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Epigenomics

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https://www.readbyqxmd.com/read/28140666/does-maternal-mental-well-being-in-pregnancy-impact-the-early-human-epigenome
#1
Joanne Ryan, Toby Mansell, Peter Fransquet, Richard Saffery
There is considerable interest in the potential nongenetic transmission of a suite of mental health conditions across generations, with epigenetics emerging as a candidate mediator of such effects. This review summarizes findings from 22 studies measuring candidate gene DNA methylation and seven epigenome-wide association studies of offspring epigenetic profile in women with adverse mental wellbeing measures (stress, depression or anxiety) in pregnancy. Despite some compelling evidence to suggest an association, there is a lack of reproducible findings, potentially linked to a number of limitations to this research and the field more broadly...
January 31, 2017: Epigenomics
https://www.readbyqxmd.com/read/28140654/genome-wide-methylation-analysis-identifies-novel-cpg-loci-for-perimembranous-ventricular-septal-defects-in-human
#2
Kim Pj Wijnands, Jun Chen, Liming Liang, Michael Mpj Verbiest, Xihong Lin, Willem A Helbing, Adriana C Gittenberger-de Groot, Peter J van der Spek, André G Uitterlinden, Régine Pm Steegers-Theunissen
AIM: Congenital heart diseases are the most common birth defects worldwide and leading cause of infant mortality. The perimembranous ventricular septal defect is most prevalent. Epigenetics may provide an underlying mechanism of the gene-environment interactions involved. MATERIALS & METHODS: We examined epigenome-wide DNA methylation using the Illumina HumanMethylation450 BeadChip in 84 case children and 196 control children. RESULTS: We identified differential methylation of a CpG locus (cg17001566) within the PRDM16 gene after Bonferroni correction (p = 9...
January 31, 2017: Epigenomics
https://www.readbyqxmd.com/read/28111986/gestational-age-predicted-by-dna-methylation-potential-clinical-and-research-utility
#3
Anna K Knight, Karen N Conneely, Alicia K Smith
No abstract text is available yet for this article.
January 23, 2017: Epigenomics
https://www.readbyqxmd.com/read/28111977/genome-wide-analysis-of-dna-methylation-and-their-associations-with-long-noncoding-rna-mrna-expression-in-non-small-cell-lung-cancer
#4
Nannan Feng, Yu Wang, Min Zheng, Xiao Yu, Hongyan Lin, Rong-Na Ma, Oumin Shi, Xiangqian Zheng, Ming Gao, Herbert Yu, Lana Garmire, Biyun Qian
AIM: The goal of this study is to identify differentially methylated (DM) loci associated with long noncoding RNA (lncRNA)/mRNA expression in non-small-cell lung cancer (NSCLC). MATERIALS & METHODS: Microarrays were used to interrogate genome-wide methylation and expression of lncRNA/mRNA in NSCLC. RESULTS: We identified 113,644 DM loci between tumors and adjacent tissues. Among them, 26,310 DM loci were associated with 1685 differentially expressed genes, and 839 genes had significant correlations between methylation and expression, of which 26 hypermethylated loci in transcription start site 200 were correlated with low gene expression...
January 23, 2017: Epigenomics
https://www.readbyqxmd.com/read/28102705/the-acetyl-code-in-rheumatoid-arthritis-and-other-rheumatic-diseases
#5
Chiara Angiolilli, Dominique L Baeten, Timothy R Radstake, Kris A Reedquist
Growing evidence supports the idea that aberrancies in epigenetic processes contribute to the onset and progression of human immune-mediated inflammatory diseases, such as rheumatoid arthritis (RA). Epigenetic regulators of histone tail modifications play a role in chromatin accessibility and transcriptional responses to inflammatory stimuli. Among these, histone deacetylases (HDACs) regulate the acetylation status of histones and nonhistone proteins, essential for immune responses. Broad-spectrum HDAC inhibitors are well-known anti-inflammatory agents and reduce disease severity in animal models of arthritis; however, selective HDAC inhibitors remain poorly studied...
January 19, 2017: Epigenomics
https://www.readbyqxmd.com/read/28097892/new-avenues-for-targeted-therapies-and-biomarkers-in-anaplastic-large-cell-lymphoma
#6
Gerda Egger, Suzanne D Turner
No abstract text is available yet for this article.
January 18, 2017: Epigenomics
https://www.readbyqxmd.com/read/28097877/the-epigenetics-of-testicular-germ-cell-tumors-looking-for-novel-disease-biomarkers
#7
Ana Laura Costa, João Lobo, Carmen Jerónimo, Rui Henrique
Testicular germ cell tumors (TGCT) are a group of heterogeneous, biologically diverse and clinically challenging neoplasms. Despite the relatively low incidence and mortality rates, a subgroup of patients with disseminated disease relapse after conventional therapy and have a dismal prognosis. Moreover, TGCT afflict mostly young men and have therapeutic peculiarities, with some patients showing resistance to cisplatin-based treatments and others being troubled by irreversible side effects, such as infertility...
January 18, 2017: Epigenomics
https://www.readbyqxmd.com/read/28093925/hypermethylation-of-antisense-long-noncoding-rnas-in-acute-lymphoblastic-leukemia
#8
Gerald Arthur, Md Almamun, Kristen Taylor
AIM: Long noncoding RNAs serve critical regulatory functions highly specific for a tissue and its developmental stage. Antisense long ncRNA (AS-lncRNA) methylation changes in acute lymphoblastic leukemia (ALL) versus normal pre-B-cell lymphoblasts were evaluated to identify potential differential methylation in this group of genes. MATERIALS & METHODS: The methylome of ALL and normal lymphoblasts was examined by the methylated CpG island recovery assay followed by NGS...
January 17, 2017: Epigenomics
https://www.readbyqxmd.com/read/27925476/immune-disease-associated-variants-in-gene-enhancers-point-to-bet-epigenetic-mechanisms-for-therapeutic-intervention
#9
David F Tough, Rab K Prinjha
Genome-wide association studies have identified thousands of single nucleotide polymorphisms in the human genome that are statistically associated with particular disease traits. In this Perspective, we review emerging data suggesting that most single nucleotide polymorphisms associated with immune-mediated diseases are found in regulatory regions of the DNA - parts of the genome that control expression of the protein encoding genes - rather than causing mutations in proteins. We discuss how the emerging understanding of particular gene regulