncover the substituent effects on nonradiative decay dynamics of uracil. Vibrational cooling in the ground states of Ura, Thy and 6-MU has been directly observed for the first time, providing solid evidence of the ultrafast (1)ππ* → S0 decay. In combination with the ground state bleaching signals, it is consolidated that their lowest (1)ππ* state decays via two parallel pathways, i.e., (1)ππ* → S0 and (1)ππ* → (1)nπ*. Moreover, the contribution of the (1)ππ* → (1)nπ* channel is found to be much smaller for Thy or 6-MU than for Ura. Different from methyl-substitution, the initial (1)ππ* state of the aza-substituent 6-AU decays primarily to the (1)nπ* state, while the (1)ππ* → S0 channel can be negligible. Our study provides a comprehensive understanding of the substituent effects on the excited-state dynamics of uracil in water.

  4. Quantitative assessment of the diagnostic role of FHIT promoter methylation in non-small cell lung cancer

    PubMed Central

    Tan, Yulong; Lu, Zhouyi; Wang, An; Tan, Lixing; Chen, Sidi; Guo, Shicheng; Wang, Jiucun; Chen, Xiaofeng

    2017-01-01

    Aberrant methylation of CpG islands acquired in promoter regions plays an important role in carcinogenesis. Accumulated evidence demonstrates FHIT gene promoter hyper-methylation is involved in non-small cell lung cancer (NSCLC). To test the diagnostic ability of FHIT methylation status on NSCLC, thirteen studies, including 2,119 samples were included in our meta-analysis. Simultaneously, four independent DNA methylation datasets from TCGA and GEO database were analyzed for validation. The pooled odds ratio of FHIT promoter methylation in cancer samples was 3.43 (95% CI: 1.85 to 6.36) compared with that in controls. In subgroup analysis, significant difference of FHIT gene promoter methylation status in NSCLC and controls was found in Asians but not in Caucasian population. In validation stage, 950 Caucasian samples, including 126 paired samples from TCGA, 568 cancer tissues and 256 normal controls from GEO database were analyzed, and all 8 CpG sites near the promoter region of FHIT gene were not significantly differentially methylated. Thus the diagnostic role of FHIT gene in the lung cancer may be relatively limited in the Caucasian population but useful in the Asians. PMID:28036263

  5. The nucleotides responsible for the direct physical contact between the chromatin insulator protein CTCF and the H19 imprinting control region manifest parent of origin-specific long-distance insulation and methylation-free domains

    PubMed Central

    Pant, Vinod; Mariano, Piero; Kanduri, Chandrasekhar; Mattsson, Anita; Lobanenkov, Victor; Heuchel, Rainer; Ohlsson, Rolf

    2003-01-01

    The repression of the maternally inherited Igf2 allele has been proposed to depend on a methylation-sensitive chromatin insulator organized by the 11 zinc finger protein CTCF at the H19 imprinting control region (ICR). Here we document that point mutations of the nucleotides in physical contact with CTCF within the endogenous H19 ICR lead to loss of CTCF binding and Igf2 imprinting only when passaged through the female germline. This effect is accompanied by a significant loss of methylation protection of the maternally derived H19 ICR. Because CTCF interacts with other imprinting control regions, it emerges as a central factor responsible for interpreting and propagating gamete-derived epigenetic marks and for organizing epigenetically controlled expression domains. PMID:12629040

  6. Involvement of the glucose moiety in the molecular recognition of methyl beta-lactoside by ricin: synthesis, conformational analysis, and binding studies of different derivatives at the C-3 region.

    PubMed

    Fernández, P; Jiménez-Barbero, J; Martín-Lomas, M; Solís, D; Díaz-Mauriño, T

    1994-04-01

    Syntheses of the 3-aminodeoxy (4), 3-deoxy-3-methyl (5), and 3-epi (6) derivatives of methyl beta-lactoside (1) have been achieved from 1 in a straightforward way, and their solution conformations in water and dimethyl sulfoxide analysed through molecular mechanics and dynamics calculations and nuclear magnetic resonance data. The overall shape of all the compounds studied is fairly similar and may be described by conformers included in a low energy region with phi = 15 +/- 45 degrees and psi = -25 +/- 30 degrees, that is ca. 5% of the total potential energy surface for the glycosidic linkages of the disaccharides. The binding of the different compounds to ricin, the galactose-specific toxin from Ricinus communis, has been investigated. The results confirm the involvement of the C-3 region in a nonpolar interaction with the protein at the periphery of the combining site.

  7. Acquired inflammatory demyelinating neuropathies.

    PubMed

    Ensrud, E R; Krivickas, L S

    2001-05-01

    The acquired demyelinating neuropathies can be divided into those with an acute onset and course and those with a more chronic course. The acute neuropathies present as Guillain-Barré syndrome and include acute inflammatory demyelinating polyradiculoneuropathy (AIDP), Miller Fisher syndrome, acute motor axonal neuropathy (AMAN), acute motor and sensory axonal neuropathy (AMSAN), and acute pandysautonomia. The chronic neuropathies are collectively known as chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) and include MADSAM (multifocal acquired demyelinating sensory and motor neuropathy, also know as Lewis-Sumner syndrome) and DADS (distal acquired demyelinating symmetric neuropathy) as variants. The clinical features, pathology, pathogenesis, diagnosis, treatment, rehabilitation, and prognosis of these neuropathies are discussed.

  8. Long-term arsenic exposure induces histone H3 Lys9 dimethylation without altering DNA methylation in the promoter region of p16(INK4a) and down-regulates its expression in the liver of mice.

    PubMed

    Suzuki, Takehiro; Nohara, Keiko

    2013-09-01

    Long-term exposure of humans to high concentrations of arsenic is associated with an increased risk of cancer. Previous studies have suggested that arsenic exposure promotes tumorigenesis by inducing changes in the expression of tumor-related genes by dysregulating DNA methylation at tumor-related gene loci. However, the causal relationships between epigenetic changes and both arsenic exposure and tumorigenesis are still unclear. In the present study, we investigated whether arsenic can change the expression of tumor-related genes by inducing epigenetic modifications before tumorigenesis. We did so by investigating the effects of long-term arsenic exposure on representative epigenetic modifications, DNA methylation and histone modifications, in the tumor-free normal liver of C57Bl/6 mice. We focused on the tumor-related genes, p16(INK4a) , RASSF1A, Ha-ras and ER-α as target genes, because their expression and promoter methylation status in mice have been reported to be affected by long-term arsenic exposure. The results showed that long-term arsenic exposure induced a significant decrease in expression of p16(INK4a) associated with an increase in level of dimethylated histone H3 lysine 9 (H3K9), a transcription-suppressive histone modification, in the promoter region, but that DNA methylation of the promoter region was unaffected. The results also showed a significant increase in recruitment of H3K9 histone methyltransferase G9a to the promoter after arsenic exposure. These findings suggest that long-term arsenic exposure may induce down-regulation of p16(INK4a) by targeting recruitment of G9a and H3K9 dimethylation without altering DNA methylation before tumorigenesis in the liver. Copyright © 2012 John Wiley & Sons, Ltd.

  9. Methyl parathion

    Integrated Risk Information System (IRIS)

    Methyl parathion ; CASRN 298 - 00 - 0 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic

  10. Methyl chlorocarbonate

    Integrated Risk Information System (IRIS)

    Methyl chlorocarbonate ; CASRN 79 - 22 - 1 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinog

  11. Methyl chloride

    Integrated Risk Information System (IRIS)

    EPA / 635 / R01 / 003 TOXICOLOGICAL REVIEW OF METHYL CHLORIDE ( CAS No . 74 - 87 - 3 ) In Support of Summary Information on the Integrated Risk Information System ( IRIS ) June 2001 U.S . Environmental Protection Agency Washington , DC DISCLAIMER This document has been reviewed in accordance with U.

  12. Methyl iodide

    Integrated Risk Information System (IRIS)

    Methyl iodide ; CASRN 74 - 88 - 4 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Effe

  13. Methyl acrylate

    Integrated Risk Information System (IRIS)

    Methyl acrylate ; CASRN 96 - 33 - 3 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Ef

  14. Methyl isocyanate

    Integrated Risk Information System (IRIS)

    Methyl isocyanate ; CASRN 624 - 83 - 9 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic

  15. The inhibition of acquired fear.

    PubMed

    Izquierdo, Iván; Cammarota, Martín; Vianna, Mónica M R; Bevilaqua, Lía R M

    2004-01-01

    A conditioned stimulus (CS) associated with a fearsome unconditioned stimulus (US) generates learned fear. Acquired fear is at the root of a variety of mental disorders, among which phobias, generalized anxiety, the posttraumatic stress disorder (PTSD) and some forms of depression. The simplest way to inhibit learned fear is to extinguish it, which is usually done by repeatedly presenting the CS alone, so that a new association, CS-"no US", will eventually overcome the previously acquired CS-US association. Extinction was first described by Pavlov as a form of "internal inhibition" and was recommended by Freud and Ferenczi in the 1920s (who called it "habituation") as the treatment of choice for phobic disorders. It is used with success till this day, often in association with anxiolytic drugs. Extinction has since then been applied, also successfully and also often in association with anxiolytics, to the treatment of panic, generalized anxiety disorders and, more recently, PTSD. Extinction of learned fear involves gene expression, protein synthesis, N-methyl-D-aspartate (NMDA) receptors and signaling pathways in the hippocampus and the amygdala at the time of the first CS-no US association. It can be enhanced by increasing the exposure to the "no US" component at the time of behavioral testing, to the point of causing the complete uninstallment of the original fear response. Some theorists have recently proposed that reiteration of the CS alone may induce a reconsolidation of the learned behavior instead of its extinction. Reconsolidation would preserve the original memory from the labilization induced by its retrieval. If true, this would of course be disastrous for the psychotherapy of fear-motivated disorders. Here we show that neither the CS nor retrieval cause anything remotely like reconsolidation, but just extinction. In fact, our findings indicate that the reconsolidation hypothesis is essentially incorrect, at least for the form of contextual fear most

  16. Hospital-acquired pneumonia

    MedlinePlus

    ... levels in the blood Sputum culture or sputum gram stain , to check what germs are causing the pneumonia ... Aspiration Immunodeficiency disorders Pneumonia - adults (community acquired) Patient Instructions Pneumonia in adults - discharge Review Date 2/2/ ...

  17. Acquired color vision deficiency.

    PubMed

    Simunovic, Matthew P

    2016-01-01

    Acquired color vision deficiency occurs as the result of ocular, neurologic, or systemic disease. A wide array of conditions may affect color vision, ranging from diseases of the ocular media through to pathology of the visual cortex. Traditionally, acquired color vision deficiency is considered a separate entity from congenital color vision deficiency, although emerging clinical and molecular genetic data would suggest a degree of overlap. We review the pathophysiology of acquired color vision deficiency, the data on its prevalence, theories for the preponderance of acquired S-mechanism (or tritan) deficiency, and discuss tests of color vision. We also briefly review the types of color vision deficiencies encountered in ocular disease, with an emphasis placed on larger or more detailed clinical investigations. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Acquired Cerebral Trauma: Epilogue.

    ERIC Educational Resources Information Center

    Bigler, Erin D., Ed.

    1988-01-01

    The article summarizes a series of articles concerning acquired cerebral trauma. Reviewed are technological advances, treatment, assessment, potential innovative therapies, long-term outcome, family impact of chronic brain injury, and prevention. (DB)

  19. Pneumonia - children - community acquired

    MedlinePlus

    ... CL, Bradley JS. Pediatric community-acquired pneumonia. In: Cherry JD, Harrison GJ, Kaplan SL, Steinback WJ, and Hotez PJ, eds. Feigin and Cherry's Textbook of Pediatric Infectious Diseases. 7th ed. Philadelphia, ...

  20. Mercury net methylation in five tropical flood plain regions of Brazil: high in the root zone of floating macrophyte mats but low in surface sediments and flooded soils.

    PubMed

    Guimarães, J R; Meili, M; Hylander, L D; de Castro e Silva, E; Roulet, M; Mauro, J B; de Lemos, R

    2000-10-16

    In aquatic systems, bottom sediments have often been considered as the main methylmercury (MeHg) production site. In tropical floodplain areas, however, floating meadows and flooded forests extend over large areas and can be important Hg methylating sites. We present here a cross-system comparison of the Hg net methylation capacity in surface sediments, flooded soils and roots of floating aquatic macrophytes, assayed by in situ incubation with 203Hg and extraction of formed Me203 Hg by acid leaching and toluene. The presence of mono-MeHg was confirmed by thin layer chromatography and other techniques. Study areas included floodplain lakes in the Amazon basin (Tapajós, Negro and Amazon rivers), the Pantanal floodplain (Paraguay river basin), freshwater coastal lagoons in Rio de Janeiro and oxbow lakes in the Mogi-Guaçú river, São Paulo state. Different Hg levels were added in assays performed in 1994-1998, but great care was taken to standardise all other test parameters, to allow data comparisons. Net MeHg production was one order of magnitude higher (mean 13.8%, range 0.28-35) in the living or decomposing roots of floating or rooted macrophyte mats (Eichhornia azurea, E. crassipes, Paspalum sp., Eleocharis sellowiana, Salvinia sp., S. rotundifolia and Scirpus cubensis) than in the surface layer of underlying lake sediments (mean 0.6%, range 0.022-2.5). Methylation in flooded soils presented a wide range and was in some cases similar to the one found in macrophyte roots but usually much lower. In a Tapajós floodplain lake, natural concentrations of MeHg in soil and sediment cores taken along a lake-forest transect agreed well with data on net methylation potentials in the same samples. E. azurea, E. crassipes and Salvinia presented the highest methylation potentials, up to 113 times higher than in sediments. Methylation in E. azurea from six lakes of the Paraguay and Cuiabá rivers, high Pantanal, was determined in the 1998 dry and wet seasons and ranged from

  1. DNA methylation pathways and their crosstalk with histone methylation

    PubMed Central

    Du, Jiamu; Johnson, Lianna M.; Jacobsen, Steven E.; Patel, Dinshaw J.

    2015-01-01

    Methylation of DNA and of histone 3 at Lys 9 (H3K9) are highly correlated with gene silencing in eukaryotes from fungi to humans. Both of these epigenetic marks need to be established at specific regions of the genome and then maintained at these sites through cell division. Protein structural domains that specifically recognize methylated DNA and methylated histones are key for targeting enzymes that catalyse these marks to appropriate genome sites. Genetic, genomic, structural and biochemical data reveal connections between these two epigenetic marks, and these domains mediate much of the crosstalk. PMID:26296162

  2. Critical period of nonpromoter DNA methylation acquisition during prenatal male germ cell development.

    PubMed

    Niles, Kirsten M; Chan, Donovan; La Salle, Sophie; Oakes, Christopher C; Trasler, Jacquetta M

    2011-01-01

    The prenatal period of germ cell development is a key time of epigenetic programming in the male, a window of development that has been shown to be influenced by maternal factors such as dietary methyl donor supply. DNA methylation occurring outside of promoter regions differs significantly between sperm and somatic tissues and has recently been linked with the regulation of gene expression during development as well as successful germline development. We examined DNA methylation at nonpromoter, intergenic sequences in purified prenatal and postnatal germ cells isolated from wildtype mice and mice deficient in the DNA methyltransferase cofactor DNMT3L. Erasure of the parental DNA methylation pattern occurred by 13.5 days post coitum (dpc) with the exception of approximately 8% of loci demonstrating incomplete erasure. For most loci, DNA methylation acquisition occurred between embryonic day 13.5 to 16.5 indicating that the key phase of epigenetic pattern establishment for intergenic sequences in male germ cells occurs prior to birth. In DNMT3L-deficient germ cells at 16.5 dpc, average DNA methylation levels were low, about 30% of wildtype levels; however, by postnatal day 6, about half of the DNMT3L deficiency-specific hypomethylated loci had acquired normal methylation levels. Those loci normally methylated earliest in the prenatal period were the least affected in the DNMT3L-deficient mice, suggesting that some loci may be more susceptible than others to perturbations occurring prenatally. These results indicate that the critical period of DNA methylation programming of nonpromoter, intergenic sequences occurs in male germline progenitor cells in the prenatal period, a time when external perturbations of epigenetic patterns could result in diminished fertility.

  3. PTSD and DNA Methylation in Select Immune Function Gene Promoter Regions: A Repeated Measures Case-control Study of U.S. Military Service Members

    DTIC Science & Technology

    2013-06-24

    other relevant exposures which may influ- ence DNA methylation, such as dietary factors (folate, vitamin B12 intake) (Fenech, 2001; Piyathilake and...of folic acid and Vitamin B12 in genomic stability of human cells. Mutat. Res. 475, 57–67. doi:10.1016/S0027- 5107(01)00069-0 Feng, J., and Fan, G...42, 746–753. Oliveira, N. F., Damm, G. R., Andia, D. C., Salmon , C., Nociti, F. H. Jr., Line, S. R., et al. (2009). DNA methylation status of the

  4. Methyl eucomate

    PubMed Central

    Li, Linglin; Zhou, Guang-Xiong; Jiang, Ren-Wang

    2008-01-01

    The crystal structure of the title compound [systematic name: methyl 3-carboxy-3-hydr­oxy-3-(4-hydroxy­benz­yl)propanoate], C12H14O6, is stabilized by inter­molecular O—H⋯O and C—H⋯O hydrogen bonds. The mol­ecules are arranged in layers, parallel to (001), which are inter­connected by the O—H⋯O hydrogen bonds. PMID:21202973

  5. Acquired Immunity to Malaria

    PubMed Central

    Doolan, Denise L.; Dobaño, Carlota; Baird, J. Kevin

    2009-01-01

    Naturally acquired immunity to falciparum malaria protects millions of people routinely exposed to Plasmodium falciparum infection from severe disease and death. There is no clear concept about how this protection works. There is no general agreement about the rate of onset of acquired immunity or what constitutes the key determinants of protection; much less is there a consensus regarding the mechanism(s) of protection. This review summarizes what is understood about naturally acquired and experimentally induced immunity against malaria with the help of evolving insights provided by biotechnology and places these insights in the context of historical, clinical, and epidemiological observations. We advocate that naturally acquired immunity should be appreciated as being virtually 100% effective against severe disease and death among heavily exposed adults. Even the immunity that occurs in exposed infants may exceed 90% effectiveness. The induction of an adult-like immune status among high-risk infants in sub-Saharan Africa would greatly diminish disease and death caused by P. falciparum. The mechanism of naturally acquired immunity that occurs among adults living in areas of hyper- to holoendemicity should be understood with a view toward duplicating such protection in infants and young children in areas of endemicity. PMID:19136431

  6. Variable maternal methylation overlapping the nc886/vtRNA2-1 locus is locked between hypermethylated repeats and is frequently altered in cancer

    PubMed Central

    Romanelli, Valeria; Nakabayashi, Kazuhiko; Vizoso, Miguel; Moran, Sebastián; Iglesias-Platas, Isabel; Sugahara, Naoko; Sugahara, Naoko; Simón, Carlos; Simón, Carlos; Hata, Kenichiro; Hata, Kenichiro; Esteller, Manel; Esteller, Manel; Court, Franck; Court, Franck; Monk, David; Monk, David

    2014-01-01

    Cancer is as much an epigenetic disease as a genetic one; however, the interplay between these two processes is unclear. Recently, it has been shown that a large proportion of DNA methylation variability can be explained by allele-specific methylation (ASM), either at classical imprinted loci or those regulated by underlying genetic variants. During a recent screen for imprinted differentially methylated regions, we identified the genomic interval overlapping the non-coding nc886 RNA (previously known as vtRNA2-1) as an atypical ASM that shows variable levels of methylation, predominantly on the maternal allele in many tissues. Here we show that the nc886 interval is the first example of a polymorphic imprinted DMR in humans. Further analysis of the region suggests that the interval subjected to ASM is approximately 2 kb in size and somatically acquired. An in depth analysis of this region in primary cancer samples with matching normal adjacent tissue from the Cancer Genome Atlas revealed that aberrant methylation in bladder, breast, colon and lung tumors occurred in approximately 27% of cases. Hypermethylation occurred more frequently than hypomethylation. Using additional normal-tumor paired samples we show that on rare occasions the aberrant methylation profile is due to loss-of-heterozygosity. This work therefore suggests that the nc886 locus is subject to variable allelic methylation that undergoes cancer-associated epigenetic changes in solid tumors. PMID:24589629

  7. Community-acquired pneumonia.

    PubMed

    Falguera, M; Ramírez, M F

    2015-11-01

    This article not only reviews the essential aspects of community-acquired pneumonia for daily clinical practice, but also highlights the controversial issues and provides the newest available information. Community-acquired pneumonia is considered in a broad sense, without excluding certain variants that, in recent years, a number of authors have managed to delineate, such as healthcare-associated pneumonia. The latter form is nothing more than the same disease that affects more frail patients, with a greater number of risk factors, both sharing an overall common approach.

  8. Acquired hypofibrinogenemia: current perspectives

    PubMed Central

    Besser, Martin W; MacDonald, Stephen G

    2016-01-01

    Acquired hypofibrinogenemia is most frequently caused by hemodilution and consumption of clotting factors. The aggressive replacement of fibrinogen has become one of the core principles of modern management of massive hemorrhage. The best method for determining the patient’s fibrinogen level remains controversial, and particularly in acquired dysfibrinogenemia, could have major therapeutic implications depending on which quantification method is chosen. This review introduces the available laboratory and point-of-care methods and discusses the relative advantages and limitations. It also discusses current strategies for the correction of hypofibrinogenemia. PMID:27713652

  9. Acquired Brain Injury Program.

    ERIC Educational Resources Information Center

    Schwartz, Stacey Hunter

    This paper reviews the Acquired Brain Injury (ABI) Program at Coastline Community College (California). The ABI Program is a two-year, for-credit educational curriculum designed to provide structured cognitive retraining for adults who have sustained an ABI due to traumatic (such as motor vehicle accident or fall) or non-traumatic(such as…

  10. Laboratory-acquired Brucellosis

    PubMed Central

    Gallo, Richard; Kelly, Molly; Limberger, Ronald J.; DeAngelis, Karen; Cain, Louise; Wallace, Barbara; Dumas, Nellie

    2004-01-01

    We report two laboratory-acquired Brucella melitensis infections that were shown to be epidemiologically related. Blood culture isolates were initially misidentified because of variable Gram stain results, which led to misdiagnoses and subsequent laboratory exposures. Notifying laboratory personnel who unknowingly processed cultures from brucellosis patients is an important preventive measure. PMID:15504276

  11. Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation

    PubMed Central

    Zhang, Qingzhu; Wang, Dong; Lang, Zhaobo; He, Li; Yang, Lan; Zeng, Liang; Li, Yanqiang; Zhao, Cheng; Huang, Huan; Zhang, Heng; Zhang, Huiming; Zhu, Jian-Kang

    2016-01-01

    DNA methylation is a conserved epigenetic mark in plants and many animals. How parental alleles interact in progeny to influence the epigenome is poorly understood. We analyzed the DNA methylomes of Arabidopsis Col and C24 ecotypes, and their hybrid progeny. Hybrids displayed nonadditive DNA methylation levels, termed methylation interactions, throughout the genome. Approximately 2,500 methylation interactions occurred at regions where parental DNA methylation levels are similar, whereas almost 1,000 were at differentially methylated regions in parents. Methylation interactions were characterized by an abundance of 24-nt small interfering RNAs. Furthermore, dysfunction of the RNA-directed DNA methylation pathway abolished methylation interactions but did not affect the increased biomass observed in hybrid progeny. Methylation interactions correlated with altered genetic variation within the genome, suggesting that they may play a role in genome evolution. PMID:27382183

  12. Desmosomes in acquired disease.

    PubMed

    Stahley, Sara N; Kowalczyk, Andrew P

    2015-06-01

    Desmosomes are cell-cell junctions that mediate adhesion and couple the intermediate filament cytoskeleton to sites of cell-cell contact. This architectural arrangement integrates adhesion and cytoskeletal elements of adjacent cells. The importance of this robust adhesion system is evident in numerous human diseases, both inherited and acquired, which occur when desmosome function is compromised. This review focuses on autoimmune and infectious diseases that impair desmosome function. In addition, we discuss emerging evidence that desmosomal genes are often misregulated in cancer. The emphasis of our discussion is placed on the way in which human diseases can inform our understanding of basic desmosome biology and in turn, the means by which fundamental advances in the cell biology of desmosomes might lead to new treatments for acquired diseases of the desmosome.

  13. Desmosomes in acquired disease

    PubMed Central

    Stahley, Sara N.; Kowalczyk, Andrew P.

    2015-01-01

    Desmosomes are cell-cell junctions that mediate adhesion and couple the intermediate filament cytoskeleton to sites of cell-cell contact. This architectural arrangement functions to integrate adhesion and cytoskeletal elements of adjacent cells. The importance of this robust adhesion system is evident in numerous human diseases, both inherited and acquired, that occur when desmosome function is compromised. This review focuses on autoimmune and infectious diseases that impair desmosome function. In addition, we discuss emerging evidence that desmosomal genes are often misregulated in cancer. The emphasis of our discussion is placed on how human diseases inform our understanding of basic desmosome biology, and in turn, how fundamental advances in the cell biology of desmosomes may lead to new treatments for acquired diseases of the desmosome. PMID:25795143

  14. Hospital-acquired thrombocytopenia.

    PubMed

    McMahon, Christine M; Cuker, Adam

    2014-10-01

    The development of thrombocytopenia is common in hospitalized patients and is associated with increased mortality. Frequent and important causes of thrombocytopenia in hospitalized patients include etiologies related to the underlying illness for which the patient is admitted, such as infection and disseminated intravascular coagulation, and iatrogenic etiologies such as drug-induced immune thrombocytopenia, heparin-induced thrombocytopenia, posttransfusion purpura, hemodilution, major surgery, and extracorporeal circuitry. This review presents a brief discussion of the pathophysiology, distinguishing clinical features, and management of these etiologies, and provides a diagnostic approach to hospital-acquired thrombocytopenia that considers the timing and severity of the platelet count fall, the presence of hemorrhage or thrombosis, the clinical context, and the peripheral blood smear. This approach may offer guidance to clinicians in distinguishing among the various causes of hospital-acquired thrombocytopenia and providing management appropriate to the etiology.

  15. Inheritance of acquired traits in plants: reinstatement of Lamarck.

    PubMed

    Sano, Hiroshi

    2010-04-01

    Since Lamarck proposed the idea of inheritance of acquired traits 200 years ago, much has been said for and against it, but the theory was finally declined after the 1930s. Despite of the negative opinions of the majority of geneticists, botanists and plant breeders have long recognized that altered properties during the growth were occasionally transmitted to the offspring. This was also the case with artificially altered properties such as dwarfism, flowering timing and plant stature, which were induced by a non-mutagenic chemical, 5-azacytidine and its derivatives. As these drugs are powerful inhibitors of DNA methylation in vivo, a close correlation between methylation and phenotypic expression was suggested. Subsequent studies showed that rice plants acquired disease resistance upon demethylation of the corresponding resistant gene, and that both resistant trait and hypomethylated status were inherited by the progeny up to nine generations. Whether or not the methylation pattern changes under natural condition was then questioned, and recent studies have indicated that it indeed naturally changes in response to environmental stresses. Whether or not the altered methylation pattern during the vegetative growth is heritable was also questioned, and studies on toadflax and rice affirmed the question, showing stable maintenance of hypermethylation in the former and hypomethylation in the latter for 250 and 10 years, respectively. The observation strongly suggested that acquired traits can be heritable as far as the acquired methylation pattern is stably transmitted. This concept is consistent with the Lamarck's theory of the inheritance of acquired traits, which therefore should be carefully reevaluated to reestablish his impaired reputation.

  16. Intermediate DNA methylation is a conserved signature of genome regulation

    PubMed Central

    Elliott, GiNell; Hong, Chibo; Xing, Xiaoyun; Zhou, Xin; Li, Daofeng; Coarfa, Cristian; Bell, Robert J.A.; Maire, Cecile L.; Ligon, Keith L.; Sigaroudinia, Mahvash; Gascard, Philippe; Tlsty, Thea D.; Harris, R. Alan; Schalkwyk, Leonard C.; Bilenky, Misha; Mill, Jonathan; Farnham, Peggy J.; Kellis, Manolis; Marra, Marco A.; Milosavljevic, Aleksandar; Hirst, Martin; Stormo, Gary D.; Wang, Ting; Costello, Joseph F.

    2015-01-01

    The role of intermediate methylation states in DNA is unclear. Here, to comprehensively identify regions of intermediate methylation and their quantitative relationship with gene activity, we apply integrative and comparative epigenomics to 25 human primary cell and tissue samples. We report 18,452 intermediate methylation regions located near 36% of genes and enriched at enhancers, exons and DNase I hypersensitivity sites. Intermediate methylation regions average 57% methylation, are predominantly allele-independent and are conserved across individuals and between mouse and human, suggesting a conserved function. These regions have an intermediate level of active chromatin marks and their associated genes have intermediate transcriptional activity. Exonic intermediate methylation correlates with exon inclusion at a level between that of fully methylated and unmethylated exons, highlighting gene context-dependent functions. We conclude that intermediate DNA methylation is a conserved signature of gene regulation and exon usage. PMID:25691127

  17. Whole-genome DNA methylation profiling using MethylCap-seq.

    PubMed

    Brinkman, Arie B; Simmer, Femke; Ma, Kelong; Kaan, Anita; Zhu, Jingde; Stunnenberg, Hendrik G

    2010-11-01

    MethylCap-seq is a robust procedure for genome-wide profiling of DNA methylation. The approach consists of the capture of methylated DNA using the MBD domain of MeCP2, and subsequent next-generation sequencing of eluted DNA. Elution of the captured methylated DNA is done in steps using a salt gradient, which stratifies the genome into fractions with different CpG density. The enrichment reached within the individual eluates allows for cost-effective deep sequence coverage. The profiles together yield a detailed genome-wide map of methylated regions and readily allows detection of DNA methylation in known and novel regions. Here, we describe principles and details of the MethylCap-seq procedure using different sources of starting material.

  18. Function and Evolution of DNA Methylation in Nasonia vitripennis

    PubMed Central

    Wang, Xu; Wheeler, David; Avery, Amanda; Rago, Alfredo; Choi, Jeong-Hyeon; Colbourne, John K.; Clark, Andrew G.; Werren, John H.

    2013-01-01

    The parasitoid wasp Nasonia vitripennis is an emerging genetic model for functional analysis of DNA methylation. Here, we characterize genome-wide methylation at a base-pair resolution, and compare these results to gene expression across five developmental stages and to methylation patterns reported in other insects. An accurate assessment of DNA methylation across the genome is accomplished using bisulfite sequencing of adult females from a highly inbred line. One-third of genes show extensive methylation over the gene body, yet methylated DNA is not found in non-coding regions and rarely in transposons. Methylated genes occur in small clusters across the genome. Methylation demarcates exon-intron boundaries, with elevated levels over exons, primarily in the 5′ regions of genes. It is also elevated near the sites of translational initiation and termination, with reduced levels in 5′ and 3′ UTRs. Methylated genes have higher median expression levels and lower expression variation across development stages than non-methylated genes. There is no difference in frequency of differential splicing between methylated and non-methylated genes, and as yet no established role for methylation in regulating alternative splicing in Nasonia. Phylogenetic comparisons indicate that many genes maintain methylation status across long evolutionary time scales. Nasonia methylated genes are more likely to be conserved in insects, but even those that are not conserved show broader expression across development than comparable non-methylated genes. Finally, examination of duplicated genes shows that those paralogs that have lost methylation in the Nasonia lineage following gene duplication evolve more rapidly, show decreased median expression levels, and increased specialization in expression across development. Methylation of Nasonia genes signals constitutive transcription across developmental stages, whereas non-methylated genes show more dynamic developmental expression

  19. The inheritance of acquired epigenetic variations.

    PubMed

    Jablonka, Eva; Lamb, Marion J

    2015-08-01

    There is evidence that the functional history of a gene in one generation can influence its expression in the next. In somatic cells, changes in gene activity are frequently associated with changes in the pattern of methylation of the cytosines in DNA; these methylation patterns are stably inherited. Recent work suggests that information about patterns of methylation and other epigenetic states can also be transmitted from parents to offspring. This evidence is the basis of a model for the inheritance of acquired epigenetic variations. According to the model, an environmental stimulus can induce heritable chromatin modifications which are very specific and predictable, and might result in an adaptive response to the stimulus. This type of response probably has most significance for adaptive evolution in organisms such as fungi and plants, which lack distinct segregation of the soma and germ line. However, in all organisms, the accumulation of specific and random chromatin modifications in the germ line may be important in speciation, because these modifications could lead to reproductive isolation between populations. Heritable chromatin variations may also alter the frequency and distribution of classical mutations and meiotic recombination. Therefore, inherited epigenetic changes in the structure of chromatin can influence neo-Darwinian evolution as well as cause a type of "Lamarckian" inheritance.

  20. Acquired Factor V Inhibitor

    PubMed Central

    Hirai, Daisuke; Yamashita, Yugo; Masunaga, Nobutoyo; Katsura, Toshiaki; Akao, Masaharu; Okuno, Yoshiaki; Koyama, Hiroshi

    2016-01-01

    Inhibitors directed against factor V rarely occur, and the clinical symptoms vary. We herein report the case of a patient who presented with a decreased factor V activity that had decreased to <3 %. We administered vitamin K and 6 units of fresh frozen plasma, but she thereafter developed an intracerebral hemorrhage. It is unclear whether surgery >10 years earlier might have caused the development of a factor V inhibitor. The treatment of acquired factor V inhibitors is mainly the transfusion of platelet concentrates and corticosteroids. Both early detection and the early initiation of the treatment of factor V inhibitor are thus considered to be important. PMID:27746446

  1. Indigenous and acquired modifications in the aminoglycoside binding sites of Pseudomonas aeruginosa rRNAs.

    PubMed

    Gutierrez, Belen; Douthwaite, Stephen; Gonzalez-Zorn, Bruno

    2013-08-01

    Aminoglycoside antibiotics remain the drugs of choice for treatment of Pseudomonas aeruginosa infections, particularly for respiratory complications in cystic-fibrosis patients. Previous studies on other bacteria have shown that aminoglycosides have their primary target within the decoding region of 16S rRNA helix 44 with a secondary target in 23S rRNA helix 69. Here, we have mapped P. aeruginosa rRNAs using MALDI mass spectrometry and reverse transcriptase primer extension to identify nucleotide modifications that could influence aminoglycoside interactions. Helices 44 and 45 contain indigenous (housekeeping) modifications at m (4)Cm1402, m (3)U1498, m (2)G1516, m (6) 2A1518, and m (6) 2A1519; helix 69 is modified at m (3)Ψ1915, with m (5)U1939 and m (5)C1962 modification in adjacent sequences. All modifications were close to stoichiometric, with the exception of m (3)Ψ1915, where about 80% of rRNA molecules were methylated. The modification status of a virulent clinical strain expressing the acquired methyltransferase RmtD was altered in two important respects: RmtD stoichiometrically modified m (7)G1405 conferring high resistance to the aminoglycoside tobramycin and, in doing so, impeded one of the methylation reactions at C1402. Mapping the nucleotide methylations in P. aeruginosa rRNAs is an essential step toward understanding the architecture of the aminoglycoside binding sites and the rational design of improved drugs against this bacterial pathogen.

  2. Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes

    PubMed Central

    Olson, Claire E.; Roberts, Steven B.

    2014-01-01

    DNA methylation patterns and functions are variable across invertebrate taxa. In order to provide a better understanding of DNA methylation in the Pacific oyster (Crassostrea gigas), we characterized the genome-wide DNA methylation profile in male gamete cells using whole-genome bisulfite sequencing. RNA-Seq analysis was performed to examine the relationship between DNA methylation and transcript expression. Methylation status of over 7.6 million CpG dinucleotides was described with a majority of methylated regions occurring among intragenic regions. Overall, 15% of the CpG dinucleotides were determined to be methylated and the mitochondrial genome lacked DNA methylation. Integrative analysis of DNA methylation and RNA-Seq data revealed a positive association between methylation status, both in gene bodies and putative promoter regions, and expression. This study provides a comprehensive characterization of the distribution of DNA methylation in the oyster male gamete tissue and suggests that DNA methylation is involved in gene regulatory activity. PMID:24987376

  3. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

    PubMed Central

    2012-01-01

    DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation, cellular specification and cancer development. Here, we describe an R package, methylKit, that rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and hydroxymethylation sequencing experiments. methylKit includes functions for clustering, sample quality visualization, differential methylation analysis and annotation features, thus automating and simplifying many of the steps for discerning statistically significant bases or regions of DNA methylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statistically significant regions of differential methylation and stratify tumor subtypes. methylKit is available at http://code.google.com/p/methylkit. PMID:23034086

  4. Factors Affecting Elevated Arsenic and Methyl Mercury Concentrations in Small Shield Lakes Surrounding Gold Mines near the Yellowknife, NT, (Canada) Region

    PubMed Central

    Houben, Adam James; D’Onofrio, Rebecca; Kokelj, Steven V; Blais, Jules M

    2016-01-01

    Gold mines in the Yellowknife, NT, region—in particular, the Giant Mine—operated from 1949–99, releasing 237,000 tonnes of waste arsenic trioxide (As2O3) dust, among other compounds, from gold ore extraction and roasting processes. For the first time, we show the geospatial distribution of roaster-derived emissions of several chemical species beyond the mine property on otherwise undisturbed taiga shield lakes within a 25 km radius of the mine, 11 years after its closing. Additionally, we demonstrate that underlying bedrock is not a significant source for the elevated concentrations in overlying surface waters. Aquatic arsenic (As) concentrations are well above guidelines for drinking water (10 μg/L) and protection for aquatic life (5 μg/L), ranging up to 136 μg/L in lakes within 4 km from the mine, to 2.0 μg/L in lakes 24 km away. High conversion ratios of methyl mercury were shown in lakes near the roaster stack as well, with MeHg concentrations reaching 44% of total mercury. The risk of elevated exposures by these metals is significant, as many lakes used for recreation and fishing near the City of Yellowknife are within this radius of elevated As and methyl Hg concentrations. PMID:27050658

  5. Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions.

    PubMed

    Prickett, Adam R; Barkas, Nikolaos; McCole, Ruth B; Hughes, Siobhan; Amante, Samuele M; Schulz, Reiner; Oakey, Rebecca J

    2013-10-01

    DNA binding factors are essential for regulating gene expression. CTCF and cohesin are DNA binding factors with central roles in chromatin organization and gene expression. We determined the sites of CTCF and cohesin binding to DNA in mouse brain, genome wide and in an allele-specific manner with high read-depth ChIP-seq. By comparing our results with existing data for mouse liver and embryonic stem (ES) cells, we investigated the tissue specificity of CTCF binding sites. ES cells have fewer unique CTCF binding sites occupied than liver and brain, consistent with a ground-state pattern of CTCF binding that is elaborated during differentiation. CTCF binding sites without the canonical consensus motif were highly tissue specific. In brain, a third of CTCF and cohesin binding sites coincide, consistent with the potential for many interactions between cohesin and CTCF but also many instances of independent action. In the context of genomic imprinting, CTCF and/or cohesin bind to a majority but not all differentially methylated regions, with preferential binding to the unmethylated parental allele. Whether the parental allele-specific methylation was established in the parental germlines or post-fertilization in the embryo is not a determinant in CTCF or cohesin binding. These findings link CTCF and cohesin with the control regions of a subset of imprinted genes, supporting the notion that imprinting control is mechanistically diverse.

  6. Both CpG Methylation and Activation-Induced Deaminase Are Required for the Fragility of the Human bcl-2 Major Breakpoint Region: Implications for the Timing of the Breaks in the t(14;18) Translocation

    PubMed Central

    Cui, Xiaoping; Lu, Zhengfei; Kurosawa, Aya; Klemm, Lars; Bagshaw, Andrew T.; Tsai, Albert G.; Gemmell, Neil; Müschen, Markus; Adachi, Noritaka; Hsieh, Chih-Lin

    2013-01-01

    The t(14;18) chromosomal translocation typically involves breakage at the bcl-2 major breakpoint region (MBR) to cause human follicular lymphoma. A theory to explain the striking propensity of the MBR breaks at three CpG clusters within the 175-bp MBR region invoked activation-induced deaminase (AID). In a test of that theory, we used here minichromosomal substrates in human pre-B cell lines. Consistent with the essential elements of the theory, we found that the MBR breakage process is indeed highly dependent on DNA methylation at the CpG sites and highly dependent on the AID enzyme to create lesions at peak locations within the MBR. Interestingly, breakage of the phosphodiester bonds at the AID-initiated MBR lesions is RAG dependent, but, unexpectedly, most are also dependent on Artemis. We found that Artemis is capable of nicking small heteroduplex structures and is even able to nick single-base mismatches. This raises the possibility that activated Artemis, derived from the unjoined D to JH DNA ends at the IgH locus on chromosome 14, nicks AID-generated TG mismatches at methyl CpG sites, and this would explain why the breaks at the chromosome 18 MBR occur within the same time window as those on chromosome 14. PMID:23263985

  7. Whole genome methylation profiling by immunoprecipitation of methylated DNA.

    PubMed

    Sharp, Andrew J

    2012-01-01

    I provide a protocol for DNA methylation profiling based on immunoprecipitation of methylated DNA using commercially available monoclonal antibodies that specifically recognize 5-methylcytosine. Quantification of the level of enrichment of the resulting DNA enables DNA methylation to be assayed for any genomic locus, including entire chromosomes or genomes if appropriate microarray or high-throughput sequencing platforms are used. In previous studies (1, 2), I have used hybridization to oligonucleotide arrays from Roche Nimblegen Inc, which allow any genomic region of interest to be interrogated, dependent on the array design. For example, using modern tiling arrays comprising millions of oligonucleotide probes, several complete human chromosomes can be assayed at densities of one probe per 100 bp or greater, sufficient to yield high-quality data. However, other methods such as quantitative real-time PCR or high-throughput sequencing can be used, giving either measurement of methylation at a single locus or across the entire genome, respectively. While the data produced by single locus assays is relatively simple to analyze and interpret, global assays such as microarrays or high-throughput sequencing require more complex statistical approaches in order to effectively identify regions of differential methylation, and a brief outline of some approaches is given.

  8. [Acquired coagulant factor inhibitors].

    PubMed

    Nogami, Keiji

    2015-02-01

    Acquired coagulation factor inhibitors are an autoimmune disease causing bleeding symptoms due to decreases in the corresponding factor (s) which result from the appearance of autoantibodies against coagulation factors (inhibitor). This disease is quite different from congenital coagulation factor deficiencies based on genetic abnormalities. In recent years, cases with this disease have been increasing, and most have anti-factor VIII autoantibodies. The breakdown of the immune control mechanism is speculated to cause this disease since it is common in the elderly, but the pathology and pathogenesis are presently unclear. We herein describe the pathology and pathogenesis of factor VIII and factor V inhibitors. Characterization of these inhibitors leads to further analysis of the coagulation process and the activation mechanisms of clotting factors. In the future, with the development of new clotting examination method (s), we anticipate that further novel findings will be obtained in this field through inhibitor analysis. In addition, detailed elucidation of the coagulation inhibitory mechanism possibly leading to hemostatic treatment strategies for acquired coagulation factor disorders will be developed.

  9. Cigarette smoking and DNA methylation

    PubMed Central

    Lee, Ken W. K.; Pausova, Zdenka

    2013-01-01

    DNA methylation is the most studied epigenetic modification, capable of controlling gene expression in the contexts of normal traits or diseases. It is highly dynamic during early embryogenesis and remains relatively stable throughout life, and such patterns are intricately related to human development. DNA methylation is a quantitative trait determined by a complex interplay of genetic and environmental factors. Genetic variants at a specific locus can influence both regional and distant DNA methylation. The environment can have varying effects on DNA methylation depending on when the exposure occurs, such as during prenatal life or during adulthood. In particular, cigarette smoking in the context of both current smoking and prenatal exposure is a strong modifier of DNA methylation. Epigenome-wide association studies have uncovered candidate genes associated with cigarette smoking that have biologically relevant functions in the etiology of smoking-related diseases. As such, DNA methylation is a potential mechanistic link between current smoking and cancer, as well as prenatal cigarette-smoke exposure and the development of adult chronic diseases. PMID:23882278

  10. Protein Methylation in Full Length Chlamydomonas Flagella

    PubMed Central

    Sloboda, Roger D.; Howard, Louisa

    2010-01-01

    Post-translational protein modification occurs extensively in eukaryotic flagella. Here we examine protein methylation, a protein modification that has only recently been reported to occur in flagella (Schneider et al. 2008). The cobalamin (vitamin B12) independent form of the enzyme methionine synthase (MetE), which catalyzes the final step in methionine production, is localized to flagella. Here we demonstrate, using immunogold scanning electron microscopy, that MetE is bound to the outer doublets of the flagellum. Methionine can be converted to S-adenosyl methionine, which then serves as the methyl donor for protein methylation reactions. Using antibodies that recognize symmetrically or asymmetrically methylated arginine residues, we identify three highly methylated proteins in intact flagella: two symmetrically methylated proteins of about 30 and 40 kDa, and one asymmetrically methylated protein of about 75 kDa. Several other relatively less methylated proteins could also be detected. Fractionation and immunoblot analysis shows that these proteins are components of the flagellar axoneme. Immunogold thin section electron microscopy indicates that the symmetrically methylated proteins are located in the central region of the axoneme, perhaps as components of the central pair complex and the radial spokes, while the asymmetrically methylated proteins are associated with the outer doublets. PMID:19472373

  11. RNA-directed DNA methylation in Arabidopsis

    PubMed Central

    Aufsatz, Werner; Mette, M. Florian; van der Winden, Johannes; Matzke, Antonius J. M.; Matzke, Marjori

    2002-01-01

    In plants, double-stranded RNA that is processed to short RNAs ≈21–24 nt in length can trigger two types of epigenetic gene silencing. Posttranscriptional gene silencing, which is related to RNA interference in animals and quelling in fungi, involves targeted elimination of homologous mRNA in the cytoplasm. RNA-directed DNA methylation involves de novo methylation of almost all cytosine residues within a region of RNA–DNA sequence identity. RNA-directed DNA methylation is presumed to be responsible for the methylation observed in protein coding regions of posttranscriptionally silenced genes. Moreover, a type of transcriptional gene silencing and de novo methylation of homologous promoters in trans can occur if a double-stranded RNA contains promoter sequences. Although RNA-directed DNA methylation has been described so far only in plants, there is increasing evidence that RNA can also target genome modifications in other organisms. To understand how RNA directs methylation to identical DNA sequences and how changes in chromatin configuration contribute to initiating or maintaining DNA methylation induced by RNA, a promoter double-stranded RNA-mediated transcriptional gene silencing system has been established in Arabidopsis. A genetic analysis of this system is helping to unravel the relationships among RNA signals, DNA methylation, and chromatin structure. PMID:12169664

  12. Wp specific methylation of highly proliferated LCLs

    SciTech Connect

    Park, Jung-Hoon; Jeon, Jae-Pil; Shim, Sung-Mi; Nam, Hye-Young; Kim, Joon-Woo; Han, Bok-Ghee; Lee, Suman . E-mail: suman@cha.ac.kr

    2007-06-29

    The epigenetic regulation of viral genes may be important for the life cycle of EBV. We determined the methylation status of three viral promoters (Wp, Cp, Qp) from EBV B-lymphoblastoid cell lines (LCLs) by pyrosequencing. Our pyrosequencing data showed that the CpG region of Wp was methylated, but the others were not. Interestingly, Wp methylation was increased with proliferation of LCLs. Wp methylation was as high as 74.9% in late-passage LCLs, but 25.6% in early-passage LCLs. From two Burkitt's lymphoma cell lines, Wp specific hypermethylation was also found (>80%). Interestingly, the expression of EBNA2 gene which located directly next to Wp was associated with its methylation. Our data suggested that Wp specific methylation may be important for the indicator of the proliferation status of LCLs, and the epigenetic viral gene regulation of EBNA2 gene by Wp should be further defined possibly with other biological processes.

  13. Acquired Porphyria Cutanea Tarda

    PubMed Central

    Koval, Andrew; Danby, C. W. E.; Petermann, H.

    1965-01-01

    Currently, the porphyrias are classified in four main groups: congenital porphyria, acute intermittent porphyria, porphyria cutanea tarda hereditaria, and porphyria cutanea tarda symptomatica. The acquired form of porphyria (porphyria cutanea tarda symptomatica) occurs in older males and is nearly always associated with chronic alcoholism and hepatic cirrhosis. The main clinical changes are dermatological, with excessive skin fragility and photosensitivity resulting in erosions and bullae. Biochemically, high levels of uroporphyrin are found in the urine and stools. Treatment to date has been symptomatic and usually unsuccessful. A case of porphyria cutanea tarda symptomatica is presented showing dramatic improvement of both the skin lesions and porphyrin levels in urine and blood following repeated phlebotomy. Possible mechanisms of action of phlebotomy on porphyria cutanea tarda symptomatica are discussed. ImagesFig. 1Fig. 2 PMID:14341652

  14. AIDS: acquired immunodeficiency syndrome.

    PubMed Central

    Gilmore, N. J.; Beaulieu, R.; Steben, M.; Laverdière, M.

    1983-01-01

    Acquired immunodeficiency syndrome, or AIDS, is a new illness that occurs in previously healthy individuals. It is characterized by immunodeficiency, opportunistic infections and unusual malignant diseases. Life-threatening single or multiple infections with viruses, mycobacteria, fungi or protozoa are common. A rare neoplasm, Kaposi's sarcoma, has developed in approximately one third of patients with AIDS. More than 800 cases of AIDS have been reported in North America, over 24 of them in Canada. The majority of patients are male homosexuals, although AIDS has also developed in abusers of intravenously administered drugs, Haitian immigrants, individuals with hemophilia, recipients of blood transfusions, prostitutes, and infants, spouses and partners of patients with AIDS. The cause of AIDS is unknown, but the features are consistent with an infectious process. Early diagnosis can be difficult owing to the nonspecific symptoms and signs of the infections and malignant diseases. Therefore, vigilance by physicians is of utmost importance. PMID:6342737

  15. AIDS: acquired immunodeficiency syndrome *

    PubMed Central

    Gilmore, N.J.; Beaulieu, R.; Steben, M.; Laverdière, M.

    1992-01-01

    Acquired immunodeficiency syndrome, or AIDS, is a new illness that occurs in previously healthy individuals. It is characterized by immunodeficiency, opportunistic infections and unusual malignant diseases. Life-threatening single or multiple infections with viruses, mycobacteria, fungi or protozoa are common. A rare neoplasm, Kaposi's sarcoma, has developed in approximately one third of patients with AIDS. More than 800 cases of AIDS have been reported in North America, over 24 of them in Canada. The majority of patients are male homosexuals, although AIDS has also developed in abusers of intravenously administered drugs, Haitian immigrants, individuals with hemophilia, recipients of blood transfusions, prostitutes, and infants, spouses and partners of patients with AIDS. The cause of AIDS is unknown, but the features are consistent with an infectious process. Early diagnosis can be difficult owing to the nonspecific symptoms and signs of the infections and malignant diseases. Therefore, vigilance by physicians is of the utmost importance. PMID:1544049

  16. Acquired epidermodysplasia verruciformis.

    PubMed

    Rogers, Heather D; Macgregor, Jennifer L; Nord, Kristin M; Tyring, Stephen; Rady, Peter; Engler, Danielle E; Grossman, Marc E

    2009-02-01

    Epidermodysplasia verruciformis (EV) is a rare autosomal recessive genodermatosis with an increased susceptibility to specific human papillomavirus (HPV) genotypes. Classically, this viral infection leads to the development of tinea versicolor-like macules on the trunk, neck, arms, and face during childhood, and over time, these lesions can progress to squamous cell carcinoma. More recently, an EV-like syndrome has been described in patients with impaired cell-mediated immunity. We describe two cases of EV-like syndrome in HIV-positive patients, review all previously reported cases of EV in patients with impaired cell-mediated immunity, introduce the term "acquired epidermodysplasia verruciformis" to describe EV developing in the immunocompromised host and examine the limited treatment options for these patients.

  17. Surgical treatment of acquired tracheocele.

    PubMed

    Porubsky, Edward A; Gourin, Christine G

    2006-06-01

    Acquired tracheoceles are rare clinical entities that can cause a variety of chronic and recurrent aerodigestive tract symptoms. The management of acquired tracheoceles is primarily conservative, but surgical intervention may be indicated for patients with refractory symptoms. We present a case of acquired tracheocele and describe a method of successful surgical management.

  18. The polymorphism (-600 C>A) of CpG methylation site at the promoter region of CYP17A1 and its association of male infertility and testosterone levels.

    PubMed

    Park, Jung-Hoon; Lee, Jinu; Kim, Cheol-Hee; Lee, Suman

    2014-01-15

    Cytochrome P450, family 17, subfamily A, polypeptide 1 (CYP17A1) is a key regulatory enzyme in the steroidogenic pathway. The functional and clinical relevance of novel CYP17A1 promoter single nucleotide polymorphism (-600 C>A, rs17115149) was investigated with male infertility. Case-control association study of CYP17A1 from 456 infertile men performed with 465 normal fertile men. The rs17115149 at the promoter region of CYP17A1 was significantly associated with Oligoasthenoteratozoospermia (OAT, P=0.0015, n=265). 5-aza-dC treatment to B lymphocyte cells increased the CYP17A1 expression. Direct bisulfite sequencing of five human tissues showed that the rs17115149 is located at -600bp (-600C>A) before transcription start site within the CpG islands of CYP17A1 promoter. This -600 Cytosine of CpG site was highly methylated in colon and stomach tissues, but low methylated in adrenal gland, kidney and testis with higher CYP17A1 RNA expression. Especially, this polymorphism is statistically significant associated with testosterone levels from infertile males (n=197, P<0.05). CYP17A1 promoter polymorphism (rs17115149, -600C>A) is a functional regulatory SNP which associated with its expression possibly by epigenetic pathway, which may signify a genetic risk factor for male infertility. © 2013 Elsevier B.V. All rights reserved.

  19. Acquired spatial dyslexia.

    PubMed

    Siéroff, E

    2015-08-10

    Acquired spatial dyslexia is a reading disorder frequently occurring after left or right posterior brain lesions. This article describes several types of spatial dyslexia with an attentional approach. After right posterior lesions, patients show left neglect dyslexia with errors on the left side of text, words, and non-words. The deficit is frequently associated with left unilateral spatial neglect. Severe left neglect dyslexia can be detected with unlimited exposure duration of words or non-words. Minor neglect dyslexia is detected with brief presentation of bilateral words, one in the left and one in the right visual field (phenomenon of contralesional extinction). Neglect dyslexia can be explained as a difficulty in orienting attention to the left side of verbal stimuli. With left posterior lesions, spatial dyslexia is also frequent but multiform. Right neglect dyslexia is frequent, but right unilateral spatial neglect is rare. Attentional dyslexia represents difficulty in selecting a stimulus, letter or word among other similar stimuli; it is a deficit of attentional selection, and the left hemisphere plays a crucial role in selection. Two other types of spatial dyslexia can be found after left posterior lesions: paradoxical ipsilesional extinction and stimulus-centred neglect dyslexia. Disconnections between left or right parietal attentional areas and the left temporal visual word form area could explain these deficits. Overall, a model of attention dissociating modulation, selection control, and selection positioning can help in understanding these reading disorders.

  20. Acquired aplastic anemia.

    PubMed

    Keohane, Elaine M

    2004-01-01

    Acquired aplastic anemia (AA) is a disorder characterized by a profound deficit of hematopoietic stem and progenitor cells, bone marrow hypocellularity, and peripheral blood pancytopenia. It primarily affects children, young adults, and those over 60 years of age. The majority of cases are idiopathic; however, idiosyncratic reactions to some drugs, chemicals, and viruses have been implicated in its etiology. An autoimmune T-cell reaction likely causes the stem cell depletion, but the precise mechanism, as well as the eliciting and target antigens, is unknown. Symptoms vary from severe life-threatening cytopenias to moderate or non-severe disease that does not require transfusion support. The peripheral blood typically exhibits pancytopenia, reticulocytopenia, and normocytic or macrocytic erythrocytes. The bone marrow is hypocellular and may exhibit dysplasia of the erythrocyte precursors. First line treatment for severe AA consists of hematopoietic stem cell transplantation in young patients with HLA identical siblings, while immunosuppression therapy is used for older patients and for those of any age who lack a HLA matched donor. Patients with AA have an increased risk of developing paroxysmal nocturnal hemoglobinuria (PNH), myelodysplastic syndrome (MDS), or acute leukemia. Further elucidation of the pathophysiology of this disease will result in a better understanding of the interrelationship among AA, PNH, and MDS, and may lead to novel targeted therapies.

  1. ICU-Acquired Weakness.

    PubMed

    Jolley, Sarah E; Bunnell, Aaron E; Hough, Catherine L

    2016-11-01

    Survivorship after critical illness is an increasingly important health-care concern as ICU use continues to increase while ICU mortality is decreasing. Survivors of critical illness experience marked disability and impairments in physical and cognitive function that persist for years after their initial ICU stay. Newfound impairment is associated with increased health-care costs and use, reductions in health-related quality of life, and prolonged unemployment. Weakness, critical illness neuropathy and/or myopathy, and muscle atrophy are common in patients who are critically ill, with up to 80% of patients admitted to the ICU developing some form of neuromuscular dysfunction. ICU-acquired weakness (ICUAW) is associated with longer durations of mechanical ventilation and hospitalization, along with greater functional impairment for survivors. Although there is increasing recognition of ICUAW as a clinical entity, significant knowledge gaps exist concerning identifying patients at high risk for its development and understanding its role in long-term outcomes after critical illness. This review addresses the epidemiologic and pathophysiologic aspects of ICUAW; highlights the diagnostic challenges associated with its diagnosis in patients who are critically ill; and proposes, to our knowledge, a novel strategy for identifying ICUAW. Copyright © 2016 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

  2. Controlling for conservation in genome-wide DNA methylation studies.

    PubMed

    Singer, Meromit; Pachter, Lior

    2015-05-30

    A commonplace analysis in high-throughput DNA methylation studies is the comparison of methylation extent between different functional regions, computed by averaging methylation states within region types and then comparing averages between regions. For example, it has been reported that methylation is more prevalent in coding regions as compared to their neighboring introns or UTRs, leading to hypotheses about novel forms of epigenetic regulation. We have identified and characterized a bias present in these seemingly straightforward comparisons that results in the false detection of differences in methylation intensities across region types. This bias arises due to differences in conservation rates, rather than methylation rates, and is broadly present in the published literature. When controlling for conservation at coding start sites the differences in DNA methylation rates disappear. Moreover, a re-evaluation of methylation rates at intronexon junctions reveals that the magnitude of previously reported differences is greatly exaggerated. We introduce two correction methods to address this bias, an inferencebased matrix completion algorithm and an averaging approach, tailored to address different underlying biological questions. We evaluate how analysis using these corrections affects the detection of differences in DNA methylation across functional boundaries. We report here on a bias in DNA methylation comparative studies that originates in conservation rate differences and manifests itself in the false discovery of differences in DNA methylation intensities and their extents. We have characterized this bias and its broad implications, and show how to control for it so as to enable the study of a variety of biological questions.

  3. Strong epigenetic similarity between maize centromeric and pericentromeric regions at the level of small RNAs, DNA methylation and H3 chromatin modifications.

    PubMed

    Gent, Jonathan I; Dong, Yuzhu; Jiang, Jiming; Dawe, R Kelly

    2012-02-01

    Both kinetochore function and sister chromatid cohesion can depend upon pericentromere chromatin structure, and factors associated with heterochromatin have been proposed to have general, conserved roles in distinguishing centromeres and pericentromeres and in conferring pericentromere-intrinsic functions. We applied genome-wide sequencing approaches to quantify RNA expression, DNA methylation and histone modification distributions in maize (Zea mays), focusing on two maize chromosomes with nearly fully sequenced centromeres and pericentromeres. Aside from the presence of the Histone H3 variant common to all centromeres, Centromeric Histone H3 (CENH3), we found no RNA expression or chromatin modifications that clearly differentiate pericentromeres from either centromeres or from chromosome arms, nor did we identify an epigenetic signature that accurately predicts CENH3 location. RNA expression and chromatin modification frequencies were broadly associated with distance from centromeres, gradually peaking or dipping toward arms. When interpreted in the context of experimental data from other systems, our results suggest that centromeres may confer essential functions (such as cohesion retention) to flanking sequence regardless of the local heterochromatin profile.

  4. Regional development of alpha-methyl-D-glucoside transport in the small intestine of chick embryos and newly-hatched chicks.

    PubMed

    Esteban, S; Moreno, M; Mestre, I; Planas, J M; Tur, J A

    1991-12-01

    A regional study of the intestinal hexose transport shows the role played by duodenum, jejunum and ileum during the chick perinatal development. From at least two days before hatching the three regions of small intestine accumulate alpha-Méthyl-D-Glucose (alpha-MG) by mediated transport mechanisms, and phloridzin inhibit about 90% of the uptakes. This ability reaches the maximal level at 1 day after hatch in the three regions. Before hatching the jejunum shows higher transport levels than the observed values in the duodenum and ileum, but the three regions show similar values at 1 day after hatch. In the following days, the alpha-MG transport ability is strongly reduced in the duodenum, slightly reduced in the jejunum and maintained in the ileum until at least 7 day-old chicks.

  5. Extinction of Oct-3/4 gene expression in embryonal carcinoma [times] fibroblast somatic cell hybrids is accompanied by changes in the methylation status, chromatin structure, and transcriptional activity of the Oct-3/4 upstream region

    SciTech Connect

    Ben-Shushan, E.; Pikarsky, E.; Klar, A.; Bergman, Y. )

    1993-02-01

    The OCT-3/4 gene provides an excellent model system with which to study the extinction phenomenon in somatic cell hybrids. The molecular mechanism that underlies the extinction of a tissue-specific transcription factor in somatic cell hybrides is evaluated and compared with its down-regulation in retinoic acid treated embryonal carcinoma cells. This study draws a connection between the shutdown of OCT-3/4 expression in retinoic acid (RA)-differentiated embryonal carcinoma (EC) cells and its extinction in hybrid cells. This repression of OCT-3/4 expression is achieved through changes in the methylation status, chromatin structure, and transcriptional activity of the OCT-3/4 upstream regulatory region. 59 refs.

  6. Acquired reactive perforating collagenosis

    PubMed Central

    Fei, Chengwen; Wang, Yao; Gong, Yu; Xu, Hui; Yu, Qian; Shi, Yuling

    2016-01-01

    Abstract Background: Reactive perforating collagenosis (RPC) is a rare form of transepithelial elimination, in which altered collagen is extruded through the epidermis. There are 2 types of RPC, acquired RPC (ARPC) and inherited RPC, while the latter is extremely rare. Here we report on 1 case of ARPC. Methods: A 73-year-old female was presented with strongly itchy papules over her back and lower limbs for 3 months. She denied the history of oozing or vesiculation. A cutaneous examination showed diffusely distributed multiple well-defined keratotic papules, 4 to 10 mm in diameter, on the bilateral lower limbs and back as well as a few papules on her chest and forearm. Scratching scars were over the resolved lesions while Koebner phenomenon was negative. The patient had a history of type 2 diabetes for 15 years. Laboratory examinations showed elevated blood glucose level. Skin lesion biopsy showed a well-circumscribed area of necrosis filled with a keratotic plug. Parakeratotic cells and lymphocytic infiltration could be seen in the necrosed area. In dermis, sparse fiber bundles were seen perforating the epidermis. These degenerated fiber bundles were notarized as collagen fiber by elastic fiber stain, suggesting a diagnosis of RPC. Results: Then a diagnosis of ARPC was made according to the onset age and the history of diabetes mellitus. She was treated with topical application of corticosteroids twice a day and oral antihistamine once a day along with compound glycyrrhizin tablets 3 times a day. And the blood glucose was controlled in a satisfying range. Two months later, a significant improvement was seen in this patient. Conclusion: Since there is no efficient therapy to RPC, moreover, ARPC is considered to be associated with some systemic diseases, the management of the coexisting disease is quite crucial. The patient in this case received a substantial improvement due to the control of blood glucose and application of compound glycyrrhizin tablets. PMID

  7. The origins of atmospheric methyl mercury

    SciTech Connect

    Prestbo, E.M.; Bloom, N.S.

    1995-12-31

    Methyl Hg in precipitation shows strong regional patterns, with highest volume weighted mean values (0.4 ng/L) in the Pacific Northwest and lowest values in Florida (<0.01 ng/l). Over most of the North Central region, average values range from 0.05 to 0.2 ng/L. Several potential sources of methyl Hg to the atmosphere have been investigated, including direct anthropogenic emissions, atmospheric methylation of Hg{sup o} or Hg(II), and emissions of methyl or dimethyl Hg from natural surfaces (oceans, bogs, or forests). Direct measurements of major total Hg sources such as coal and waste combustors, and sewage treatment facilities suggest that direct anthropogenic emissions are an insignificant source of methyl Hg to the atmosphere. The gas phase reaction of methyl halides with Hg{sup o} also appears to be an insignificant source of methyl Hg to the atmosphere. Recent laboratory experiments have provided a likely mechanism for atmospheric Hg methylation via a complex reaction involving acetate, sulfite, and iron. From a series of field measurements, another source appears to be the degradation of dimethyl mercury emitted by the upwelling of deep ocean water.

  8. Effects of Novel ncRNA Molecules, p15-piRNAs, on the Methylation of DNA and Histone H3 of the CDKN2B Promoter Region in U937 Cells.

    PubMed

    Wu, Dansen; Fu, Haiying; Zhou, Huarong; Su, Junnan; Zhang, Feng; Shen, Jianzhen

    2015-12-01

    Non-coding RNAs (ncRNAs) play key roles in epigenetic events. However, the exact mechanism of ncRNA guidance, particularly piwi-interacting RNAs (piRNAs), for the targeting of epigenetic regulatory factors to specific gene regions is unclear. Although piRNA function was first established in germ-line cells, piRNA may be crucial in cancer cells. This study investigated the potential roles of CDKN2B-related piRNA in leukemia cells to provide a potential tumorigenesis model of leukemia. CDKN2B-related piRNAs, hsa_piR_014637 and hsa_piR_011186 were transduced into the leukemia cell line U937 to study the effect of these two piRNAs on cell-cycle progression, apoptosis, heterochromatin formation, CDKN2B methylation and expression. Our results show that over-expressing hsa_piR_011186 promoted cell-cycle progression and decreased apoptosis. We also observed inhibition of CDKN2B gene expression. These effects were likely mediated by novel piRC (piRNA complex) of CDKN2B-related piRNA that associate with DNMT1, Suv39H1 and/or EZH2 proteins to modulate the methylation of DNA and histone H3 in the promoter region of the CDKN2B gene. The novel piRC complex facilitated epigenetic modifications on the promoter of cell-cycle regulating genes, providing an expanded view of the role of piRNA in the progression of leukemia cells. © 2015 Wiley Periodicals, Inc.

  9. The effects of endothelin-1 and NG-nitro-L-arginine methyl ester on regional haemodynamics in conscious rats with streptozotocin-induced diabetes mellitus.

    PubMed Central

    Kiff, R. J.; Gardiner, S. M.; Compton, A. M.; Bennett, T.

    1991-01-01

    1. Resting haemodynamic status and responses to endothelin-1 (0.0004, 0.04, 0.4 nmol kg-1) and NG-nitro-L-arginine methyl ester (L-NAME, 10 mg kg-1) were assessed in conscious, Wistar rats treated with streptozotocin (STZ) to induce diabetes mellitus, and in control animals treated with saline. 2. In the resting state, STZ-treated rats had a bradycardia relative to control animals (291 +/- 13 and 337 +/- 10 beats min-1, respectively), but mean arterial blood pressures were the same in the two groups (STZ-treated 109 +/- 3; control 114 +/- 4 mmHg). However, the STZ-treated rats had raised renal (105 +/- 9 units) and mesenteric (114 +/- 16 units) vascular conductances and reduced hindquarters vascular conductance (26 +/- 4 units) relative to control rats (renal, 80 +/- 6; mesenteric, 75 +/- 7; hindquarters, 37 +/- 3 units). 3. Increasing doses of endothelin-1 caused similar, early falls and subsequent rises in mean arterial blood pressures in both groups of rats. Although there were initial hindquarters vasodilatations with endothelin-1 that were not different in STZ-treated and control rats, there were subsequent renal and mesenteric vasoconstrictions that were greater in the former. Hence, the similar rises in mean arterial blood pressures must have been accompanied by a greater reduction in cardiac output in the STZ-treated rats. 4. L-NAME caused similar renal and mesenteric vasoconstrictions in control and STZ-treated rats, but there was a smaller pressor effect and an attenuated hindquarters vasoconstrictor response to L-NAME in STZ-treated rats.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1884094

  10. Methyl nutrients, DNA methylation, and cardiovascular disease.

    PubMed

    Glier, Melissa B; Green, Timothy J; Devlin, Angela M

    2014-01-01

    Diet plays an important role in the development and prevention of cardiovascular disease (CVD), but the molecular mechanisms are not fully understood. DNA methylation has been implicated as an underlying molecular mechanism that may account for the effect of dietary factors on the development and prevention of CVD. DNA methylation is an epigenetic process that provides "marks" in the genome by which genes are set to be transcriptionally activated or silenced. Epigenomic marks are heritable but are also responsive to environmental shifts, such as changes in nutritional status, and are especially vulnerable during development. S-adenosylmethionine is the methyl group donor for DNA methylation and several nutrients are required for the production of S-adenosylmethionine. These methyl nutrients include vitamins (folate, riboflavin, vitamin B12, vitamin B6, choline) and amino acids (methionine, cysteine, serine, glycine). As such, imbalances in the metabolism of these nutrients have the potential to affect DNA methylation. The focus of this review is to provide an overview on the current understanding of the relationship between methyl nutrient status and DNA methylation patterns and the potential role of this interaction in CVD pathology. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma.

    PubMed

    Decock, Anneleen; Ongenaert, Maté; Cannoodt, Robrecht; Verniers, Kimberly; De Wilde, Bram; Laureys, Geneviève; Van Roy, Nadine; Berbegall, Ana P; Bienertova-Vasku, Julie; Bown, Nick; Clément, Nathalie; Combaret, Valérie; Haber, Michelle; Hoyoux, Claire; Murray, Jayne; Noguera, Rosa; Pierron, Gaelle; Schleiermacher, Gudrun; Schulte, Johannes H; Stallings, Ray L; Tweddle, Deborah A; De Preter, Katleen; Speleman, Frank; Vandesompele, Jo

    2016-01-12

    Accurate assessment of neuroblastoma outcome prediction remains challenging. Therefore, this study aims at establishing novel prognostic tumor DNA methylation biomarkers. In total, 396 low- and high-risk primary tumors were analyzed, of which 87 were profiled using methyl-CpG-binding domain (MBD) sequencing for differential methylation analysis between prognostic patient groups. Subsequently, methylation-specific PCR (MSP) assays were developed for 78 top-ranking differentially methylated regions and tested on two independent cohorts of 132 and 177 samples, respectively. Further, a new statistical framework was used to identify a robust set of MSP assays of which the methylation score (i.e. the percentage of methylated assays) allows accurate outcome prediction. Survival analyses were performed on the individual target level, as well as on the combined multimarker signature. As a result of the differential DNA methylation assessment by MBD sequencing, 58 of the 78 MSP assays were designed in regions previously unexplored in neuroblastoma, and 36 are located in non-promoter or non-coding regions. In total, 5 individual MSP assays (located in CCDC177, NXPH1, lnc-MRPL3-2, lnc-TREX1-1 and one on a region from chromosome 8 with no further annotation) predict event-free survival and 4 additional assays (located in SPRED3, TNFAIP2, NPM2 and CYYR1) also predict overall survival. Furthermore, a robust 58-marker methylation signature predicting overall and event-free survival was established. In conclusion, this study encompasses the largest DNA methylation biomarker study in neuroblastoma so far. We identified and independently validated several novel prognostic biomarkers, as well as a prognostic 58-marker methylation signature.

  12. Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma

    PubMed Central

    Decock, Anneleen; Ongenaert, Maté; Cannoodt, Robrecht; Verniers, Kimberly; De Wilde, Bram; Laureys, Geneviève; Van Roy, Nadine; Berbegall, Ana P.; Bienertova-Vasku, Julie; Bown, Nick; Clément, Nathalie; Combaret, Valérie; Haber, Michelle; Hoyoux, Claire; Murray, Jayne; Noguera, Rosa; Pierron, Gaelle; Schleiermacher, Gudrun; Schulte, Johannes H.; Stallings, Ray L.; Tweddle, Deborah A.; De Preter, Katleen; Speleman, Frank; Vandesompele, Jo

    2016-01-01

    Accurate assessment of neuroblastoma outcome prediction remains challenging. Therefore, this study aims at establishing novel prognostic tumor DNA methylation biomarkers. In total, 396 low- and high-risk primary tumors were analyzed, of which 87 were profiled using methyl-CpG-binding domain (MBD) sequencing for differential methylation analysis between prognostic patient groups. Subsequently, methylation-specific PCR (MSP) assays were developed for 78 top-ranking differentially methylated regions and tested on two independent cohorts of 132 and 177 samples, respectively. Further, a new statistical framework was used to identify a robust set of MSP assays of which the methylation score (i.e. the percentage of methylated assays) allows accurate outcome prediction. Survival analyses were performed on the individual target level, as well as on the combined multimarker signature. As a result of the differential DNA methylation assessment by MBD sequencing, 58 of the 78 MSP assays were designed in regions previously unexplored in neuroblastoma, and 36 are located in non-promoter or non-coding regions. In total, 5 individual MSP assays (located in CCDC177, NXPH1, lnc-MRPL3-2, lnc-TREX1-1 and one on a region from chromosome 8 with no further annotation) predict event-free survival and 4 additional assays (located in SPRED3, TNFAIP2, NPM2 and CYYR1) also predict overall survival. Furthermore, a robust 58-marker methylation signature predicting overall and event-free survival was established. In conclusion, this study encompasses the largest DNA methylation biomarker study in neuroblastoma so far. We identified and independently validated several novel prognostic biomarkers, as well as a prognostic 58-marker methylation signature. PMID:26646589

  13. 16 CFR 801.2 - Acquiring and acquired persons.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Acquiring and acquired persons. 801.2 Section 801.2 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976 COVERAGE RULES § 801.2...

  14. 16 CFR 801.2 - Acquiring and acquired persons.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 16 Commercial Practices 1 2012-01-01 2012-01-01 false Acquiring and acquired persons. 801.2 Section 801.2 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976 COVERAGE RULES § 801.2...

  15. Methyl salicylate overdose

    MedlinePlus

    Methyl salicylate (oil of wintergreen) is a chemical that smells like wintergreen. It is used in many over- ... muscle ache creams. It is related to aspirin. Methyl salicylate overdose occurs when someone swallows a dangerous amount ...

  16. Hematopoietic stem and progenitor cells acquire distinct DNA-hypermethylation during in vitro culture.

    PubMed

    Weidner, Carola Ingrid; Walenda, Thomas; Lin, Qiong; Wölfler, Monika Martina; Denecke, Bernd; Costa, Ivan Gesteira; Zenke, Martin; Wagner, Wolfgang

    2013-11-28

    Hematopoietic stem and progenitor cells (HPCs) can be maintained in vitro, but the vast majority of their progeny loses stemness during culture. In this study, we compared DNA-methylation (DNAm) profiles of freshly isolated and culture-expanded HPCs. Culture conditions of CD34(+) cells - either with or without mesenchymal stromal cells (MSCs) - had relatively little impact on DNAm, although proliferation is greatly increased by stromal support. However, all cultured HPCs - even those which remained CD34(+) - acquired significant DNA-hypermethylation. DNA-hypermethylation occurred particularly in up-stream promoter regions, shore-regions of CpG islands, binding sites for PU.1, HOXA5 and RUNX1, and it was reflected in differential gene expression and variant transcripts of DNMT3A. Low concentrations of DNAm inhibitors slightly increased the frequency of colony-forming unit initiating cells. Our results demonstrate that HPCs acquire DNA-hypermethylation at specific sites in the genome which is relevant for the rapid loss of stemness during in vitro manipulation.

  17. Acquired ciliary circumscribed grey hair (ACCG).

    PubMed

    Romero, A G; Calatayud, J C

    2001-12-01

    Grey-haired areas usually occur due to aging or inheritance. A case is described of abrupt occurrence of a focal circumscribed grey-hair in the eyebrow region (a single hair) in a 27-year-old woman. The phenomenon was named acquired ciliary circumscribed grey-hair (ACCG). Qualitative and semiquantitative findings were obtained by microanalytical studies. In addition to morphological differences from control hair, the ACCG hair showed a high percentage of sulfur (99.8%) and absence of oligoelements.

  18. Profiling genome-wide DNA methylation.

    PubMed

    Yong, Wai-Shin; Hsu, Fei-Man; Chen, Pao-Yang

    2016-01-01

    DNA methylation is an epigenetic modification that plays an important role in regulating gene expression and therefore a broad range of biological processes and diseases. DNA methylation is tissue-specific, dynamic, sequence-context-dependent and trans-generationally heritable, and these complex patterns of methylation highlight the significance of profiling DNA methylation to answer biological questions. In this review, we surveyed major methylation assays, along with comparisons and biological examples, to provide an overview of DNA methylation profiling techniques. The advances in microarray and sequencing technologies make genome-wide profiling possible at a single-nucleotide or even a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, genomic region coverage, and bioinformatics analysis, and selecting a feasible method requires knowledge of these methods. We first introduce the biological background of DNA methylation and its pattern in plants, animals and fungi. We present an overview of major experimental approaches to profiling genome-wide DNA methylation and hydroxymethylation and then extend to the single-cell methylome. To evaluate these methods, we outline their strengths and weaknesses and perform comparisons across the different platforms. Due to the increasing need to compute high-throughput epigenomic data, we interrogate the computational pipeline for bisulfite sequencing data and also discuss the concept of identifying differentially methylated regions (DMRs). This review summarizes the experimental and computational concepts for profiling genome-wide DNA methylation, followed by biological examples. Overall, this review provides researchers useful guidance for the selection of a profiling method suited to specific research questions.

  19. Expression of KCNQ1OT1, CDKN1C, H19, and PLAGL1 and the methylation patterns at the KvDMR1 and H19/IGF2 imprinting control regions is conserved between human and bovine

    PubMed Central

    2012-01-01

    Background Beckwith-Wiedemann syndrome (BWS) is a loss-of-imprinting pediatric overgrowth syndrome. The primary features of BWS include macrosomia, macroglossia, and abdominal wall defects. Secondary features that are frequently observed in BWS patients are hypoglycemia, nevus flammeus, polyhydramnios, visceromegaly, hemihyperplasia, cardiac malformations, and difficulty breathing. BWS is speculated to occur primarily as the result of the misregulation of imprinted genes associated with two clusters on chromosome 11p15.5, namely the KvDMR1 and H19/IGF2. A similar overgrowth phenotype is observed in bovine and ovine as a result of embryo culture. In ruminants this syndrome is known as large offspring syndrome (LOS). The phenotypes associated with LOS are increased birth weight, visceromegaly, skeletal defects, hypoglycemia, polyhydramnios, and breathing difficulties. Even though phenotypic similarities exist between the two syndromes, whether the two syndromes are epigenetically similar is unknown. In this study we use control Bos taurus indicus X Bos taurus taurus F1 hybrid bovine concepti to characterize baseline imprinted gene expression and DNA methylation status of imprinted domains known to be misregulated in BWS. This work is intended to be the first step in a series of experiments aimed at determining if LOS will serve as an appropriate animal model to study BWS. Results The use of F1 B. t. indicus x B. t. taurus tissues provided us with a tool to unequivocally determine imprinted status of the regions of interest in our study. We found that imprinting is conserved between the bovine and human in imprinted genes known to be associated with BWS. KCNQ1OT1 and PLAGL1 were paternally-expressed while CDKN1C and H19 were maternally-expressed in B. t. indicus x B. t. taurus F1 concepti. We also show that in bovids, differential methylation exists at the KvDMR1 and H19/IGF2 ICRs. Conclusions Based on these findings we conclude that the imprinted gene expression of

  20. SMAP: a streamlined methylation analysis pipeline for bisulfite sequencing.

    PubMed

    Gao, Shengjie; Zou, Dan; Mao, Likai; Zhou, Quan; Jia, Wenlong; Huang, Yi; Zhao, Shancen; Chen, Gang; Wu, Song; Li, Dongdong; Xia, Fei; Chen, Huafeng; Chen, Maoshan; Ørntoft, Torben F; Bolund, Lars; Sørensen, Karina D

    2015-01-01

    DNA methylation has important roles in the regulation of gene expression and cellular specification. Reduced representation bisulfite sequencing (RRBS) has prevailed in methylation studies due to its cost-effectiveness and single-base resolution. The rapid accumulation of RRBS data demands well designed analytical tools. To streamline the data processing of DNA methylation from multiple RRBS samples, we present a flexible pipeline named SMAP, whose features include: (i) handling of single-and/or paired-end diverse bisulfite sequencing data with reduced false-positive rates in differentially methylated regions; (ii) detection of allele-specific methylation events with improved algorithms; (iii) a built-in pipeline for detection of novel single nucleotide polymorphisms (SNPs); (iv) support of multiple user-defined restriction enzymes; (v) conduction of all methylation analyses in a single-step operation when well configured. Simulation and experimental data validated the high accuracy of SMAP for SNP detection and methylation identification. Most analyses required in methylation studies (such as estimation of methylation levels, differentially methylated cytosine groups, and allele-specific methylation regions) can be executed readily with SMAP. All raw data from diverse samples could be processed in parallel and 'packetized' streams. A simple user guide to the methylation applications is also provided.

  1. CpG island methylator phenotype in colorectal cancer

    PubMed Central

    Toyota, Minoru; Ahuja, Nita; Ohe-Toyota, Mutsumi; Herman, James G.; Baylin, Stephen B.; Issa, Jean-Pierre J.

    1999-01-01

    Aberrant methylation of promoter region CpG islands is associated with transcriptional inactivation of tumor-suppressor genes in neoplasia. To understand global patterns of CpG island methylation in colorectal cancer, we have used a recently developed technique called methylated CpG island amplification to examine 30 newly cloned differentially methylated DNA sequences. Of these 30 clones, 19 (63%) were progressively methylated in an age-dependent manner in normal colon, 7 (23%) were methylated in a cancer-specific manner, and 4 (13%) were methylated only in cell lines. Thus, a majority of CpG islands methylated in colon cancer are also methylated in a subset of normal colonic cells during the process of aging. In contrast, methylation of the cancer-specific clones was found exclusively in a subset of colorectal cancers, which appear to display a CpG island methylator phenotype (CIMP). CIMP+ tumors also have a high incidence of p16 and THBS1 methylation, and they include the majority of sporadic colorectal cancers with microsatellite instability related to hMLH1 methylation. We thus define a pathway in colorectal cancer that appears to be responsible for the majority of sporadic tumors with mismatch repair deficiency. PMID:10411935

  2. Site-specific methylation of CpG nucleotides in the hTERT promoter region can control the expression of hTERT during malignant progression of colorectal carcinoma.

    PubMed

    Choi, Jee-Hye; Park, Soo Hyun; Park, Jina; Park, Borae G; Cha, Seong-Jae; Kong, Kwang-Hoon; Lee, Kwang-Ho; Park, Ae Ja

    2007-09-28

    Expression of hTERT has been recognized an important factor in cellular aging and immortalization. Therefore, to analyze regulatory mechanism of hTERT expression, we investigated the CpG methylation pattern of the hTERT promoter as an epigenetic mechanism and its implication in transcriptional regulation of hTERT using tissues of colorectal carcinoma. As a result, we were able to observe an increased pattern of hTERT expression according to the malignant progression of colorectal carcinoma. Additionally, we could find that hTERT expression was induced when the P1 and P2 region of hTERT were sufficiently hypermethylated and, oppositely, the G1 region of hTERT was hypomethylated. Importantly, we could find three specific CpG sites (7th CpG of P2 and 11th and 2nd-10th CpGs of P1) closely related with the increasing of hTERT expression. These findings may provide important clues to deducing the expression mechanisms of hTERT.

  3. Revised genomic consensus for the hypermethylated CpG island region of the human L1 transposon and integration sites of full length L1 elements from recombinant clones made using methylation-tolerant host strains.

    PubMed Central

    Crowther, P J; Doherty, J P; Linsenmeyer, M E; Williamson, M R; Woodcock, D M

    1991-01-01

    Efficient recovery of clones from the 5' end of the human L1 dispersed repetitive elements necessitates the use of deletion mcr- host strains since this region contains a CpG island which is hypermethylated in vivo. Clones recovered with conventional mcr+ hosts seem to have been derived preferentially from L1 members which have accumulated mutations that have removed sites of methylation. We present a revised consensus from the 5' presumptive control region of these elements. This revised consensus contains a consensus RNA polymerase III promoter which would permit the synthesis of transcripts from the 5' end of full length L1 elements. Such potential transcripts are likely to exhibit a high degree of secondary structure. In addition, we have determined the flanking sequences for 6 full length L1 elements. The majority of full length L1 clones show no convincing evidence for target site duplication in the insertion site as commonly observed with truncated L1 elements. These data would be consistent with two mechanisms of integration of transposing L1 elements with different mechanisms predominating for full length and truncated elements. PMID:1710354

  4. Enrichment of methylated DNA by methyl-CpG immunoprecipitation.

    PubMed

    Sonnet, Miriam; Baer, Constance; Rehli, Michael; Weichenhan, Dieter; Plass, Christoph

    2013-01-01

    Normal DNA methylation is an epigenetic modification required for proper development. Aberrant DNA methylation, in contrast, is frequently observed in many different malignancies including leukemias and lymphomas. Global DNA methylation profiling addresses the methylated sequences (methylome) of patient genomes to identify disease-specific methylation patterns. Workload in methylome analyses can be considerably reduced by methylome enrichment using proteins or antibodies with high affinity to methylated DNA. Methyl-CpG Immunoprecipitation (MCIp) employs an immobilized recombinant human methyl-CpG binding domain protein 2, MBD2, which binds methylated CpGs in double-stranded DNA. Elution with increasing salt concentrations allows the fractionated enrichment of different degrees of methylation.

  5. DNA Methylation Signatures of the Plant Chromomethyltransferases

    PubMed Central

    Baulcombe, David C.

    2016-01-01

    DNA methylation in plants is traditionally partitioned into CG, CHG and CHH contexts (with H any nucleotide but G). By investigating DNA methylation patterns in trinucleotide contexts in four angiosperm species, we show that such a representation hides spatial and functional partitioning of different methylation pathways and is incomplete. CG methylation (mCG) is largely context-independent whereas, at CHG motifs, there is under-representation of mCCG in pericentric regions of A. thaliana and tomato and throughout the chromosomes of maize and rice. In A. thaliana the biased representation of mCCG in heterochromatin is related to specificities of H3K9 methyltransferase SUVH family members. At CHH motifs there is an over-representation of different variant forms of mCHH that, similarly to mCCG hypomethylation, is partitioned into the pericentric regions of the two dicots but dispersed in the monocot chromosomes. The over-represented mCHH motifs in A. thaliana associate with specific types of transposon including both class I and II elements. At mCHH the contextual bias is due to the involvement of various chromomethyltransferases whereas the context-independent CHH methylation in A. thaliana and tomato is mediated by the RNA-directed DNA methylation process that is most active in the gene-rich euchromatin. This analysis therefore reveals that the sequence context of the methylome of plant genomes is informative about the mechanisms associated with maintenance of methylation and the overlying chromatin structure. PMID:27997534

  6. DNA Methylation Signatures of the Plant Chromomethyltransferases.

    PubMed

    Gouil, Quentin; Baulcombe, David C

    2016-12-01

    DNA methylation in plants is traditionally partitioned into CG, CHG and CHH contexts (with H any nucleotide but G). By investigating DNA methylation patterns in trinucleotide contexts in four angiosperm species, we show that such a representation hides spatial and functional partitioning of different methylation pathways and is incomplete. CG methylation (mCG) is largely context-independent whereas, at CHG motifs, there is under-representation of mCCG in pericentric regions of A. thaliana and tomato and throughout the chromosomes of maize and rice. In A. thaliana the biased representation of mCCG in heterochromatin is related to specificities of H3K9 methyltransferase SUVH family members. At CHH motifs there is an over-representation of different variant forms of mCHH that, similarly to mCCG hypomethylation, is partitioned into the pericentric regions of the two dicots but dispersed in the monocot chromosomes. The over-represented mCHH motifs in A. thaliana associate with specific types of transposon including both class I and II elements. At mCHH the contextual bias is due to the involvement of various chromomethyltransferases whereas the context-independent CHH methylation in A. thaliana and tomato is mediated by the RNA-directed DNA methylation process that is most active in the gene-rich euchromatin. This analysis therefore reveals that the sequence context of the methylome of plant genomes is informative about the mechanisms associated with maintenance of methylation and the overlying chromatin structure.

  7. Structure and methylation-associated silencing of a gene within a homozygously deleted region of human chromosome band 8p22

    SciTech Connect

    MacGrogan, D.; Levy, A.; Bookstein, R.

    1996-07-01

    The structure and expression pattern of a human gene located within a homozygously deleted region of a metastatic prostate cancer have been characterized. Multiple cDNA fragments of this gene were isolated by hybrid capture with yeast artificial chromosome hybrid capture with yeast artificial chromosome clones covering the deletion region. Eleven coding exons spanned 205-220 kb of the 730- to 970-kb deletion. The predicted amino acid sequence was 43% identical to that of an accessory or regulatory subunit of the oligosaccharyltransferase enzyme complex in Saccharomyces cerevisiae. Hydrophobicity profiles of all three gene products were similar and showed four putative membrane-spanning domains in the molecules` C-terminal halves, suggesting a general conservation of function. The gene was expressed as an {approximately}1.5-kb mRNA in most nonlymphoid human cells/tissues including prostate, lung, liver, and colon. Expression was detected in many epithelial tumor cell lines, but was undetectable by Northern blot or RT-PCR in 14 of 15 colorectal, 1 of 8 lung, and 1 of 4 liver cancer cell lines. Lack of expression in tumor cell lines was highly correlated with hypermethylation of a CpG island located at the gene`s 5{prime} end. These findings form a basis for further work on this candidate tumor suppressor gene. 36 refs., 9 figs., 2 tabs.

  8. DNA methylation as a target of epigenetic therapeutics in cancer.

    PubMed

    Li, Keqin K; Li, Fangcheng; Li, Qiushi S; Yang, Kun; Jin, Bilian

    2013-02-01

    Epigenetic alterations have been implicated in the development and progression of human cancer. It is noteworthy that epigenetic modifications, in contrast to genetic mutations, are intrinsically reversible. This triggers an impressive interest of researchers in treatment of cancer patients via targeting epigenetic mechanisms, leading to subsequent intensive investigations of epigenetic drugs as a novel therapeutic intervention. DNA methylation, the major form of epigenetic modifications, is catalyzed by the maintenance DNA methyltransferase (DNMT) 1 and/or the de novo methyltransferases DNMT3A and DNMT3B. Aberrant expression of DNMTs and disruption of DNA methylation are closely associated with multiple forms of cancer, although the exact mechanisms underlying this link remain elusive. An array of tumor suppressor genes (TSGs) frequently sustain promoter hypermethylation, which results in epigenetic silencing of these genes and makes cancer cells acquire growth advantages. DNA demethylating agents, re-activating TSGs via inhibiting hypermethylation of their promoter regions, are currently being tested in clinical trials, and several of them are already applied in clinics. DNA demethylating agents, used either alone or in combination with other agents, such as chemotherapeutic drugs and the histone deacetylase inhibitors, have shown to be effective in treatment of cancer, although only in a small set of patients. In this review, we examine and discuss the most recent advances in epigenetic therapy of cancer, with a focus on DNA demethylating agents.

  9. Gene methylation in gastric cancer.

    PubMed

    Qu, Yiping; Dang, Siwen; Hou, Peng

    2013-09-23

    Gastric cancer is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide. Over 70% of new cases and deaths occur in developing countries. In the early years of the molecular biology revolution, cancer research mainly focuses on genetic alterations, including gastric cancer. Epigenetic mechanisms are essential for normal development and maintenance of tissue-specific gene expression patterns in mammals. Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Recent advancements in the rapidly evolving field of cancer epigenetics have shown extensive reprogramming of every component of the epigenetic machinery in cancer, including DNA methylation, histone modifications, nucleosome positioning, noncoding RNAs, and microRNAs. Aberrant DNA methylation in the promoter regions of gene, which leads to inactivation of tumor suppressor and other cancer-related genes in cancer cells, is the most well-defined epigenetic hallmark in gastric cancer. The advantages of gene methylation as a target for detection and diagnosis of cancer in biopsy specimens and non-invasive body fluids such as serum and gastric washes have led to many studies of application in gastric cancer. This review focuses on the most common and important phenomenon of epigenetics, DNA methylation, in gastric cancer and illustrates the impact epigenetics has had on this field. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  10. Blockade of DNA methylation enhances the therapeutic effect of gefitinib in non-small cell lung cancer cells.

    PubMed

    Li, Xiao-You; Wu, Jian-Zhong; Cao, Hai-Xia; Ma, Rong; Wu, Jian-Qiu; Zhong, Yue-Jiao; Feng, Ji-Feng

    2013-05-01

    The sensitivity of lung cancer to epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) has been found to be associated with mutations in the tyrosine kinase domain of EGFR. However, not all mutations are sensitive to gefitinib. While CpG island methylation in the promoter region of the EGFR gene and transcriptional silencing are common in solid tumors, the role of the EGFR gene promoter methylation in affecting resistance to TKIs in non-small cell lung cancer (NSCLC) remains unknown. In this study, we examined the correlation between EGFR gene promoter methylation and the therapeutic effect of gefitinib in NSCLC cells. Three NSCLC cell lines with different EGFR mutation statuses and levels of sensitivity to EGFR-TKIs were used in this study: H1650 (del E746-A750), H1299 (wild-type EGFR) and PC-9 (del E746-A750). Cells were treated with gefitinib or 5-aza-2'-deoxy cytidine (5-aza-CdR), a methylation inhibitor, alone or in combination. Subsequently, the methylation status of the EGFR gene promoter was examined by methylation-specific PCR (MSP). Cell survival and apoptosis assays were performed using the Cell Counting Kit-8 (CCK-8) and flow cytometry. In addition, western blot analysis and quantitative real-time PCR were used to examine the expression levels of EGFR protein and mRNA. Our study showed that the promoter region of the EGFR gene in PC-9 cells was unmethylated, and that the cells were sensitive to gefitinib. By contrast, the promoter region of the EGFR gene in the H1650 and H1299 cells was methylated, and the cells were resistant to gefitinib. Of note, the combination treatment with 5-aza-CdR and gefitinib further enhanced the growth inhibitory effects and led to the induction of apoptosis, while a significant reduction in the expression of EGFR protein and mRNA was observed in the H1650 and H1299 cells. These results suggest that blockade of DNA methylation may enhance the antitumor effects of EGFR-TKIs and gefitinib in NSCLC cells

  11. Genomic targeting of methylated DNA: influence of methylation on transcription, replication, chromatin structure, and histone acetylation.

    PubMed

    Schübeler, D; Lorincz, M C; Cimbora, D M; Telling, A; Feng, Y Q; Bouhassira, E E; Groudine, M

    2000-12-01

    We have developed a strategy to introduce in vitro-methylated DNA into defined chromosomal locations. Using this system, we examined the effects of methylation on transcription, chromatin structure, histone acetylation, and replication timing by targeting methylated and unmethylated constructs to marked genomic sites. At two sites, which support stable expression from an unmethylated enhancer-reporter construct, introduction of an in vitro-methylated but otherwise identical construct results in specific changes in transgene conformation and activity, including loss of the promoter DNase I-hypersensitive site, localized hypoacetylation of histones H3 and H4 within the reporter gene, and a block to transcriptional initiation. Insertion of methylated constructs does not alter the early replication timing of the loci and does not result in de novo methylation of flanking genomic sequences. Methylation at the promoter and gene is stable over time, as is the repression of transcription. Surprisingly, sequences within the enhancer are demethylated, the hypersensitive site forms, and the enhancer is hyperacetylated. Nevertheless, the enhancer is unable to activate the methylated and hypoacetylated reporter. Our findings suggest that CpG methylation represses transcription by interfering with RNA polymerase initiation via a mechanism that involves localized histone deacetylation. This repression is dominant over a remodeled enhancer but neither results in nor requires region-wide changes in DNA replication or chromatin structure.

  12. Genomic Targeting of Methylated DNA: Influence of Methylation on Transcription, Replication, Chromatin Structure, and Histone Acetylation

    PubMed Central

    Schübeler, Dirk; Lorincz, Matthew C.; Cimbora, Daniel M.; Telling, Agnes; Feng, Yong-Quing; Bouhassira, Eric E.; Groudine, Mark

    2000-01-01

    We have developed a strategy to introduce in vitro-methylated DNA into defined chromosomal locations. Using this system, we examined the effects of methylation on transcription, chromatin structure, histone acetylation, and replication timing by targeting methylated and unmethylated constructs to marked genomic sites. At two sites, which support stable expression from an unmethylated enhancer-reporter construct, introduction of an in vitro-methylated but otherwise identical construct results in specific changes in transgene conformation and activity, including loss of the promoter DNase I-hypersensitive site, localized hypoacetylation of histones H3 and H4 within the reporter gene, and a block to transcriptional initiation. Insertion of methylated constructs does not alter the early replication timing of the loci and does not result in de novo methylation of flanking genomic sequences. Methylation at the promoter and gene is stable over time, as is the repression of transcription. Surprisingly, sequences within the enhancer are demethylated, the hypersensitive site forms, and the enhancer is hyperacetylated. Nevertheless, the enhancer is unable to activate the methylated and hypoacetylated reporter. Our findings suggest that CpG methylation represses transcription by interfering with RNA polymerase initiation via a mechanism that involves localized histone deacetylation. This repression is dominant over a remodeled enhancer but neither results in nor requires region-wide changes in DNA replication or chromatin structure. PMID:11094062

  13. DNA Methylation and BMI: Investigating Identified Methylation Sites at HIF3A in a Causal Framework

    PubMed Central

    Richmond, Rebecca C.; Ward, Mary E.; Fraser, Abigail; Lyttleton, Oliver; McArdle, Wendy L.; Ring, Susan M.; Gaunt, Tom R.; Lawlor, Debbie A.; Davey Smith, George; Relton, Caroline L.

    2016-01-01

    Multiple differentially methylated sites and regions associated with adiposity have now been identified in large-scale cross-sectional studies. We tested for replication of associations between previously identified CpG sites at HIF3A and adiposity in ∼1,000 mother-offspring pairs from the Avon Longitudinal Study of Parents and Children (ALSPAC). Availability of methylation and adiposity measures at multiple time points, as well as genetic data, allowed us to assess the temporal associations between adiposity and methylation and to make inferences regarding causality and directionality. Overall, our results were discordant with those expected if HIF3A methylation has a causal effect on BMI and provided more evidence for causality in the reverse direction (i.e., an effect of BMI on HIF3A methylation). These results are based on robust evidence from longitudinal analyses and were also partially supported by Mendelian randomization analysis, although this latter analysis was underpowered to detect a causal effect of BMI on HIF3A methylation. Our results also highlight an apparent long-lasting intergenerational influence of maternal BMI on offspring methylation at this locus, which may confound associations between own adiposity and HIF3A methylation. Further work is required to replicate and uncover the mechanisms underlying the direct and intergenerational effect of adiposity on DNA methylation. PMID:26861784

  14. Age and Region-Specific Responses of Microglia, but not Astrocytes, Suggest a Role in Selective Vulnerability of Dopamine Neurons After 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine Exposure in Monkeys

    PubMed Central

    KANAAN, NICHOLAS M.; KORDOWER, JEFFREY H.; COLLIER, TIMOTHY J.

    2012-01-01

    Little is known about the effects of aging, the strongest risk factor for Parkinson’s disease (PD), on glial responses to dopamine (DA) neuron degeneration in midbrain subregions that display selective vulnerability to degeneration. We evaluated the impact of aging on astrocytes and microglia in a regionally specific manner in a monkey model of PD. 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) was delivered unilaterally via the internal carotid artery of young, middle-aged, and old-aged rhesus monkeys. Astrocytes and microglia were identified using glial fibrillary acidic protein and human leukocyte antigen-DR (HLA-DR) immunolabeling, respectively. Glial reactivity was assessed using (1) stereological cell counting, (2) fluorescence intensity, and (3) a morphology rating scale. In the midbrain contralateral and ipsilateral to the MPTP injection, astrocyte number and intensity did not change with age. In both sides of the midbrain, cellular morphology suggested astrocyte hypertrophy in middle-age dissipated in old-age, irrespective of DA subregion and regional differences in vulnerability to degeneration. In the contralateral midbrain, microglia became mildly activated (increased cell number and intensity, and morphological changes) with advancing age. Inflammation was evident at 3 months postlesion by severe microglial activation in the ipsilateral midbrain. HLA-DR fluorescence intensity and an abundance of activated microglia (based on morphological criteria) were consistently exacerbated in the vtSN of both sides of the midbrain. These results suggest the glial responses accompanying aging and DA neuron degeneration following a toxic insult represent persistent alterations in the microenvironment of surviving DA neurons that are important factors in understanding regional differences in susceptibility to degeneration. PMID:18484101

  15. Genome-Wide Methylation Analyses in Glioblastoma Multiforme

    PubMed Central

    Lai, Rose K.; Chen, Yanwen; Guan, Xiaowei; Nousome, Darryl; Sharma, Charu; Canoll, Peter; Bruce, Jeffrey; Sloan, Andrew E.; Cortes, Etty; Vonsattel, Jean-Paul; Su, Tao; Delgado-Cruzata, Lissette; Gurvich, Irina; Santella, Regina M.; Ostrom, Quinn; Lee, Annette; Gregersen, Peter; Barnholtz-Sloan, Jill

    2014-01-01

    Few studies had investigated genome-wide methylation in glioblastoma multiforme (GBM). Our goals were to study differential methylation across the genome in gene promoters using an array-based method, as well as repetitive elements using surrogate global methylation markers. The discovery sample set for this study consisted of 54 GBM from Columbia University and Case Western Reserve University, and 24 brain controls from the New York Brain Bank. We assembled a validation dataset using methylation data of 162 TCGA GBM and 140 brain controls from dbGAP. HumanMethylation27 Analysis Bead-Chips (Illumina) were used to interrogate 26,486 informative CpG sites in both the discovery and validation datasets. Global methylation levels were assessed by analysis of L1 retrotransposon (LINE1), 5 methyl-deoxycytidine (5m-dC) and 5 hydroxylmethyl-deoxycytidine (5hm-dC) in the discovery dataset. We validated a total of 1548 CpG sites (1307 genes) that were differentially methylated in GBM compared to controls. There were more than twice as many hypomethylated genes as hypermethylated ones. Both the discovery and validation datasets found 5 tumor methylation classes. Pathway analyses showed that the top ten pathways in hypomethylated genes were all related to functions of innate and acquired immunities. Among hypermethylated pathways, transcriptional regulatory network in embryonic stem cells was the most significant. In the study of global methylation markers, 5m-dC level was the best discriminant among methylation classes, whereas in survival analyses, high level of LINE1 methylation was an independent, favorable prognostic factor in the discovery dataset. Based on a pathway approach, hypermethylation in genes that control stem cell differentiation were significant, poor prognostic factors of overall survival in both the discovery and validation datasets. Approaches that targeted these methylated genes may be a future therapeutic goal. PMID:24586730

  16. Genome-wide methylation analyses in glioblastoma multiforme.

    PubMed

    Lai, Rose K; Chen, Yanwen; Guan, Xiaowei; Nousome, Darryl; Sharma, Charu; Canoll, Peter; Bruce, Jeffrey; Sloan, Andrew E; Cortes, Etty; Vonsattel, Jean-Paul; Su, Tao; Delgado-Cruzata, Lissette; Gurvich, Irina; Santella, Regina M; Ostrom, Quinn; Lee, Annette; Gregersen, Peter; Barnholtz-Sloan, Jill

    2014-01-01

    Few studies had investigated genome-wide methylation in glioblastoma multiforme (GBM). Our goals were to study differential methylation across the genome in gene promoters using an array-based method, as well as repetitive elements using surrogate global methylation markers. The discovery sample set for this study consisted of 54 GBM from Columbia University and Case Western Reserve University, and 24 brain controls from the New York Brain Bank. We assembled a validation dataset using methylation data of 162 TCGA GBM and 140 brain controls from dbGAP. HumanMethylation27 Analysis Bead-Chips (Illumina) were used to interrogate 26,486 informative CpG sites in both the discovery and validation datasets. Global methylation levels were assessed by analysis of L1 retrotransposon (LINE1), 5 methyl-deoxycytidine (5m-dC) and 5 hydroxylmethyl-deoxycytidine (5hm-dC) in the discovery dataset. We validated a total of 1548 CpG sites (1307 genes) that were differentially methylated in GBM compared to controls. There were more than twice as many hypomethylated genes as hypermethylated ones. Both the discovery and validation datasets found 5 tumor methylation classes. Pathway analyses showed that the top ten pathways in hypomethylated genes were all related to functions of innate and acquired immunities. Among hypermethylated pathways, transcriptional regulatory network in embryonic stem cells was the most significant. In the study of global methylation markers, 5m-dC level was the best discriminant among methylation classes, whereas in survival analyses, high level of LINE1 methylation was an independent, favorable prognostic factor in the discovery dataset. Based on a pathway approach, hypermethylation in genes that control stem cell differentiation were significant, poor prognostic factors of overall survival in both the discovery and validation datasets. Approaches that targeted these methylated genes may be a future therapeutic goal.

  17. Profound parental bias associated with chromosome 14 acquired uniparental disomy indicates targeting of an imprinted locus

    PubMed Central

    Chase, A; Leung, W; Tapper, W; Jones, A V; Knoops, L; Rasi, C; Forsberg, L A; Guglielmelli, P; Zoi, K; Hall, V; Chiecchio, L; Eder-Azanza, L; Bryant, C; Lannfelt, L; Docherty, L; White, H E; Score, J; Mackay, D J G; Vannucchi, A M; Dumanski, J P; Cross, N C P

    2015-01-01

    Acquired uniparental disomy (aUPD) is a common finding in myeloid malignancies and typically acts to convert a somatically acquired heterozygous mutation to homozygosity. We sought to identify the target of chromosome 14 aUPD (aUPD14), a recurrent abnormality in myeloid neoplasms and population cohorts of elderly individuals. We identified 29 cases with aUPD14q that defined a minimal affected region (MAR) of 11.2 Mb running from 14q32.12 to the telomere. Exome sequencing (n=7) did not identify recurrently mutated genes, but methylation-specific PCR at the imprinted MEG3-DLK1 locus located within the MAR demonstrated loss of maternal chromosome 14 and gain of paternal chromosome 14 (P<0.0001), with the degree of methylation imbalance correlating with the level of aUPD (r=0.76; P=0.0001). The absence of driver gene mutations in the exomes of three individuals with aUPD14q but no known haematological disorder suggests that aUPD14q may be sufficient to drive clonal haemopoiesis. Analysis of cases with both aUPD14q and JAK2 V617F (n=11) indicated that aUPD14q may be an early event in some cases but a late event in others. We conclude that aUPD14q is a recurrent abnormality that targets an imprinted locus and may promote clonal haemopoiesis either as an initiating event or as a secondary change. PMID:26114957

  18. Profound parental bias associated with chromosome 14 acquired uniparental disomy indicates targeting of an imprinted locus.

    PubMed

    Chase, A; Leung, W; Tapper, W; Jones, A V; Knoops, L; Rasi, C; Forsberg, L A; Guglielmelli, P; Zoi, K; Hall, V; Chiecchio, L; Eder-Azanza, L; Bryant, C; Lannfelt, L; Docherty, L; White, H E; Score, J; Mackay, D J G; Vannucchi, A M; Dumanski, J P; Cross, N C P

    2015-10-01

    Acquired uniparental disomy (aUPD) is a common finding in myeloid malignancies and typically acts to convert a somatically acquired heterozygous mutation to homozygosity. We sought to identify the target of chromosome 14 aUPD (aUPD14), a recurrent abnormality in myeloid neoplasms and population cohorts of elderly individuals. We identified 29 cases with aUPD14q that defined a minimal affected region (MAR) of 11.2 Mb running from 14q32.12 to the telomere. Exome sequencing (n=7) did not identify recurrently mutated genes, but methylation-specific PCR at the imprinted MEG3-DLK1 locus located within the MAR demonstrated loss of maternal chromosome 14 and gain of paternal chromosome 14 (P<0.0001), with the degree of methylation imbalance correlating with the level of aUPD (r=0.76; P=0.0001). The absence of driver gene mutations in the exomes of three individuals with aUPD14q but no known haematological disorder suggests that aUPD14q may be sufficient to drive clonal haemopoiesis. Analysis of cases with both aUPD14q and JAK2 V617F (n=11) indicated that aUPD14q may be an early event in some cases but a late event in others. We conclude that aUPD14q is a recurrent abnormality that targets an imprinted locus and may promote clonal haemopoiesis either as an initiating event or as a secondary change.

  19. A systematic comparison of quantitative high-resolution DNA methylation analysis and methylation-specific PCR

    PubMed Central

    Claus, Rainer; Wilop, Stefan; Hielscher, Thomas; Sonnet, Miriam; Dahl, Edgar; Galm, Oliver; Jost, Edgar; Plass, Christoph

    2012-01-01

    Assessment of DNA methylation has become a critical factor for the identification, development and application of methylation based biomarkers. Here we describe a systematic comparison of a quantitative high-resolution mass spectrometry-based approach (MassARRAY), pyrosequencing and the broadly used methylation-specific PCR (MSP) technique analyzing clinically relevant epigenetically silenced genes in acute myeloid leukemia (AML). By MassARRAY and pyrosequencing, we identified significant DNA methylation differences at the ID4 gene promoter and in the 5′ region of members of the SFRP gene family in 62 AML patients compared with healthy controls. We found a good correlation between data obtained by MassARRAY and pyrosequencing (correlation coefficient R2 = 0.88). MSP-based assessment of the identical samples showed less pronounced differences between AML patients and controls. By direct comparison of MSP-derived and MassARRAY-based methylation data as well as pyrosequencing, we could determine overestimation of DNA methylation data by MSP. We found sequence-context dependent highly variable cut-off values of quantitative DNA methylation values serving as discriminator for the two MSP methylation categories. Moreover, good agreements between quantitative methods and MSP could not be achieved for all investigated loci. Significant correlation of the quantitative assessment but not of MSP-derived methylation data with clinically important characteristics in our patient cohort demonstrated clinical relevance of quantitative DNA methylation assessment. Taken together, while MSP is still the most commonly applied technique for DNA methylation assessment, our data highlight advantages of quantitative approaches for precise characterization and reliable biomarker use of aberrant DNA methylation in primary patient samples, particularly. PMID:22647397

  20. A Novel Mutation in a Critical Region for the Methyl Donor Binding in DNMT3B Causes Immunodeficiency, Centromeric Instability, and Facial Anomalies Syndrome (ICF).

    PubMed

    Rechavi, Erez; Lev, Atar; Eyal, Eran; Barel, Ortal; Kol, Nitzan; Barhom, Sarit Farage; Pode-Shakked, Ben; Anikster, Yair; Somech, Raz; Simon, Amos J

    2016-11-01

    Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is an extremely rare autosomal recessive disease. The immune phenotype is characterized by hypogammaglobulinemia in the presence of B cells. T cell lymphopenia also develops in some patients. We sought to further investigate the immune defect in an ICF patient with a novel missense mutation in DNMT3B and a severe phenotype. Patient lymphocytes were examined for subset counts, immunoglobulin levels, T and B cell de novo production (via excision circles) and receptor repertoire diversity. Mutated DNMT3B protein structure was modeled to assess the effect of a mutation located outside of the catalytic region on protein function. A novel homozygous missense mutation, Ala585Thr, was found in DNMT3B. The patient had decreased B cell counts with hypogammaglobulinemia, and normal T cell counts. CD4(+) T cells decreased over time, leading to an inversion of the CD4(+) to CD8(+) ratio. Excision circle copy numbers were normal, signifying normal de novo lymphocyte production, but the ratio between naïve and total B cells was low, indicating decreased in vivo B cell replication. T and B cell receptor repertoires displayed normal diversity. Computerized modeling of the mutated Ala585 residue suggested reduced thermostability, possibly affecting the enzyme kinetics. Our results highlight the existence of a T cell defect that develops over time in ICF patient, in addition to the known B cell dysfunction. With intravenous immunoglobulin (IVIG) treatment ameliorating the B cell defect, the extent of CD4(+) lymphopenia may determine the severity of ICF immunodeficiency.

  1. [DNA methylation and epigenetics].

    PubMed

    Vaniushin, B F

    2006-09-01

    In eukaryotic cells, nuclear DNA is subject to enzymatic methylation with the formation of 5-methylcytosine residues, mostly within the CG and CNG sequences. In plants and animals this DNA methylation is species-, tissue-, and organelle-specific. It changes (decreases) with age and is regulated by hormones. On the other hand, genome methylation can control hormonal signal. Replicative and post-replicative DNA methylation types are distinguished. They are mediated by multiple DNA methyltransferases with different site-specificity. Replication is accompanied by the appearance of hemimethylated DNA sites. Pronounced asymmetry of the DNA strand methylation disappears to the end of the cell cycle. A model of methylation-regulated DNA replication is proposed. DNA methylation controls all genetic processes in the cell (replication, transcription, DNA repair, recombination, and gene transposition). It is the mechanism of cell differentiation, gene discrimination and silencing. In animals, suppression of DNA methylation stops development (embryogenesis), switches on apoptosis, and is usually lethal. Disruption of DNA methylation pattern results in the malignant cell transformation and serves as one of the early diagnostic features of carcinogenesis. In malignant cell the pattern of DNA methylation, as well as the set of DNA methyltransferase activities, differs from that in normal cell. In plants inhibition of DNA methylation is accompanied by the induction of seed storage and florescence genes. In eukaryotes one and the same gene can be simultaneously methylated both at cytosine and adenine residues. It can be thus suggested, that the plant cell contains at least two different, and probably, interdependent systems of DNA methylation. The first eukaryotic adenine DNA methyltransferase was isolated from plants. This enzyme methylates DNA with the formation of N6-methyladenine residues in the sequence TGATCA (TGATCA-->TGm6ATCA). Plants possess AdoMet-dependent endonucleases

  2. Histone Arginine Methylation

    PubMed Central

    Lorenzo, Alessandra Di; Bedford, Mark T.

    2012-01-01

    Arginine methylation is a common posttranslational modification (PTM). This type of PTM occurs on both nuclear and cytoplasmic proteins, and is particularly abundant on shuttling proteins. In this review, we will focus on one aspect of this PTM: the diverse roles that arginine methylation of the core histone tails play in regulating chromatin function. A family of nine protein arginine methyltransferases (PRMTs) catalyze methylation reactions, and a subset target histones. Importantly, arginine methylation of histone tails can promote or prevent the docking of key transcriptional effector molecules, thus playing a central role in the orchestration of the histone code. PMID:21074527

  3. The glycine binding site of the N-methyl-D-aspartate receptor subunit NR1: identification of novel determinants of co-agonist potentiation in the extracellular M3-M4 loop region.

    PubMed Central

    Hirai, H; Kirsch, J; Laube, B; Betz, H; Kuhse, J

    1996-01-01

    The N-methyl-D-aspartate (NMDA) subtype of ionotropic glutamate receptors is a heterooligomeric membrane protein composed of homologous subunits. Here, the contribution of the M3-M4 loop of the NR1 subunit to the binding of glutamate and the co-agonist glycine was investigated by site-directed mutagenesis. Substitution of the phenylalanine residues at positions 735 or 736 of the M3-M4 loop produced a 15- to 30-fold reduction in apparent glycine affinity without affecting the binding of glutamate and the competitive glycine antagonist 7-chlorokynurenic acid; mutation of both residues caused a >100-fold decrease in glycine affinity. These residues are found in a C-terminal region of the M3-M4 loop that shows significant sequence similarity to bacterial amino acid-binding proteins. Epitope tagging revealed both the N-terminus and the M3-M4 loop to be exposed extracellularly, whereas a C-terminal epitope was localized intracellularly. These results indicate that the M3-M4 loop is part of the ligand-binding pocket of the NR1 subunit and provide the basis for a refined model of the glycine-binding site of the NMDA receptor. Images Fig. 3 Fig. 4 PMID:8650214

  4. DNA methylation profiles at birth and child ADHD symptoms.

    PubMed

    van Mil, Nina H; Steegers-Theunissen, Régine P M; Bouwland-Both, Marieke I; Verbiest, Michael M P J; Rijlaarsdam, Jolien; Hofman, Albert; Steegers, Eric A P; Heijmans, Bastiaan T; Jaddoe, Vincent W V; Verhulst, Frank C; Stolk, Lisette; Eilers, Paul H C; Uitterlinden, André G; Tiemeier, Henning

    2014-02-01

    Attention deficit/hyperactivity disorder (ADHD) is a common and highly heritable psychiatric disorder. In addition, early life environmental factors contribute to the occurrence of ADHD. Recently, DNA methylation has emerged as a mechanism potentially mediating genetic and environmental effects. Here, we investigated whether newborn DNA methylation patterns of selected candidate genes involved in psychiatric disorders or fetal growth are associated with ADHD symptoms in childhood. Participants were 426 children from a large population based cohort of Dutch national origin. Behavioral data were obtained at age 6 years with the Child Behavior Checklist. For the current study, 11 regions at 7 different genes were selected. DNA methylation levels of cord blood DNA were measured for the 11 regions combined and for each region separately. We examined the association between DNA methylation levels at different regions and ADHD symptoms with linear mixed models. DNA methylation levels were negatively associated with ADHD symptom score in the overall analysis of all 11 regions. This association was largely explained by associations of DRD4 and 5-HTT regions. Other candidate genes showed no association between DNA methylation levels and ADHD symptom score. Associations between DNA methylation levels and ADHD symptom score were attenuated by co-occurring Oppositional defiant disorder and total symptoms. Lower DNA methylation levels of the 7 genes assessed at birth, were associated with more ADHD symptoms of the child at 6 years of age. Further studies are needed to confirm our results and to investigate the possible underlying mechanism.

  5. DNA Methylation Patterns in the Hypothalamus of Female Pubertal Goats

    PubMed Central

    Li, Xiumei; Gao, Xiaoxiao; Zhang, Kaifa; Luo, Lei; Ding, Jianping; Zhang, Yunhai; Li, Yunsheng; Cao, Hongguo; Ling, Yinghui; Zhang, Xiaorong; Liu, Ya; Fang, Fugui

    2016-01-01

    Female pubertal development is tightly controlled by complex mechanisms, including neuroendocrine and epigenetic regulatory pathways. Specific gene expression patterns can be influenced by DNA methylation changes in the hypothalamus, which can in turn regulate timing of puberty onset. In order to understand the relationship between DNA methylation changes and gene expression patterns in the hypothalamus of pubertal goats, whole-genome bisulfite sequencing and RNA-sequencing analyses were carried out. There was a decline in DNA methylation levels in the hypothalamus during puberty and 268 differentially methylated regions (DMR) in the genome, with differential patterns in different gene regions. There were 1049 genes identified with distinct expression patterns. High levels of DNA methylation were detected in promoters, introns and 3′-untranslated regions (UTRs). Levels of methylation decreased gradually from promoters to 5′-UTRs and increased from 5′-UTRs to introns. Methylation density analysis demonstrated that methylation level variation was consistent with the density in the promoter, exon, intron, 5′-UTRs and 3′-UTRs. Analyses of CpG island (CGI) sites showed that the enriched gene contents were gene bodies, intergenic regions and introns, and these CGI sites were hypermethylated. Our study demonstrated that DNA methylation changes may influence gene expression profiles in the hypothalamus of goats during the onset of puberty, which may provide new insights into the mechanisms involved in pubertal onset. PMID:27788248

  6. DNA Methylation Patterns in the Hypothalamus of Female Pubertal Goats.

    PubMed

    Yang, Chen; Ye, Jing; Li, Xiumei; Gao, Xiaoxiao; Zhang, Kaifa; Luo, Lei; Ding, Jianping; Zhang, Yunhai; Li, Yunsheng; Cao, Hongguo; Ling, Yinghui; Zhang, Xiaorong; Liu, Ya; Fang, Fugui

    2016-01-01

    Female pubertal development is tightly controlled by complex mechanisms, including neuroendocrine and epigenetic regulatory pathways. Specific gene expression patterns can be influenced by DNA methylation changes in the hypothalamus, which can in turn regulate timing of puberty onset. In order to understand the relationship between DNA methylation changes and gene expression patterns in the hypothalamus of pubertal goats, whole-genome bisulfite sequencing and RNA-sequencing analyses were carried out. There was a decline in DNA methylation levels in the hypothalamus during puberty and 268 differentially methylated regions (DMR) in the genome, with differential patterns in different gene regions. There were 1049 genes identified with distinct expression patterns. High levels of DNA methylation were detected in promoters, introns and 3'-untranslated regions (UTRs). Levels of methylation decreased gradually from promoters to 5'-UTRs and increased from 5'-UTRs to introns. Methylation density analysis demonstrated that methylation level variation was consistent with the density in the promoter, exon, intron, 5'-UTRs and 3'-UTRs. Analyses of CpG island (CGI) sites showed that the enriched gene contents were gene bodies, intergenic regions and introns, and these CGI sites were hypermethylated. Our study demonstrated that DNA methylation changes may influence gene expression profiles in the hypothalamus of goats during the onset of puberty, which may provide new insights into the mechanisms involved in pubertal onset.

  7. DNA methylation abnormalities in congenital heart disease.

    PubMed

    Serra-Juhé, Clara; Cuscó, Ivon; Homs, Aïda; Flores, Raquel; Torán, Núria; Pérez-Jurado, Luis A

    2015-01-01

    Congenital heart defects represent the most common malformation at birth, occurring also in ∼50% of individuals with Down syndrome. Congenital heart defects are thought to have multifactorial etiology, but the main causes are largely unknown. We have explored the global methylation profile of fetal heart DNA in comparison to blood DNA from control subjects: an absolute correlation with the type of tissue was detected. Pathway analysis revealed a significant enrichment of differential methylation at genes related to muscle contraction and cardiomyopathies in the developing heart DNA. We have also searched for abnormal methylation profiles on developing heart-tissue DNA of syndromic and non-syndromic congenital heart defects. On average, 3 regions with aberrant methylation were detected per sample and 18 regions were found differentially methylated between groups. Several epimutations were detected in candidate genes involved in growth regulation, apoptosis and folate pathway. A likely pathogenic hypermethylation of several intragenic sites at the MSX1 gene, involved in outflow tract morphogenesis, was found in a fetus with isolated heart malformation. In addition, hypermethylation of the GATA4 gene was present in fetuses with Down syndrome with or without congenital heart defects, as well as in fetuses with isolated heart malformations. Expression deregulation of the abnormally methylated genes was detected. Our data indicate that epigenetic alterations of relevant genes are present in developing heart DNA in fetuses with both isolated and syndromic heart malformations. These epimutations likely contribute to the pathogenesis of the malformation by cis-acting effects on gene expression.

  8. Methylation plotter: a web tool for dynamic visualization of DNA methylation data.

    PubMed

    Mallona, Izaskun; Díez-Villanueva, Anna; Peinado, Miguel A

    2014-01-01

    Methylation plotter is a Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality. The user is asked to introduce a file containing the methylation status of a genomic region. This file can contain up to 100 samples and 100 CpGs. Optionally, the user can assign a group for each sample (i.e. whether a sample is a tumoral or normal tissue). After the data upload, the tool produces different graphical representations of the results following the most commonly used styles to display this type of data. They include an interactive plot that summarizes the status of every CpG site and for every sample in lollipop or grid styles. Methylation values ranging from 0 (unmethylated) to 1 (fully methylated) are represented using a gray color gradient. A practical feature of the tool allows the user to choose from different types of arrangement of the samples in the display: for instance, sorting by overall methylation level, by group, by unsupervised clustering or just following the order in which data were entered. In addition to the detailed plot, Methylation plotter produces a methylation profile plot that summarizes the status of the scrutinized region, a boxplot that sums up the differences between groups (if any) and a dendrogram that classifies the data by unsupervised clustering. Coupled with this analysis, descriptive statistics and testing for differences at both CpG and group levels are provided. The implementation is based in R/shiny, providing a highly dynamic user interface that generates quality graphics without the need of writing R code. Methylation plotter is freely available at http://gattaca.imppc.org:3838/methylation_plotter/.

  9. Methylation plotter: a web tool for dynamic visualization of DNA methylation data

    PubMed Central

    2014-01-01

    Methylation plotter is a Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality. The user is asked to introduce a file containing the methylation status of a genomic region. This file can contain up to 100 samples and 100 CpGs. Optionally, the user can assign a group for each sample (i.e. whether a sample is a tumoral or normal tissue). After the data upload, the tool produces different graphical representations of the results following the most commonly used styles to display this type of data. They include an interactive plot that summarizes the status of every CpG site and for every sample in lollipop or grid styles. Methylation values ranging from 0 (unmethylated) to 1 (fully methylated) are represented using a gray color gradient. A practical feature of the tool allows the user to choose from different types of arrangement of the samples in the display: for instance, sorting by overall methylation level, by group, by unsupervised clustering or just following the order in which data were entered. In addition to the detailed plot, Methylation plotter produces a methylation profile plot that summarizes the status of the scrutinized region, a boxplot that sums up the differences between groups (if any) and a dendrogram that classifies the data by unsupervised clustering. Coupled with this analysis, descriptive statistics and testing for differences at both CpG and group levels are provided. The implementation is based in R/shiny, providing a highly dynamic user interface that generates quality graphics without the need of writing R code. Methylation plotter is freely available at http://gattaca.imppc.org:3838/methylation_plotter/. PMID:25260021

  10. 16 CFR 801.2 - Acquiring and acquired persons.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... ultimate parent entitles of their respective “persons,” created a joint venture, corporation V, and that... acquisitions which comprise a single transaction. (d)(1)(i) Mergers and consolidations are transactions subject.... Examples: 1. Corporation A (the ultimate parent entity included within person “A”) proposes to acquire Y, a...

  11. 16 CFR 801.2 - Acquiring and acquired persons.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... ultimate parent entitles of their respective “persons,” created a joint venture, corporation V, and that... acquisitions which comprise a single transaction. (d)(1)(i) Mergers and consolidations are transactions subject.... Examples: 1. Corporation A (the ultimate parent entity included within person “A”) proposes to acquire Y, a...

  12. 16 CFR 801.2 - Acquiring and acquired persons.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... ultimate parent entitles of their respective “persons,” created a joint venture, corporation V, and that... acquisitions which comprise a single transaction. (d)(1)(i) Mergers and consolidations are transactions subject.... Examples: 1. Corporation A (the ultimate parent entity included within person “A”) proposes to acquire Y, a...

  13. [Acquired immunodeficiency syndrome in pediatric patients].

    PubMed

    Molina Moguel, J L; Ruiz Illezcas, R; Forsbach Sánchez, S; Carreño Alvarez, S; Picco Díaz, I

    1990-12-01

    The object of this study was to determine how many of the patients treated at the Pediatric Odontology Clinic, a branch of the Maxillo-Facial Surgery Service at the Veinte de Noviembre Regional Hospital, ISSSTE, are VIH-positive of show serious manifestations of Acquired Immuno-Deficiency Syndrome (AIDS). For such purpose, 100 pediatric patients suffering from different systemic or local diseases were evaluated, the most common being hematological alterations. Results evidenced the presence of VIH in the blood of five of the pediatric subjects, all suffering from Hemophilia.

  14. Triple arthrodesis for adult acquired flatfoot.

    PubMed

    Catanzariti, Alan R; Dix, Brian T; Richardson, Phillip E; Mendicino, Robert W

    2014-07-01

    The primary goal of triple arthrodesis for stage III and IV adult acquired flatfoot is to obtain a well-aligned plantigrade foot that will support the ankle in optimal alignment. Ancillary procedures including posterior muscle group lengthening, medial displacement calcaneal osteotomy, medial column stabilization, peroneus brevis tenotomy, or transfer and harvest of regional bone graft are often necessary to achieve adequate realignment. Image intensification is helpful in confirming optimal realignment before fixation. Results of triple arthrodesis are enhanced with adequate preparation of joint surfaces, bone graft/orthobiologics, 2-point fixation of all 3 tritarsal joints, and a vertical heel position. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. DNA methylation and gene expression in Mimulus guttatus.

    PubMed

    Colicchio, Jack M; Miura, Fumihito; Kelly, John K; Ito, Takashi; Hileman, Lena C

    2015-07-07

    The presence of methyl groups on cytosine nucleotides across an organism's genome (methylation) is a major regulator of genome stability, crossing over, and gene regulation. The capacity for DNA methylation to be altered by environmental conditions, and potentially passed between generations, makes it a prime candidate for transgenerational epigenetic inheritance. Here we conduct the first analysis of the Mimulus guttatus methylome, with a focus on the relationship between DNA methylation and gene expression. We present a whole genome methylome for the inbred line Iron Mountain 62 (IM62). DNA methylation varies across chromosomes, genomic regions, and genes. We develop a model that predicts gene expression based on DNA methylation (R(2) = 0.2). Post hoc analysis of this model confirms prior relationships, and identifies novel relationships between methylation and gene expression. Additionally, we find that DNA methylation is significantly depleted near gene transcriptional start sites, which may explain the recently discovered elevated rate of recombination in these same regions. The establishment here of a reference methylome will be a useful resource for the continued advancement of M. guttatus as a model system. Using a model-based approach, we demonstrate that methylation patterns are an important predictor of variation in gene expression. This model provides a novel approach for differential methylation analysis that generates distinct and testable hypotheses regarding gene expression.

  16. DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip.

    PubMed

    Walker, Denise L; Bhagwate, Aditya Vijay; Baheti, Saurabh; Smalley, Regenia L; Hilker, Christopher A; Sun, Zhifu; Cunningham, Julie M

    2015-01-01

    To compare the performance of four sequence-based and one microarray methods for DNA methylation profiling. DNA from two cell lines were profiled by reduced representation bisulfite sequencing, methyl capture sequencing (SS-Meth Seq), NimbleGen SeqCapEpi CpGiant(Nimblegen MethSeq), methylated DNA immunoprecipitation (MeDIP) and the Human Methylation 450 Bead Chip (Meth450K). Despite differences in genome-wide coverage, high correlation and concordance were observed between different methods. Significant overlap of differentially methylated regions was identified between sequenced-based platforms. MeDIP provided the best coverage for the whole genome and gene body regions, while RRBS and Nimblegen MethSeq were superior for CpGs in CpG islands and promoters. Methylation analyses can be achieved by any of the five methods but understanding their differences may better address the research question being posed.

  17. Aberrant DNA methylation imprints in aborted bovine clones.

    PubMed

    Liu, Jing-He; Yin, Shen; Xiong, Bo; Hou, Yi; Chen, Da-Yuan; Sun, Qing-Yuan

    2008-04-01

    Genomic imprinting plays a very important role during development and its abnormality may heavily undermine the developmental potential of bovine embryos. Because of limited resources of the cow genome, bovine genomic imprinting, both in normal development and in somatic cell nuclear transfer (SCNT) cloning, is not well documented. DNA methylation is thought to be a major factor for the establishment of genomic imprinting. In our study, we determined the methylation status of differential methylated regions (DMRs) of four imprinted genes in four spontaneously aborted SCNT-cloned fetuses (AF). Firstly, abnormal methylation imprints were observed in each individual to different extents. In particular, Peg3 and MAOA were either seriously demethylated or showed aberrant methylation patterns in four aborted clones we tested, but Xist and Peg10 exhibited relatively better maintained methylation status in AF1 and AF4. Secondly, two aborted fetuses, AF2 and AF3 exhibited severe aberrant methylation imprints of four imprinted genes. Finally, MAOA showed strong heterogeneous methylation patterns of its DMR in normal somatic adult tissue, but largely variable methylation levels and relatively homogeneous methylation patterns in aborted cloned fetuses. Our data indicate that the aborted cloned fetuses exhibited abnormal methylation imprints, to different extent, in aborted clones, which partially account for the higher abortion and developmental abnormalities during bovine cloning.

  18. Differential methylation during maize leaf growth targets developmentally regulated genes.

    PubMed

    Candaele, Jasper; Demuynck, Kirin; Mosoti, Douglas; Beemster, Gerrit T S; Inzé, Dirk; Nelissen, Hilde

    2014-03-01

    DNA methylation is an important and widespread epigenetic modification in plant genomes, mediated by DNA methyltransferases (DMTs). DNA methylation is known to play a role in genome protection, regulation of gene expression, and splicing and was previously associated with major developmental reprogramming in plants, such as vernalization and transition to flowering. Here, we show that DNA methylation also controls the growth processes of cell division and cell expansion within a growing organ. The maize (Zea mays) leaf offers a great tool to study growth processes, as the cells progressively move through the spatial gradient encompassing the division zone, transition zone, elongation zone, and mature zone. Opposite to de novo DMTs, the maintenance DMTs were transcriptionally regulated throughout the growth zone of the maize leaf, concomitant with differential CCGG methylation levels in the four zones. Surprisingly, the majority of differentially methylated sequences mapped on or close to gene bodies and not to repeat-rich loci. Moreover, especially the 5' and 3' regions of genes, which show overall low methylation levels, underwent differential methylation in a developmental context. Genes involved in processes such as chromatin remodeling, cell cycle progression, and growth regulation, were differentially methylated. The presence of differential methylation located upstream of the gene anticorrelated with transcript expression, while gene body differential methylation was unrelated to the expression level. These data indicate that DNA methylation is correlated with the decision to exit mitotic cell division and to enter cell expansion, which adds a new epigenetic level to the regulation of growth processes.

  19. Acquired pericentric inversion of chromosome 9 in acute myeloid leukemia.

    PubMed

    Udayakumar, A M; Pathare, A V; Dennison, D; Raeburn, J A

    2009-01-01

    Pericentric inversion of chromosome 9 involving the qh region is relatively common as a constitutional genetic aberration without any apparent phenotypic consequences. However, it has not been established as an acquired abnormality in cancer. Among the three patients reported so far in the literature with acquired inv(9), only one had acute myeloid leukemia (AML). Here we describe an unique case where both chromosomes 9 presented with an acquired pericentric inversion with breakpoints at 9p13 and 9q12 respectively, in a AML patient with aberrant CD7 and CD9 positivity. Additionally, one der(9) also showed short arm deletion at 9p21 to the centromeric region and including the p16 gene. The constitutional karyotype was normal. This is probably the first report describing an acquired inv(9) involving both chromosomes 9 in AML. The possible significance of this inversion is discussed.

  20. 12 CFR 583.1 - Acquire.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... AND LOAN HOLDING COMPANIES § 583.1 Acquire. The term acquire means to acquire, directly or indirectly, ownership or control through an acquisition of shares, an acquisition of assets or assumption of liabilities...

  1. DNA methylation profiling of human chromosomes 6, 20 and 22

    PubMed Central

    Eckhardt, Florian; Lewin, Joern; Cortese, Rene; Rakyan, Vardhman K.; Attwood, John; Burger, Matthias; Burton, John; Cox, Tony V.; Davies, Rob; Down, Thomas A.; Haefliger, Carolina; Horton, Roger; Howe, Kevin; Jackson, David K.; Kunde, Jan; Koenig, Christoph; Liddle, Jennifer; Niblett, David; Otto, Thomas; Pettett, Roger; Seemann, Stefanie; Thompson, Christian; West, Tony; Rogers, Jane; Olek, Alex; Berlin, Kurt; Beck, Stephan

    2011-01-01

    DNA methylation constitutes the most stable type of epigenetic modifications modulating the transcriptional plasticity of mammalian genomes. Using bisulfite DNA sequencing, we report high-resolution methylation reference profiles of human chromosomes 6, 20 and 22, providing a resource of about 1.9 million CpG methylation values derived from 12 different tissues. Analysis of 6 annotation categories, revealed evolutionary conserved regions to be the predominant sites for differential DNA methylation and a core region surrounding the transcriptional start site as informative surrogate for promoter methylation. We find 17% of the 873 analyzed genes differentially methylated in their 5′-untranslated regions (5′-UTR) and about one third of the differentially methylated 5′-UTRs to be inversely correlated with transcription. While our study was controlled for factors reported to affect DNA methylation such as sex and age, we did not find any significant attributable effects. Our data suggest DNA methylation to be ontogenetically more stable than previously thought. PMID:17072317

  2. Acquired aplastic anemia in children.

    PubMed

    Hartung, Helge D; Olson, Timothy S; Bessler, Monica

    2013-12-01

    This article provides a practice-based and concise review of the etiology, diagnosis, and management of acquired aplastic anemia in children. Bone marrow transplantation, immunosuppressive therapy, and supportive care are discussed in detail. The aim is to provide the clinician with a better understanding of the disease and to offer guidelines for the management of children with this uncommon yet serious disorder.

  3. Duplicated Information Acquired by Libraries.

    ERIC Educational Resources Information Center

    White, Carl M.

    The object of this study is to make a start toward determining the extent of duplicated information that is being acquired in spite of customary precautions to avoid it. Referring to a specific case, the percentages in Table II show the frequency of appearance in five other works of 19 items in Mitchell's "Encyclopedia of American Politics." While…

  4. Musicality: instinct or acquired skill?

    PubMed

    Marcus, Gary F

    2012-10-01

    Is the human tendency toward musicality better thought of as the product of a specific, evolved instinct or an acquired skill? Developmental and evolutionary arguments are considered, along with issues of domain-specificity. The article also considers the question of why humans might be consistently and intensely drawn to music if musicality is not in fact the product of a specifically evolved instinct.

  5. Acquired Equivalence Changes Stimulus Representations

    ERIC Educational Resources Information Center

    Meeter, M.; Shohamy, D.; Myers, C. E.

    2009-01-01

    Acquired equivalence is a paradigm in which generalization is increased between two superficially dissimilar stimuli (or antecedents) that have previously been associated with similar outcomes (or consequents). Several possible mechanisms have been proposed, including changes in stimulus representations, either in the form of added associations or…

  6. Assessing combined methylation-sensitive high resolution melting and pyrosequencing for the analysis of heterogeneous DNA methylation

    PubMed Central

    2011-01-01

    Heterogeneous DNA methylation leads to difficulties in accurate detection and quantification of methylation. Methylation-sensitive high resolution melting (MS-HRM) is unique among regularly used methods for DNA methylation analysis in that heterogeneous methylation can be readily identified, although not quantified, by inspection of the melting curves. Bisulfite pyrosequencing has been used to estimate the level of heterogeneous methylation by quantifying methylation levels present at individual CpG dinucleotides. Sequentially combining the two methodologies using MS-HRM to screen the amplification products prior to bisulfite pyrosequencing would be advantageous. This would not only replace the quality control step using agarose gel analysis prior to the pyrosequencing step but would also provide important qualitative information in its own right. We chose to analyze DAPK1 as it is an important tumor suppressor gene frequently heterogeneously methylated in a number of malignancies, including chronic lymphocytic leukemia (CLL). A region of the DAPK1 promoter was analyzed in ten CLL samples by MS-HRM. By using a biotinylated primer, bisulfite pyrosequencing could be used to directly analyze the samples. MS-HRM revealed the presence of various extents of heterogeneous DAPK1 methylation in all CLL samples. Further analysis of the biotinylated MS-HRM products by bisulfite pyrosequencing provided quantitative information for each CpG dinucleotide analyzed, and confirmed the presence of heterogeneous DNA methylation. Whereas each method could be used individually, MS-HRM and bisulfite pyrosequencing provided complementary information for the assessment of heterogeneous methylation. PMID:21364322

  7. Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation.

    PubMed

    Cheong, Clara Y; Chng, Keefe; Ng, Shilen; Chew, Siew Boom; Chan, Louiza; Ferguson-Smith, Anne C

    2015-05-01

    Genomic imprinting is an epigenetic mechanism resulting in parental allele-specific gene expression. Defects in normal imprinting are found in cancer, assisted reproductive technologies, and several human syndromes. In mouse models, germline-derived DNA methylation is shown to regulate imprinting. Though imprinting is largely conserved between mammals, species- and tissue-specific domains of imprinted expression exist. Using the cynomolgus macaque (Macaca fascicularis) to assess primate-specific imprinting, we present a comprehensive view of tissue-specific imprinted expression and DNA methylation at established imprinted gene clusters. For example, like mouse and unlike human, macaque IGF2R is consistently imprinted, and the PLAGL1, INPP5F transcript variant 2, and PEG3 imprinting control regions are not methylated in the macaque germline but acquire this post-fertilization. Methylome data from human early embryos appear to support this finding. These suggest fundamental differences in imprinting control mechanisms between primate species and rodents at some imprinted domains, with implications for our understanding of the epigenetic programming process in humans and its influence on disease.

  8. Analysis of DNA methylation of potential age-related methylation sites in canine peripheral blood leukocytes.

    PubMed

    Ito, Genta; Yoshimura, Kuniko; Momoi, Yasuyuki

    2017-04-08

    Reliable methodology for predicting the age of mature dogs is currently unavailable. In this study, amplicon sequencing of 50 blood samples obtained from diseased dogs was used to measure methylation in seven DNA regions. Significant correlations between methylation level and age were identified in four of the seven regions. These four regions were then tested in samples from 31 healthy toy poodles, and correlations were detected in two regions. The age of another 11 dogs was predicted using data from the diseased dogs and the healthy poodles. The mean difference between the actual and calculated ages was 34.3 and 23.1 months, respectively. Further research is needed to identify additional sites of age-related methylation and allow accurate age prediction in dogs.

  9. The clinical characteristics of 80 cases of acquired immunodeficiency syndrome-associated Kaposi’s sarcoma in Xinjiang Autonomous Region and the effect of different treatments on the prognosis

    PubMed Central

    Yang, Tongtong; He, Li; Wan, Xuefeng; Maimaitiaili, Wubuli; Song, Yuxia; Zhang, Yuexin; Lu, Xiaobo

    2015-01-01

    To analyze the clinical features of AIDS-related Kaposi’s sarcoma (AIDS-KS) patients in Xinjiang Autonomous Region and the impact of CD4 +T lymphocyte count, highly active antiretroviral therapy (HAART) and systemic chemotherapy on the prognosis. The clinical information of 80 AIDS-KS patients admitted in Sixth People’s Hospital of Xinjiang Autonomous Region from January 2008 to August 2014 was retrospectively reviewed. Population characteristics, extent of lesions, KS progress, CD4 +T lymphocyte count, combined opportunistic infections, treatment and prognosis of these patients were analyzed. The 80 patients were divided into five groups according to treatment methods, including HAART, HAART + chemotherapy, chemotherapy + HAART, chemotherapy, and untreated groups. The efficacy and prognosis of the five groups were compared. Among the 80 patients, 74 (92.50%) patients were Uygur. The average age was 39.5±9.9 years and male-to-female ratio was 3:1. The median of baseline CD4 +T lymphocyte count was 152.5 cells/μL and the interquartile was 233.25 cells/μL. CD4 +T lymphocyte counts were significantly increased after treatment in HAART, HAART + chemotherapy, and chemotherapy + HAART groups (P < 0.05). CD4 +T lymphocyte count in chemotherapy groups was significantly reduced after treatment (P < 0.05). The untreated group had the highest mortality rate (33.3%). In HAART group, KS-associated immune reconstitution inflammatory response syndrome (KS-IRIS) appeared in 45.5% cases and 2 death cases were caused by KS-IRIS. In Xinjiang Autonomous Region, the incidence of AIDS-KS is high in young Uygur male people. HAART followed by chemotherapy has ideal efficacy, reduces the incidence of KS-IRIS and improves the prognosis. PMID:26770484

  10. META2: Intercellular DNA Methylation Pairwise Annotation and Integrative Analysis.

    PubMed

    Tang, Binhua

    2016-01-01

    Genome-wide deciphering intercellular differential DNA methylation as well as its roles in transcriptional regulation remains elusive in cancer epigenetics. Here we developed a toolkit META2 for DNA methylation annotation and analysis, which aims to perform integrative analysis on differentially methylated loci and regions through deep mining and statistical comparison methods. META2 contains multiple versatile functions for investigating and annotating DNA methylation profiles. Benchmarked with T-47D cell, we interrogated the association within differentially methylated CpG (DMC) and region (DMR) candidate count and region length and identified major transition zones as clues for inferring statistically significant DMRs; together we validated those DMRs with the functional annotation. Thus META2 can provide a comprehensive analysis approach for epigenetic research and clinical study.

  11. META2: Intercellular DNA Methylation Pairwise Annotation and Integrative Analysis

    PubMed Central

    2016-01-01

    Genome-wide deciphering intercellular differential DNA methylation as well as its roles in transcriptional regulation remains elusive in cancer epigenetics. Here we developed a toolkit META2 for DNA methylation annotation and analysis, which aims to perform integrative analysis on differentially methylated loci and regions through deep mining and statistical comparison methods. META2 contains multiple versatile functions for investigating and annotating DNA methylation profiles. Benchmarked with T-47D cell, we interrogated the association within differentially methylated CpG (DMC) and region (DMR) candidate count and region length and identified major transition zones as clues for inferring statistically significant DMRs; together we validated those DMRs with the functional annotation. Thus META2 can provide a comprehensive analysis approach for epigenetic research and clinical study. PMID:28116291

  12. Horizontal transfer of DNA methylation patterns into bacterial chromosomes.

    PubMed

    Shin, Jung-Eun; Lin, Chris; Lim, Han N

    2016-05-19

    Horizontal gene transfer (HGT) is the non-inherited acquisition of novel DNA sequences. HGT is common and important in bacteria because it enables the rapid generation of new phenotypes such as antibiotic resistance. Here we show that in vivo and in vitro DNA methylation patterns can be horizontally transferred into bacterial chromosomes to program cell phenotypes. The experiments were performed using a synthetic system in Escherichia coli where different DNA methylation patterns within the cis-regulatory sequence of the agn43 gene turn on or off a fluorescent reporter (CFP). With this system we demonstrated that DNA methylation patterns not only accompany the horizontal transfer of genes into the bacterial cytoplasm but can be transferred into chromosomes by: (i) bacteriophage P1 transduction; and (ii) transformation of extracellular synthetic DNA. We also modified the experimental system by replacing CFP with the SgrS small RNA, which regulates glucose and methyl α-D-glucoside uptake, and showed that horizontally acquired DNA methylation patterns can increase or decrease cell fitness. That is, horizontally acquired DNA methylation patterns can result in the selection for and against cells that have HGT. Findings from these proof-of-concept experiments have applications in synthetic biology and potentially broad implications for bacterial adaptation and evolution. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. H19-DMR allele-specific methylation analysis reveals epigenetic heterogeneity of CTCF binding site 6 but not of site 5 in head-and-neck carcinomas: a pilot case-control analysis.

    PubMed

    De Castro Valente Esteves, Leda Isabel; De Karla Cervigne, Nilva; Do Carmo Javaroni, Afonso; Magrin, José; Kowalski, Luiz Paulo; Rainho, Cláudia Aparecida; Rogatto, Silvia Regina

    2006-02-01

    Aberrant methylation of seven potential binding sites of the CTCF factor in the differentially methylated region upstream of the H19 gene (H19-DMR) has been suggested as critical for the regulation of IGF2 and H19 imprinted genes. In this study, we analyzed the allele-specific methylation pattern of CTCF binding sites 5 and 6 using methylation-sensitive restriction enzyme PCR followed by RFLP analysis in matched tumoral and lymphocyte DNA from head-and-neck squamous cell carcinoma (HNSCC) patients, as well as in lymphocyte DNA from control individuals who were cancer-free. The monoallelic methylation pattern was maintained in CTCF binding site 5 in 22 heterozygous out of 91 samples analyzed. Nevertheless, a biallelic methylation pattern was detected in CTCF binding site 6 in a subgroup of HNSCC patients as a somatic acquired feature of tumor cells. An atypical biallelic methylation was also observed in both tumor and lymphocyte DNA from two patients, and at a high frequency in the control group (29 out of 64 informative controls). Additionally, we found that the C/T transition detected by HhaI RFLP suppressed one dinucleotide CpG in critical CTCF binding site 6, of a mutation showing polymorphic frequencies. Although a heterogeneous methylation pattern was observed after DNA sequencing modified by sodium bisulfite, the biallelic methylation pattern was confirmed in 9 out of 10 HNSCCs. These findings are likely to be relevant in the epigenetic regulation of the DMR, especially in pathological conditions in which the imprinting of IGF2 and H19 genes is disrupted.

  14. DNA methylation and application in forensic sciences.

    PubMed

    Kader, Farzeen; Ghai, Meenu

    2015-04-01

    DNA methylation of cytosine residues is a stable epigenetic alteration, beginning as early as foetal development in the uterus and continuously evolving throughout life. DNA methylation as well as other epigenetic modifications such as chromatin remodelling and histone modifications are indispensable in mammalian development. Methylation is to a large extent influenced by the ageing process, diets and lifestyle choices. Our understanding of this crucial modification may even contribute to the treatment and prevention of age-related illnesses in the very near future. Genome-wide methylation analysis using high throughput DNA technologies has discovered numerous differentially methylated regions (tDMRs) which differ in levels of methylation in various cell types and tissues. TDMRs have been useful in various applications, particularly medicine and forensic sciences. Forensic scientists are constantly seeking exciting and novel methods to aid in the reconstruction of crime scenes, and the analysis of tDMRs represents a new and reliable technique to identify biological fluids and tissues found at the scene of a violent act. Not only has research been able to unequivocally identify various fluids and tissues, but methods to determine the sex, age and phenotype of donors has been developed. New tDMRs in genes are being searched for consistently to serve as novel markers in forensic DNA analysis.

  15. An Ill Wind: Methyl Bromide Use Near California Schools, 1998.

    ERIC Educational Resources Information Center

    Ross, Zev; Walker, Bill

    A California study investigates the use of the toxic pesticide methyl bromide near the state's public schools, explains why proposed safety rules have failed to protect children and others from exposure, and examines regions at particular exposure risk. Study results show an increasing exposure to methyl bromide near schools already at risk while…

  16. THE SEARCH FOR A COMPLEX MOLECULE IN A SELECTED HOT CORE REGION: A RIGOROUS ATTEMPT TO CONFIRM TRANS-ETHYL METHYL ETHER TOWARD W51 e1/e2

    SciTech Connect

    Carroll, P. Brandon; McGuire, Brett A.; Blake, Geoffrey A.; Apponi, A. J.; Ziurys, L. M.; Remijan, Anthony

    2015-01-20

    An extensive search has been conducted to confirm transitions of trans-ethyl methyl ether (tEME, C{sub 2}H{sub 5}OCH{sub 3}), toward the high-mass star forming region W51 e1/e2 using the 12 m Telescope of the Arizona Radio Observatory at wavelengths from 2 mm and 3 mm. In short, we cannot confirm the detection of tEME toward W51 e1/e2 and our results call into question the initial identification of this species by Fuchs et al. Additionally, re-evaluation of the data from the original detection indicates that tEME is not present toward W51 e1/e2 in the abundance reported by Fuchs and colleagues. Typical peak-to-peak noise levels for the present observations of W51 e1/e2 were between 10 and 30 mK, yielding an upper limit of the tEME column density of ≤1.5 × 10{sup 15} cm{sup –2}. This would make tEME at least a factor of two times less abundant than dimethyl ether (CH{sub 3}OCH{sub 3}) toward W51 e1/e2. We also performed an extensive search for this species toward the high-mass star forming region Sgr B2(N-LMH) with the National Radio Astronomy Observatory 100 m Green Bank Telescope. No transitions of tEME were detected and we were able to set an upper limit to the tEME column density of ≤4 × 10{sup 14} cm{sup –2} toward this source. Thus, we are able to show that tEME is not a new molecular component of the interstellar medium and that an exacting assessment must be carried out when assigning transitions of new molecular species to astronomical spectra to support the identification of large organic interstellar molecules.

  17. Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions

    PubMed Central

    Menigatti, M; Staiano, T; Manser, C N; Bauerfeind, P; Komljenovic, A; Robinson, M; Jiricny, J; Buffoli, F; Marra, G

    2013-01-01

    Epigenetic silencing of protein-encoding genes is common in early-stage colorectal tumorigenesis. Less is known about the methylation-mediated silencing of genes encoding microRNAs (miRNAs), which are also important epigenetic modulators of gene expression. Using quantitative PCR, we identified 56 miRNAs that were expressed in normal colorectal mucosa and in HT29 colorectal cancer cells treated with demethylating agents but not in untreated HT29 cells, suggesting that they probably undergo methylation-induced silencing during colorectal tumorigenesis. One of these, miR-195, had recently been reported to be underexpressed in colorectal cancers and to exert tumor-suppressor effects in colorectal cancer cells. We identified the transcription start site (TSS) for primary miRNA (pri-miR)-497/195, the primary precursor that yields miR-195 and another candidate on our list, miR-497, and a single CpG island upstream to the TSS, which controls expression of both miRNAs. Combined bisulfite restriction analysis and bisulfite genomic sequencing studies revealed monoallelic methylation of this island in normal colorectal mucosa (50/50 samples) and full methylation in most colorectal adenomas (38/50; 76%). The hypermethylated precancerous lesions displayed significantly downregulated expression of both miRNAs. Similar methylation patterns were observed at two known imprinted genes, MEG3 and GNAS-AS1, which encode several of the 56 miRNAs on our list. Imprinting at these loci was lost in over half the adenomas (62% at MEG3 and 52% at GNAS-AS1). Copy-number alterations at MEG3, GNAS-AS1 and pri-miR-497/195, which are frequent in colorectal cancers, were less common in adenomas and confined to tumors displaying differential methylation at the involved locus. Our data show that somatically acquired, epigenetic changes at monoallelically methylated regions encoding miRNAs are relatively frequent in sporadic colorectal adenomas and might contribute to the onset and progression of

  18. Age-related DNA methylation in normal breast tissue and its relationship with invasive breast tumor methylation.

    PubMed

    Johnson, Kevin C; Koestler, Devin C; Cheng, Chao; Christensen, Brock C

    2014-02-01

    Age is a key risk factor for breast cancer and epigenetic alterations may contribute to age-related increases in breast cancer risk, though the relation of age-related methylation in normal breast tissues with altered methylation in breast tumors is unclear. We investigated the relation of age with DNA methylation in normal breast tissues genome-wide using two data sets from the Gene Expression Omnibus (GEO) database (GSE32393 and GSE31979). We validated our observations in an independent set of normal breast tissues, examined age-related methylation in normal breast for enrichment of genomic features, and compared age-related methylation in normal tissue with methylation alterations in breast tumors. Between the two array-based methylation data sets, there were 204 CpG loci with significant (P<0.05) and consistent age-related methylation, 97% of which were increases in methylation. Our validation sets confirmed the direction of age-related DNA methylation changes in all measured regions. Among the 204 age-related CpG loci, we observed a significant enrichment for CpG islands (P = 8.7E-6) and polycomb group protein target genes (P = 0.03). In addition, 24 of the 204 CpGs with age-related methylation in normal breast were significantly differentially methylated between normal and breast tumor tissues. We identified consistent age-related methylation changes in normal breast tissue that are further altered in breast tumors and may represent early events contributing to breast carcinogenesis. This work identifies age-related methylation in normal breast tissue and begins to deconstruct the contribution of aging to epigenetic alterations present in breast tumors.

  19. Nursing home-acquired pneumonia.

    PubMed

    El Solh, Ali A

    2009-02-01

    Nursing home-acquired pneumonia (NHAP) was first described in 1978. Since then there has been much written regarding NHAP and its management despite the lack of well-designed studies in this patient population. The most characteristic features of patients with NHAP are the atypical presentation, which may lead to delay in diagnosis and therapy. The microbial etiology of pneumonia encompasses a wide spectrum that spans microbes recovered from patients with community-acquired pneumonia to organisms considered specific only to nosocomial settings. Decision to transfer a nursing home patient to an acute care facility depends on a host of factors, which include the level of staffing available at the nursing home, patients' advance directives, and complexity of treatment. The presence of risk factors for multidrug-resistant pathogens dictates approach to therapy. Prevention remains the cornerstone of reducing the incidence of disease. Despite the advance in medical services, mortality from NHAP remains high.

  20. Bovine DNA methylation imprints are established in an oocyte size-specific manner, which are coordinated with the expression of the DNMT3 family proteins.

    PubMed

    O'Doherty, Alan M; O'Shea, Lynne C; Fair, Trudee

    2012-03-01

    A subset of genes, known as imprinted genes, is present in the mammalian genome. Genomic imprinting governs the monoallelic expression of these genes, depending on whether the gene was inherited from the sperm or the egg. This parent-of-origin specific gene expression is generally dependent on the epigenetic modification, DNA methylation, and the DNA methylation status of CpG dinucleotides residing in loci known as differentially methylated regions (DMRs). The enzymatic machinery responsible for the addition of methyl (-CH(3)) groups to the cytosine residue in the CpG dinucleotides are known as DNA methyltransferases (DNMTs). Correct establishment and maintenance of methylation patterns at imprinted genes has been associated with placental function and regulation of embryonic/fetal development. Much work has been carried out on imprinted genes in mouse and human; however, little is known about the methylation dynamics in the bovine oocyte. The primary objective of the present study was to characterize the establishment of methylation at maternally imprinted genes in bovine growing oocytes and to determine if the expression of the bovine DNMTs-DNMT3A, DNMT3B, and DNMT3L-was coordinated with DNA methylation during oocyte development. To this end, a panel of maternally imprinted genes was selected (SNRPN, MEST, IGF2R, PEG10, and PLAGL1) and putative DMRs for MEST, IGF2R, PEG10, and PLAGL1 were identified within the 5' regions for each gene; the SNRPN DMR has been reported previously. Conventional bisulfite sequencing revealed that methylation marks were acquired at all five DMRs investigated in an oocyte size-dependent fashion. This was confirmed for a selection of genes using pyrosequencing analysis. Furthermore, mRNA expression and protein analysis revealed that DNMT3A, DNMT3B, and DNMT3L are also present in the bovine oocyte during its growth phase. This study demonstrates for the first time that an increase in bovine imprinted gene DMR methylation occurs during

  1. [Acquired disorders of color vision].

    PubMed

    Lascu, Lidia; Balaş, Mihaela

    2002-01-01

    This article is a general view of acquired disorders of color vision. The revision of the best known methods and of the etiopathogenic classification is not very important in ophthalmology but on the other hand, the detection of the blue defect advertise and associated ocular pathology. There is a major interest in serious diseases as multiple sclerosis, AIDS, diabetes melitus, when the first ocular sign can be a defect in the color vision.

  2. ENZYMOLOGY OF ARSENIC METHYLATION

    EPA Science Inventory

    Enzymology of Arsenic Methylation

    David J. Thomas, Pharmacokinetics Branch, Experimental Toxicology Division, National
    Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park...

  3. Thiophanate-methyl

    Integrated Risk Information System (IRIS)

    Integrated Risk Information System ( IRIS ) Chemical Assessment Summary U.S . Environmental Protection Agency National Center for Environmental Assessment This IRIS Summary has been removed from the IRIS database and is available for historical reference purposes . ( July 2016 ) Thiophanate - methyl

  4. ENZYMOLOGY OF ARSENIC METHYLATION

    EPA Science Inventory

    Enzymology of Arsenic Methylation

    David J. Thomas, Pharmacokinetics Branch, Experimental Toxicology Division, National
    Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park...

  5. Community-acquired bacterial meningitis.

    PubMed

    van de Beek, Diederik; Brouwer, Matthijs; Hasbun, Rodrigo; Koedel, Uwe; Whitney, Cynthia G; Wijdicks, Eelco

    2016-11-03

    Meningitis is an inflammation of the meninges and subarachnoid space that can also involve the brain cortex and parenchyma. It can be acquired spontaneously in the community - community-acquired bacterial meningitis - or in the hospital as a complication of invasive procedures or head trauma (nosocomial bacterial meningitis). Despite advances in treatment and vaccinations, community-acquired bacterial meningitis remains one of the most important infectious diseases worldwide. Streptococcus pneumoniae and Neisseria meningitidis are the most common causative bacteria and are associated with high mortality and morbidity; vaccines targeting these organisms, which have designs similar to the successful vaccine that targets Haemophilus influenzae type b meningitis, are now being used in many routine vaccination programmes. Experimental and genetic association studies have increased our knowledge about the pathogenesis of bacterial meningitis. Early antibiotic treatment improves the outcome, but the growing emergence of drug resistance as well as shifts in the distribution of serotypes and groups are fuelling further development of new vaccines and treatment strategies. Corticosteroids were found to be beneficial in high-income countries depending on the bacterial species. Further improvements in the outcome are likely to come from dampening the host inflammatory response and implementing preventive measures, especially the development of new vaccines.

  6. Acquired causes of intestinal malabsorption.

    PubMed

    van der Heide, F

    2016-04-01

    This review focuses on the acquired causes, diagnosis, and treatment of intestinal malabsorption. Intestinal absorption is a complex process that depends on many variables, including the digestion of nutrients within the intestinal lumen, the absorptive surface of the small intestine, the membrane transport systems, and the epithelial absorptive enzymes. Acquired causes of malabsorption are classified by focussing on the three phases of digestion and absorption: 1) luminal/digestive phase, 2) mucosal/absorptive phase, and 3) transport phase. Most acquired diseases affect the luminal/digestive phase. These include short bowel syndrome, extensive small bowel inflammation, motility disorders, and deficiencies of digestive enzymes or bile salts. Diagnosis depends on symptoms, physical examination, and blood and stool tests. There is no gold standard for the diagnosis of malabsorption. Further testing should be based on the specific clinical context and the suspected underlying disease. Therapy is directed at nutritional support by enteral or parenteral feeding and screening for and supplementation of deficiencies in vitamins and minerals. Early enteral feeding is important for intestinal adaptation in short bowel syndrome. Medicinal treatment options for diarrhoea in malabsorption include loperamide, codeine, cholestyramine, or antibiotics. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. METHYL GREEN-PYRONIN

    PubMed Central

    Kurnick, N. B.

    1950-01-01

    1. Methyl green stains selectively highly polymerized desoxyribonucleic acid, and fails to stain, to any significant extent, depolymerized desoxyribonucleic acid and ribonucleic acid. 2. Pyronin stains preferentially low polymers of nucleic acid. 3. Triphenylmethane dyes with two amino groups appear to share the selectivity of methyl green. Those with three amino groups are not selective. 4. A stereochemical hypothesis is offered to account for these observations. PMID:15402708

  8. Aberrant DNA methylation reprogramming in bovine SCNT preimplantation embryos

    PubMed Central

    Zhang, Sheng; Chen, Xin; Wang, Fang; An, Xinglan; Tang, Bo; Zhang, Xueming; Sun, Liguang; Li, Ziyi

    2016-01-01

    DNA methylation reprogramming plays important roles in mammalian embryogenesis. Mammalian somatic cell nuclear transfer (SCNT) embryos with reprogramming defects fail to develop. Thus, we compared DNA methylation reprogramming in preimplantation embryos from bovine SCNT and in vitro fertilization (IVF) and analyzed the influence of vitamin C (VC) on the reprogramming of DNA methylation. The results showed that global DNA methylation followed a typical pattern of demethylation and remethylation in IVF preimplantation embryos; however, the global genome remained hypermethylated in SCNT preimplantation embryos. Compared with the IVF group, locus DNA methylation reprogramming showed three patterns in the SCNT group. First, some pluripotency genes (POU5F1 and NANOG) and repeated elements (satellite I and α-satellite) showed insufficient demethylation and hypermethylation in the SCNT group. Second, a differentially methylated region (DMR) of an imprint control region (ICR) in H19 exhibited excessive demethylation and hypomethylation. Third, some pluripotency genes (CDX2 and SOX2) were hypomethylated in both the IVF and SCNT groups. Additionally, VC improved the DNA methylation reprogramming of satellite I, α-satellite and H19 but not that of POU5F1 and NANOG in SCNT preimplantation embryos. These results indicate that DNA methylation reprogramming was aberrant and that VC influenced DNA methylation reprogramming in SCNT embryos in a locus-specific manner. PMID:27456302

  9. Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease

    PubMed Central

    Gilsbach, Ralf; Preissl, Sebastian; Grüning, Björn A.; Schnick, Tilman; Burger, Lukas; Benes, Vladimir; Würch, Andreas; Bönisch, Ulrike; Günther, Stefan; Backofen, Rolf; Fleischmann, Bernd K.; Schübeler, Dirk; Hein, Lutz

    2014-01-01

    The heart is a highly specialized organ with essential function for the organism throughout life. The significance of DNA methylation in shaping the phenotype of the heart remains only partially known. Here we generate and analyse DNA methylomes from highly purified cardiomyocytes of neonatal, adult healthy and adult failing hearts. We identify large genomic regions that are differentially methylated during cardiomyocyte development and maturation. Demethylation of cardiomyocyte gene bodies correlates strongly with increased gene expression. Silencing of demethylated genes is characterized by the polycomb mark H3K27me3 or by DNA methylation. De novo methylation by DNA methyltransferases 3A/B causes repression of fetal cardiac genes, including essential components of the cardiac sarcomere. Failing cardiomyocytes partially resemble neonatal methylation patterns. This study establishes DNA methylation as a highly dynamic process during postnatal growth of cardiomyocytes and their adaptation to pathological stress in a process tightly linked to gene regulation and activity. PMID:25335909

  10. Lysine methylation regulates the pRb tumour suppressor protein.

    PubMed

    Munro, S; Khaire, N; Inche, A; Carr, S; La Thangue, N B

    2010-04-22

    The pRb tumour suppressor protein has a central role in coordinating early cell cycle progression. An important level of control imposed on pRb occurs through post-translational modification, for example, phosphorylation. We describe here a new level of regulation on pRb, mediated through the targeted methylation of lysine residues, by the methyltransferase Set7/9. Set7/9 methylates the C-terminal region of pRb, both in vitro and in cells, and methylated pRb interacts with heterochromatin protein HP1. pRb methylation is required for pRb-dependent cell cycle arrest and transcriptional repression, as well as pRb-dependent differentiation. Our results indicate that methylation can influence the properties of pRb, and raise the interesting possibility that methylation modulates pRb tumour suppressor activity.

  11. Detection of DNA Methylation by Whole-Genome Bisulfite Sequencing.

    PubMed

    Li, Qing; Hermanson, Peter J; Springer, Nathan M

    2018-01-01

    DNA methylation plays an important role in the regulation of the expression of transposons and genes. Various methods have been developed to assay DNA methylation levels. Bisulfite sequencing is considered to be the "gold standard" for single-base resolution measurement of DNA methylation levels. Coupled with next-generation sequencing, whole-genome bisulfite sequencing (WGBS) allows DNA methylation to be evaluated at a genome-wide scale. Here, we described a protocol for WGBS in plant species with large genomes. This protocol has been successfully applied to assay genome-wide DNA methylation levels in maize and barley. This protocol has also been successfully coupled with sequence capture technology to assay DNA methylation levels in a targeted set of genomic regions.

  12. Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease.

    PubMed

    Gilsbach, Ralf; Preissl, Sebastian; Grüning, Björn A; Schnick, Tilman; Burger, Lukas; Benes, Vladimir; Würch, Andreas; Bönisch, Ulrike; Günther, Stefan; Backofen, Rolf; Fleischmann, Bernd K; Schübeler, Dirk; Hein, Lutz

    2014-10-22

    The heart is a highly specialized organ with essential function for the organism throughout life. The significance of DNA methylation in shaping the phenotype of the heart remains only partially known. Here we generate and analyse DNA methylomes from highly purified cardiomyocytes of neonatal, adult healthy and adult failing hearts. We identify large genomic regions that are differentially methylated during cardiomyocyte development and maturation. Demethylation of cardiomyocyte gene bodies correlates strongly with increased gene expression. Silencing of demethylated genes is characterized by the polycomb mark H3K27me3 or by DNA methylation. De novo methylation by DNA methyltransferases 3A/B causes repression of fetal cardiac genes, including essential components of the cardiac sarcomere. Failing cardiomyocytes partially resemble neonatal methylation patterns. This study establishes DNA methylation as a highly dynamic process during postnatal growth of cardiomyocytes and their adaptation to pathological stress in a process tightly linked to gene regulation and activity.

  13. Evaluation of the Naturally Acquired Antibody Immune Response to the Pv200L N-terminal Fragment of Plasmodium vivax Merozoite Surface Protein-1 in Four Areas of the Amazon Region of Brazil

    PubMed Central

    Storti-Melo, Luciane M.; Souza-Neiras, Wanessa C.; Cassiano, Gustavo C.; Taveira, Leonardo C.; Cordeiro, Antônio J.; Couto, Vanja S. C. A.; Póvoa, Marinete M.; Cunha, Maristela G.; Echeverry, Diana M.; Rossit, Andréa R. B.; Arévalo-Herrera, Myriam; Herrera, Sócrates; Machado, Ricardo L. D.

    2011-01-01

    Frequency and levels of IgG antibodies to an N-terminal fragment of the Plasmodium vivax MSP-1 (Pv200L) protein, in individuals naturally exposed to malaria in four endemic areas of Brazil, were evaluated by enzyme-linked immunosorbent assay. Plasma samples of 261 P. vivax-infected individuals from communities of Macapá, Novo Repartimento, Porto Velho, and Plácido de Castro in the Amazonian region with different malaria transmission intensities. A high mean number of studied individuals (89.3%) presented with antibodies to the Pv200L that correlated with the number of previous malaria infections; there were significant differences in the frequency of the responders (71.9–98.7) and in the antibody levels (1:200–1:51,200) among the four study areas. Results of this study provide evidence that Pv200L is a naturally immunogenic fragment of the PvMSP-1 and is associated with the degree of exposure to parasites. The fine specificity of antibodies to Pv200L is currently being assessed. PMID:21292879

  14. DNA methylation and differentiation.

    PubMed Central

    Michalowsky, L A; Jones, P A

    1989-01-01

    The methylation of specific cytosine residues in DNA has been implicated in regulating gene expression and facilitating functional specialization of cellular phenotypes. Generally, the demethylation of certain CpG sites correlates with transcriptional activation of genes. 5-Azacytidine is an inhibitor of DNA methylation and has been widely used as a potent activator of suppressed genetic information. Treatment of cells with 5-azacytidine results in profound phenotypic alterations. The drug-induced hypomethylation of DNA apparently perturbs DNA-protein interactions that may consequently alter transcriptional activity and cell determination. The inhibitory effect of cytosine methylation may be exerted via altered DNA-protein interactions specifically or may be transduced by a change in the conformation of chromatin. Recent studies have demonstrated that cytosine methylation also plays a central role in parental imprinting, which in turn determines the differential expression of maternal and paternal genomes during embryogenesis. In other words, methylation is the mechanism whereby the embryo retains memory of the gametic origin of each component of genetic information. A memory of this type would probably persist during DNA replication and cell division as methylation patterns are stable and heritable. PMID:2466640

  15. Structural and spectroscopic characterization of methyl isocyanate, methyl cyanate, methyl fulminate, and acetonitrile N-oxide using highly correlated ab initio methods.

    PubMed

    Dalbouha, S; Senent, M L; Komiha, N; Domínguez-Gómez, R

    2016-09-28

    Various astrophysical relevant molecules obeying the empirical formula C2H3NO are characterized using explicitly correlated coupled cluster methods (CCSD(T)-F12). Rotational and rovibrational parameters are provided for four isomers: methyl isocyanate (CH3NCO), methyl cyanate (CH3OCN), methyl fulminate (CH3ONC), and acetonitrile N-oxide (CH3CNO). A CH3CON transition state is inspected. A variational procedure is employed to explore the far infrared region because some species present non-rigidity. Second order perturbation theory is used for the determination of anharmonic frequencies, rovibrational constants, and to predict Fermi resonances. Three species, methyl cyanate, methyl fulminate, and CH3CON, show a unique methyl torsion hindered by energy barriers. In methyl isocyanate, the methyl group barrier is so low that the internal top can be considered a free rotor. On the other hand, acetonitrile N-oxide presents a linear skeleton, C3v symmetry, and free internal rotation. Its equilibrium geometry depends strongly on electron correlation. The remaining isomers present a bend skeleton. Divergences between theoretical rotational constants and previous parameters fitted from observed lines for methyl isocyanate are discussed on the basis of the relevant rovibrational interaction and the quasi-linearity of the molecular skeleton.

  16. Structural and spectroscopic characterization of methyl isocyanate, methyl cyanate, methyl fulminate, and acetonitrile N-oxide using highly correlated ab initio methods

    NASA Astrophysics Data System (ADS)

    Dalbouha, S.; Senent, M. L.; Komiha, N.; Domínguez-Gómez, R.

    2016-09-01

    Various astrophysical relevant molecules obeying the empirical formula C2H3NO are characterized using explicitly correlated coupled cluster methods (CCSD(T)-F12). Rotational and rovibrational parameters are provided for four isomers: methyl isocyanate (CH3NCO), methyl cyanate (CH3OCN), methyl fulminate (CH3ONC), and acetonitrile N-oxide (CH3CNO). A CH3CON transition state is inspected. A variational procedure is employed to explore the far infrared region because some species present non-rigidity. Second order perturbation theory is used for the determination of anharmonic frequencies, rovibrational constants, and to predict Fermi resonances. Three species, methyl cyanate, methyl fulminate, and CH3CON, show a unique methyl torsion hindered by energy barriers. In methyl isocyanate, the methyl group barrier is so low that the internal top can be considered a free rotor. On the other hand, acetonitrile N-oxide presents a linear skeleton, C3v symmetry, and free internal rotation. Its equilibrium geometry depends strongly on electron correlation. The remaining isomers present a bend skeleton. Divergences between theoretical rotational constants and previous parameters fitted from observed lines for methyl isocyanate are discussed on the basis of the relevant rovibrational interaction and the quasi-linearity of the molecular skeleton.

  17. The methylation status of plant genomic DNA influences PCR efficiency.

    PubMed

    Kiselev, K V; Dubrovina, A S; Tyunin, A P

    2015-03-01

    During the polymerase chain reaction (PCR), which is a versatile and widely used method, certain DNA sequences are rapidly amplified through thermocycling. Although there are numerous protocols of PCR optimization for different applications, little is known about the effect of DNA modifications, such as DNA methylation, on PCR efficiency. Recent studies show that cytosine methylation alters DNA mechanical properties and suggest that DNA methylation may directly or indirectly influence the effectiveness of DNA amplification during PCR. In the present study, using plant DNA, we found that highly methylated plant DNA genomic regions were amplified with lower efficiencies compared to that for the regions methylated at a lower level. The correlation was observed when amplifying stilbene synthase (STS1, STS10) genes of Vitis amurensis, the Actin2 gene of Arabidopsis thaliana, the internal transcribed spacer (AtITS), and tRNAPro of A. thaliana. The level of DNA methylation within the analyzed DNA regions has been analyzed with bisulfite sequencing. The obtained data show that efficient PCRs of highly methylated plant DNA regions can be hampered. Proteinase K treatment of the plant DNA prior to PCR and using HotTaq DNA polymerase improved amplification of the highly methylated plant DNA regions. We suggest that increased DNA denaturation temperatures of the highly methylated DNA and contamination with DNA-binding proteins contribute to the hampered PCR amplification of highly methylated DNA. The data show that it is necessary to use current DNA purification protocols and commercial kits with caution to ensure appropriate PCR product yield and prevent bias toward unmethylated DNA amplification in PCRs. Copyright © 2014 Elsevier GmbH. All rights reserved.

  18. Acquired dorsal intraspinal epidermoid cyst in an adult female

    PubMed Central

    Singh, Kulwant; Pandey, Sharad; Gupta, Praveen Kumar; Sharma, Vivek; Santhosh, Deepa; Ghosh, Amrita

    2016-01-01

    Background: Epidermoid and dermoid cyst comprise <1% of spinal tumors and may be congenital (hamartoma) or acquired (iatrogenic) in origin. Epidermoid cysts within the neuraxis are rare benign neoplasms that are most commonly located in the intracranial region. Case Description: Here, we report the a case of an acquired intradural extramedullary epidermoid cyst involving the thoracic region in an adult female who had no associated history of an accompanying congenital spinal deformity. Conclusion: Early diagnosis and immediate surgical intervention reduce patient morbidity. Near complete or subtotal excision of the cyst wall is warranted to prevent inadvertent injury to the spinal cord thus minimizing neurological morbidity. PMID:26904369

  19. SNP-based prediction of the human germ cell methylation landscape.

    PubMed

    Xie, Hehuang; Wang, Min; Bischof, Jared; Bonaldo, Maria de Fatima; Soares, Marcelo Bento

    2009-05-01

    Base substitution occurs at a high rate at CpG dinucleotides due to the frequent methylation of CpG and the deamination of methylated cytosine to thymine. If these substitutions occur in germ cells, they constitute a heritable mutation that may eventually rise to polymorphic frequencies, hence resulting in a SNP that is methylation associated. In this study, we sought to identify clusters of methylation associated SNPs as a basis for prediction of methylation landscapes of germ cell genomes. Genomic regions enriched with methylation associated SNPs, namely "methylation associated SNP clusters", were identified with an agglomerative hierarchical clustering algorithm. Repetitive elements, segmental duplications, and syntenic tandem DNA repeats were enriched in methylation associated SNP clusters. The frequency of methylation associated SNPs in Alu Y/S elements exhibited a gradient pattern suggestive of linear spreading, being higher in proximity to methylation associated SNP clusters and lower closer to CpG islands. Interestingly, methylation associated SNP clusters were over-represented near the transcriptional initiation sites of immune response genes. We propose a de novo DNA methylation model during germ cell development whereby a pattern is established by long-range chromatic interactions through syntenic repeats combined with regional methylation spreading from methylation associated SNP clusters.

  20. Perinatal high methyl donor alters gene expression in IGF system in male offspring without altering DNA methylation

    PubMed Central

    Amarger, Valérie; Giudicelli, Fanny; Pagniez, Anthony; Parnet, Patricia

    2017-01-01

    Aim: To investigate the effect of a protein restriction and a supplementation with methyl donor nutrients during fetal and early postnatal life on the expression and epigenetic state of imprinted genes from the IGF system. Materials & methods: Pregnant female rats were fed a protein-restricted diet supplemented or not with methyl donor. Results: Gene expression of the Igf2, H19, Igf1, Igf2r and Plagl1 genes in the liver of male offspring at birth and weaning was strongly influenced by maternal diet. Whereas the methylation profiles of the Igf2, H19 and Igf2r genes were remarkably stable, DNA methylation of Plagl1 promoter was slightly modified. Conclusion: DNA methylation of most, but not all, imprinted gene regulatory regions was resistant to methyl group nutritional supply. PMID:28344827

  1. Perinatal high methyl donor alters gene expression in IGF system in male offspring without altering DNA methylation.

    PubMed

    Amarger, Valérie; Giudicelli, Fanny; Pagniez, Anthony; Parnet, Patricia

    2017-03-01

    To investigate the effect of a protein restriction and a supplementation with methyl donor nutrients during fetal and early postnatal life on the expression and epigenetic state of imprinted genes from the IGF system. Pregnant female rats were fed a protein-restricted diet supplemented or not with methyl donor. Gene expression of the Igf2, H19, Igf1, Igf2r and Plagl1 genes in the liver of male offspring at birth and weaning was strongly influenced by maternal diet. Whereas the methylation profiles of the Igf2, H19 and Igf2r genes were remarkably stable, DNA methylation of Plagl1 promoter was slightly modified. DNA methylation of most, but not all, imprinted gene regulatory regions was resistant to methyl group nutritional supply.

  2. Community-Acquired Pneumonia in Latin America.

    PubMed

    Iannella, Hernán A; Luna, Carlos M

    2016-12-01

    Community-acquired pneumonia (CAP) is associated with significant morbidity and mortality in Latin America and the Caribbean (LAC) region. Poverty, socioeconomic factors, and malnutrition influence the incidence and outcome of CAP in LAC. In LAC, Streptococcus pneumoniae is the most frequent microorganism responsible for CAP, (incidence: 24-78%); the incidence of atypical microorganisms is similar to other regions of the world. Human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) is a growing problem in the LAC region, with the Caribbean being the second most affected area worldwide after Sub-Saharan Africa. Pneumococcal pneumonia remains the most common cause of CAP in HIV-infected patients, but Pneumocystis jirovecii and tuberculosis (TB) are also common in this population. The heterogeneity of the health care systems and social inequity between different countries in LAC, and even between different settings inside the same country, is a difficult issue. TB, including multidrug-resistant TB, is several times more common in South American and Central American countries compared with North America. Furthermore, hantaviruses circulating in the Americas (new world hantaviruses) generate a severe respiratory disease called hantavirus pulmonary syndrome, with an associated mortality as high as 50%. More than 30 hantaviruses have been reported in the Western Hemisphere, with more frequent cases registered in the southern cone (Argentina, Chile, Uruguay, Paraguay, Bolivia, and Brazil). Respiratory viruses (particularly influenza) remain an important cause of morbidity and mortality, particularly in the elderly. Low rates of vaccination (against influenza as well as pneumococcus) may heighten the risk of these infections in low- and middle-income countries. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  3. Asymmetric DNA methylation of CpG dyads is a feature of secondary DMRs associated with the Dlk1/Gtl2 imprinting cluster in mouse.

    PubMed

    Guntrum, Megan; Vlasova, Ekaterina; Davis, Tamara L

    2017-01-01

    Differential DNA methylation plays a critical role in the regulation of imprinted genes. The differentially methylated state of the imprinting control region is inherited via the gametes at fertilization, and is stably maintained in somatic cells throughout development, influencing the expression of genes across the imprinting cluster. In contrast, DNA methylation patterns are more labile at secondary differentially methylated regions which are established at imprinted loci during post-implantation development. To investigate the nature of these more variably methylated secondary differentially methylated regions, we adopted a hairpin linker bisulfite mutagenesis approach to examine CpG dyad methylation at differentially methylated regions associated with the murine Dlk1/Gtl2 imprinting cluster on both complementary strands. We observed homomethylation at greater than 90% of the methylated CpG dyads at the IG-DMR, which serves as the imprinting control element. In contrast, homomethylation was only observed at 67-78% of the methylated CpG dyads at the secondary differentially methylated regions; the remaining 22-33% of methylated CpG dyads exhibited hemimethylation. We propose that this high degree of hemimethylation could explain the variability in DNA methylation patterns at secondary differentially methylated regions associated with imprinted loci. We further suggest that the presence of 5-hydroxymethylation at secondary differentially methylated regions may result in hemimethylation and methylation variability as a result of passive and/or active demethylation mechanisms.

  4. Vibration and DFT analysis of 2-methyl-3-nitrophenyl isocyanate and 4-methyl-2-nitrophenyl isocyanate.

    PubMed

    Tonannavar, J; Prasannakumar, Sushanti; Savanur, J; Yenagi, Jayashree

    2012-09-01

    Vibrational spectra of 2-methyl-3-nitrophenyl isocyanate and 4-methyl-2-nitrophenyl isocyanate, in the spectral region 4000-100 cm(-1), have been measured and assigned. Conformational and harmonic frequency analyses have been performed at B3LYP/6-311G(∗) level of calculations. The two stable conformers, cis and trans, have been computed for each of the molecules. It has been determined that the trans conformer has lower energy than the cis by 3.954 kJ/mol for 2-methyl-3-nitrophenyl isocyanate; whereas the cis conformer has lower energy than the trans by 10.230 kJ/mol for 4-methyl-2-nitrophenyl isocyanate. The vibration structure of 2-methyl-3-nitrophenyl isocyanate conforms to the combined behavior of its both conformers from which the deviation is shown by the structure of 4-methyl-2-nitrophenyl isocyanate which follows only the trans conformer. The occurrence of symmetric mode of the methyl group at higher frequency near 2944-20 cm(-1) is attributed to the phenyl ring strain caused by the substituents. As for the other stretching and bending modes, mutually exclusive pattern appears to work for the molecules: The nitro group's non-coplanarity with the phenyl ring is more evident in 4-methyl-2-nitrophenyl isocyanate where the asymmetric mode was assigned to the band at 1569cm(-1), whereas the symmetric mode at lower frequency 1339cm(-1). Occasional doublet appearance of the strong asymmetric absorption near 2282cm(-1) due to isocyanate moiety has been observed in the present study and is assumed to arise from the torsional vibration motion of the moiety rendered by the small energy gap between the conformers of 2-methyl-3-nitrophenyl isocyanate.

  5. 40 CFR 180.451 - Tribenuron methyl; tolerances for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... residues of the herbicide tribenuron methyl and its metabolites and degradates in or on the commodities in.... Tolerances with regional registration, as defined in § 180.1(n) are established for residues of the herbicide...

  6. 40 CFR 180.451 - Tribenuron methyl; tolerances for residues.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... residues of the herbicide tribenuron methyl and its metabolites and degradates in or on the commodities in.... Tolerances with regional registration, as defined in § 180.1(l) are established for residues of the herbicide...

  7. 40 CFR 180.451 - Tribenuron methyl; tolerances for residues.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... residues of the herbicide tribenuron methyl and its metabolites and degradates in or on the commodities in.... Tolerances with regional registration, as defined in § 180.1(l) are established for residues of the herbicide...

  8. 40 CFR 180.451 - Tribenuron methyl; tolerances for residues.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... residues of the herbicide tribenuron methyl and its metabolites and degradates in or on the commodities in.... Tolerances with regional registration, as defined in § 180.1(l) are established for residues of the herbicide...

  9. 40 CFR 180.451 - Tribenuron methyl; tolerances for residues.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... residues of the herbicide tribenuron methyl and its metabolites and degradates in or on the commodities in.... Tolerances with regional registration, as defined in § 180.1(l) are established for residues of the herbicide...

  10. Acquired Upper Extremity Growth Arrest.

    PubMed

    Gauger, Erich M; Casnovsky, Lauren L; Gauger, Erica J; Bohn, Deborah C; Van Heest, Ann E

    2017-01-01

    This study reviewed the clinical history and management of acquired growth arrest in the upper extremity in pediatric patients. The records of all patients presenting from 1996 to 2012 with radiographically proven acquired growth arrest were reviewed. Records were examined to determine the etiology and site of growth arrest, management, and complications. Patients with tumors or hereditary etiology were excluded. A total of 44 patients (24 boys and 20 girls) with 51 physeal arrests who presented at a mean age of 10.6 years (range, 0.8-18.2 years) were included in the study. The distal radius was the most common site (n=24), followed by the distal humerus (n=8), metacarpal (n=6), distal ulna (n=5), proximal humerus (n=4), radial head (n=3), and olecranon (n=1). Growth arrest was secondary to trauma (n=22), infection (n=11), idiopathy (n=6), inflammation (n=2), compartment syndrome (n=2), and avascular necrosis (n=1). Twenty-six patients (59%) underwent surgical intervention to address deformity caused by the physeal arrest. Operative procedures included ipsilateral unaffected bone epiphysiodesis (n=21), shortening osteotomy (n=10), lengthening osteotomy (n=8), excision of physeal bar or bone fragment (n=2), angular correction osteotomy (n=1), and creation of single bone forearm (n=1). Four complications occurred; 3 of these required additional procedures. Acquired upper extremity growth arrest usually is caused by trauma or infection, and the most frequent site is the distal radius. Growth disturbances due to premature arrest can be treated effectively with epiphysiodesis or osteotomy. In this series, the specific site of anatomic growth arrest was the primary factor in determining treatment. [Orthopedics. 2017; 40(1):e95-e103.]. Copyright 2016, SLACK Incorporated.

  11. 49 CFR 173.193 - Bromoacetone, methyl bromide, chloropicrin and methyl bromide or methyl chloride mixtures, etc.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... methyl bromide or methyl chloride mixtures, etc. 173.193 Section 173.193 Transportation Other Regulations... bromide, chloropicrin and methyl bromide or methyl chloride mixtures, etc. (a) Bromoacetone must be...) Bromoacetone, methyl bromide, chloropicrin and methyl bromide mixtures, chloropicrin and methyl...

  12. 49 CFR 173.193 - Bromoacetone, methyl bromide, chloropicrin and methyl bromide or methyl chloride mixtures, etc.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... methyl bromide or methyl chloride mixtures, etc. 173.193 Section 173.193 Transportation Other Regulations... bromide, chloropicrin and methyl bromide or methyl chloride mixtures, etc. (a) Bromoacetone must be...) Bromoacetone, methyl bromide, chloropicrin and methyl bromide mixtures, chloropicrin and methyl...

  13. Ribosomal RNA methylation in Staphylococcus aureus and Escherichia coli: effect of the "MLS" (erythromycin resistance) methylase.

    PubMed

    Thakker-Varia, S; Ranzini, A C; Dubin, D T

    1985-09-01

    Classical acquired resistance to erythromycin in Staphylococcus aureus ("MLS," or macrolide-lincosamide-streptogramin, resistance) was shown by Weisblum and colleagues to be a direct consequence of the conversion of one or more adenosine residues of 23S rRNA, within the subsequence(s) GA3G, to N6-dimethyladenosine (m62A). The methylation reaction is effected by a class of methylase, whose genes are typically plasmid- or transposon-associated, and whose synthesis is inducible by erythromycin. Using a recently obtained clinical MLS isolate of S. aureus, we have further defined the methylation locus as YGG X m62A X AAGAC; and have shown that this subsequence occurs once in the 23S RNA and that it is essentially completely methylated in all copies of 23S RNA that accumulate in induced cultures. Similar findings were obtained with laboratory S. aureus strains containing two well-characterized evolutionary variants (ermB, ermC) of MLS methylase genes. Analyses of a strain of E. coli containing the ermC gene indicated that the specificity of the methylase gene was unchanged, but that its expression was muted. Even after prolonged periods of induction, the strain manifested only partial resistance to erythromycin, and only about one-third of the copies of the MLS subsequence were methylated in such "induced" cultures. Since the E. coli 23S RNA sequence is known in its entirety, localization of the MLS subsequence is in this case unambiguous; as inferred by homology arguments applied earlier to the S. aureus data, the subsequence is in a highly conserved region of 23S RNA considered to contribute to the peptidyl transferase center of the ribosome.

  14. Software for Acquiring Image Data for PIV

    NASA Technical Reports Server (NTRS)

    Wernet, Mark P.; Cheung, H. M.; Kressler, Brian

    2003-01-01

    PIV Acquisition (PIVACQ) is a computer program for acquisition of data for particle-image velocimetry (PIV). In the PIV system for which PIVACQ was developed, small particles entrained in a flow are illuminated with a sheet of light from a pulsed laser. The illuminated region is monitored by a charge-coupled-device camera that operates in conjunction with a data-acquisition system that includes a frame grabber and a counter-timer board, both installed in a single computer. The camera operates in "frame-straddle" mode where a pair of images can be obtained closely spaced in time (on the order of microseconds). The frame grabber acquires image data from the camera and stores the data in the computer memory. The counter/timer board triggers the camera and synchronizes the pulsing of the laser with acquisition of data from the camera. PIVPROC coordinates all of these functions and provides a graphical user interface, through which the user can control the PIV data-acquisition system. PIVACQ enables the user to acquire a sequence of single-exposure images, display the images, process the images, and then save the images to the computer hard drive. PIVACQ works in conjunction with the PIVPROC program which processes the images of particles into the velocity field in the illuminated plane.

  15. Perioperatively acquired disorders of coagulation

    PubMed Central

    Grottke, Oliver; Fries, Dietmar; Nascimento, Bartolomeu

    2015-01-01

    Purpose of review To provide an overview of acquired coagulopathies that can occur in various perioperative clinical settings. Also described are coagulation disturbances linked to antithrombotic medications and currently available strategies to reverse their antithrombotic effects in situations of severe hemorrhage. Recent findings Recent studies highlight the link between low fibrinogen and decreased fibrin polymerization in the development of acquired coagulopathy. Particularly, fibrin(ogen) deficits are observable after cardiopulmonary bypass in cardiac surgery, on arrival at the emergency room in trauma patients, and with ongoing bleeding after child birth. Regarding antithrombotic therapy, although new oral anticoagulants offer the possibility of efficacy and relative safety compared with vitamin K antagonists, reversal of their anticoagulant effect with nonspecific agents, including prothrombin complex concentrate, has provided conflicting results. Specific antidotes, currently being developed, are not yet licensed for clinical use, but initial results are promising. Summary Targeted hemostatic therapy aims to correct coagulopathies in specific clinical settings, and reduce the need for allogeneic transfusions, thus preventing massive transfusion and its deleterious outcomes. Although there are specific guidelines for reversing anticoagulation in patients treated with antiplatelet agents or warfarin, there is currently little evidence to advocate comprehensive recommendations to treat drug-induced coagulopathy associated with new oral anticoagulants. PMID:25734869

  16. WAYS OF ACQUIRING FLYING PHOBIA.

    PubMed

    Schindler, Bettina; Vriends, Noortje; Margraf, Jürgen; Stieglitz, Rolf-Dieter

    2016-02-01

    The few studies that have explored how flying phobia is acquired have produced contradictory results. We hypothesized that classical conditioning plays a role in acquiring flying phobia and investigated if vicarious (model) learning, informational learning through media, and experiencing stressful life events at the time of onset of phobia also play a role. Thirty patients with flying phobia and thirty healthy controls matched on age, sex, and education were interviewed with the Mini-DIPS, the short German version of the Anxiety Disorders Interview Schedule (DSM-IV diagnostic criteria) and the Fear-of-Flying History Interview. Fifty Percent of patients with flying phobia and 53% of healthy controls reported frightening events in the air. There was no significant difference between the two samples. Thus there were not more classical conditioning events for patients with flying phobia. There also was no significant difference between the two samples for vicarious (model) learning: 37% of flying phobia patients and 23% of healthy controls felt influenced by model learning. The influence of informational learning through media was significantly higher for the clinical sample (70%) than for the control group (37%). Patients with flying phobia experienced significantly more stressful life events in the period of their frightening flight experience (60%) than healthy controls (19%). Frightening experiences while flying are quite common, but not everybody develops a flying phobia. Stressful life events and other factors might enhance conditionability. Informational learning through negative media reports probably reinforces the development of flying phobia. Clinical implications are discussed. © 2015 Wiley Periodicals, Inc.

  17. Foodborne listeriosis acquired in hospitals.

    PubMed

    Silk, Benjamin J; McCoy, Morgan H; Iwamoto, Martha; Griffin, Patricia M

    2014-08-15

    Listeriosis is characterized by bacteremia or meningitis. We searched for listeriosis case series and outbreak investigations published in English by 2013, and assessed the strength of evidence for foodborne acquisition among patients who ate hospital food. We identified 30 reports from 13 countries. Among the case series, the median proportion of cases considered to be hospital-acquired was 25% (range, 9%-67%). The median number of outbreak-related illnesses considered to be hospital-acquired was 4.0 (range, 2-16). All patients were immunosuppressed in 18 of 24 (75%) reports with available data. Eight outbreak reports with strong evidence for foodborne acquisition in a hospital implicated sandwiches (3 reports), butter, precut celery, Camembert cheese, sausage, and tuna salad (1 report each). Foodborne acquisition of listeriosis among hospitalized patients is well documented internationally. The number of listeriosis cases could be reduced substantially by establishing hospital policies for safe food preparation for immunocompromised patients and by not serving them higher-risk foods.

  18. [Psychosocial aspects of acquired immunodeficiency syndrome].

    PubMed

    de Moura, L; Jacquemin, A

    1991-04-01

    Psychosocial aspects which arise with regard to people directly or indirectly involved with AIDS: patients, relatives and professional staff, are studied. The results show that the population assisted in the Ribeirão Preto region is predominantly young, male and drug-addicted. The patients with "positive" results show reactions similar to those described by Kluber-Ross (1977) for terminal patients. The behavior observed in relatives forms a continuum which varies from the negation of the illness to the overprotection of the patient. For the professionals, perplexity is the most common reaction when they face a population which is different from that with which they are used to dealing. Finally, the data acquired indicate that the psychologist can help the professionals to deal with the reactions of the patients by integrating them into their organic and emotional aspects.

  19. Modeling of the oxidation of methyl esters - Validation for methyl hexanoate, methyl heptanoate, and methyl decanoate in a jet-stirred reactor

    SciTech Connect

    Glaude, Pierre Alexandre; Herbinet, Olivier; Bax, Sarah; Biet, Joffrey; Warth, Valerie; Battin-Leclerc, Frederique

    2010-11-15

    The modeling of the oxidation of methyl esters was investigated and the specific chemistry, which is due to the presence of the ester group in this class of molecules, is described. New reactions and rate parameters were defined and included in the software EXGAS for the automatic generation of kinetic mechanisms. Models generated with EXGAS were successfully validated against data from the literature (oxidation of methyl hexanoate and methyl heptanoate in a jet-stirred reactor) and a new set of experimental results for methyl decanoate. The oxidation of this last species was investigated in a jet-stirred reactor at temperatures from 500 to 1100 K, including the negative temperature coefficient region, under stoichiometric conditions, at a pressure of 1.06 bar and for a residence time of 1.5 s: more than 30 reaction products, including olefins, unsaturated esters, and cyclic ethers, were quantified and successfully simulated. Flow rate analysis showed that reactions pathways for the oxidation of methyl esters in the low-temperature range are similar to that of alkanes. (author)

  20. CGGBP1 mitigates cytosine methylation at repetitive DNA sequences.

    PubMed

    Agarwal, Prasoon; Collier, Paul; Fritz, Markus Hsi-Yang; Benes, Vladimir; Wiklund, Helena Jernberg; Westermark, Bengt; Singh, Umashankar

    2015-05-16

    CGGBP1 is a repetitive DNA-binding transcription regulator with target sites at CpG-rich sequences such as CGG repeats and Alu-SINEs and L1-LINEs. The role of CGGBP1 as a possible mediator of CpG methylation however remains unknown. At CpG-rich sequences cytosine methylation is a major mechanism of transcriptional repression. Concordantly, gene-rich regions typically carry lower levels of CpG methylation than the repetitive elements. It is well known that at interspersed repeats Alu-SINEs and L1-LINEs high levels of CpG methylation constitute a transcriptional silencing and retrotransposon inactivating mechanism. Here, we have studied genome-wide CpG methylation with or without CGGBP1-depletion. By high throughput sequencing of bisulfite-treated genomic DNA we have identified CGGBP1 to be a negative regulator of CpG methylation at repetitive DNA sequences. In addition, we have studied CpG methylation alterations on Alu and L1 retrotransposons in CGGBP1-depleted cells using a novel bisulfite-treatment and high throughput sequencing approach. The results clearly show that CGGBP1 is a possible bidirectional regulator of CpG methylation at Alus, and acts as a repressor of methylation at L1 retrotransposons.

  1. Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA.

    PubMed

    Osakabe, Akihisa; Adachi, Fumiya; Arimura, Yasuhiro; Maehara, Kazumitsu; Ohkawa, Yasuyuki; Kurumizaka, Hitoshi

    2015-10-01

    DNA methylation occurs on CpG sites and is important to form pericentric heterochromatin domains. The satellite 2 sequence, containing seven CpG sites, is located in the pericentric region of human chromosome 1 and is highly methylated in normal cells. In contrast, the satellite 2 region is reportedly hypomethylated in cancer cells, suggesting that the methylation status may affect the chromatin structure around the pericentric regions in tumours. In this study, we mapped the nucleosome positioning on the satellite 2 sequence in vitro and found that DNA methylation modestly affects the distribution of the nucleosome positioning. The micrococcal nuclease assay revealed that the DNA end flexibility of the nucleosomes changes, depending on the DNA methylation status. However, the structures and thermal stabilities of the nucleosomes are unaffected by DNA methylation. These findings provide new information to understand how DNA methylation functions in regulating pericentric heterochromatin formation and maintenance in normal and malignant cells.

  2. Management of Travel-Related Illness Acquired in Haiti.

    PubMed

    Walters, Michele

    2015-12-01

    Management of travel-related diseases acquired in Haiti begins with the identification of tropical diseases that are prevalent in the region. Knowledge of various tropical disease incubation periods and presenting symptoms is crucial to ensure rapid triage and management of care.

  3. DNA Methylation is Developmentally Regulated for Genes Essential for Cardiogenesis

    PubMed Central

    Chamberlain, Alyssa A.; Lin, Mingyan; Lister, Rolanda L.; Maslov, Alex A.; Wang, Yidong; Suzuki, Masako; Wu, Bingruo; Greally, John M.; Zheng, Deyou; Zhou, Bin

    2014-01-01

    Background DNA methylation is a major epigenetic mechanism altering gene expression in development and disease. However, its role in the regulation of gene expression during heart development is incompletely understood. The aim of this study is to reveal DNA methylation in mouse embryonic hearts and its role in regulating gene expression during heart development. Methods and Results We performed the genome‐wide DNA methylation profiling of mouse embryonic hearts using methyl‐sensitive, tiny fragment enrichment/massively parallel sequencing to determine methylation levels at ACGT sites. The results showed that while global methylation of 1.64 million ACGT sites in developing hearts remains stable between embryonic day (E) 11.5 and E14.5, a small fraction (2901) of them exhibit differential methylation. Gene Ontology analysis revealed that these sites are enriched at genes involved in heart development. Quantitative real‐time PCR analysis of 350 genes with differential DNA methylation showed that the expression of 181 genes is developmentally regulated, and 79 genes have correlative changes between methylation and expression, including hyaluronan synthase 2 (Has2). Required for heart valve formation, Has2 expression in the developing heart valves is downregulated at E14.5, accompanied with increased DNA methylation in its enhancer. Genetic knockout further showed that the downregulation of Has2 expression is dependent on DNA methyltransferase 3b, which is co‐expressed with Has2 in the forming heart valve region, indicating that the DNA methylation change may contribute to the Has2 enhancer's regulating function. Conclusions DNA methylation is developmentally regulated for genes essential to heart development, and abnormal DNA methylation may contribute to congenital heart disease. PMID:24947998

  4. Self-reported smoking, serum cotinine, and blood DNA methylation.

    PubMed

    Zhang, Yan; Florath, Ines; Saum, Kai-Uwe; Brenner, Hermann

    2016-04-01

    Epigenome-wide profiling of DNA methylation pattern with respect to tobacco smoking has given rise to a new measure of smoking exposure. We investigated the relationships of methylation markers with both cotinine, an established marker of internal smoking exposure, and self-reported smoking. Blood DNA methylation levels across the genome and serum cotinine were measured in 1000 older adults aged 50-75 years. Epigenome-wide scans were performed to identify methylation markers associated with cotinine. The inter-dose-response relationships between the number of cigarettes smoked per day, cotinine concentration, and DNA methylation were modeled by restricted cubic spline regression. Of 61 CpGs that passed the genome-wide significance threshold (p<1.13×10(-7)), 40 CpGs in 25 chromosomal regions were successfully replicated, showing 0.2-3% demethylation per 10ng/ml increases in cotinine. The strongest associations were observed for several loci at AHRR, F2RL3, 2q37.1, 6p21.33, and GFI1 that were previously identified to be related to self-reported smoking. One locus at RAB34 was newly discovered. Both cotinine and methylation markers exhibited non-linear relationships with the number of cigarettes smoked per day, where the highest rates of increase in cotinine and decreases in methylation were observed at low smoking intensity (1-15 cigarettes/day) and plateaued at high smoking intensity (>15-20 cigarettes/day). A clear linear relationship was observed between cotinine concentration and methylation level. Both cotinine and methylation markers showed similar accuracy in distinguishing current from never smoker, but only methylation markers distinguished former from never smoker with high accuracy. Our study corroborates and expands the list of smoking-associated DNA methylation markers. Methylation levels were linearly related to cotinine concentration and provided accurate measures for both current and past smoking exposure. Copyright © 2016 Elsevier Inc. All rights

  5. Bejel: acquirable only in childhood?

    PubMed

    Rothschild, Bruce M; Rothschild, Christine; Naples, Virginia; Billard, Michel; Panero, Barbara

    2006-10-01

    Bejel clearly has a long history in the Middle East and the Sudan, but was it transmitted to Europe? As the major manifestation of bejel is presence of periosteal reaction in 20-40% of afflicted populations, absence of significant population frequency of periosteal reaction in Europe would exclude that diagnosis. Examination of skeletal populations from continental Europe revealed no significant periosteal reaction at the time of and immediately subsequent to the Crusades. Thus, there is no evidence for bejel in Europe, in spite of clear contact (the mechanism of bejel transmission in children) between warring groups, at least during the Crusades. This supports the hypothesis that bejel is a childhood-acquired disease and apparently cannot be contracted in adulthood.

  6. Inheritance of cytosine methylation patterns in purebred versus hybrid chicken lines.

    PubMed

    Xu, Q; Sun, D X; Li, J L; Liu, R; Wang, Y C; Zhang, Y

    2013-07-30

    We used methylation-sensitive amplified polymo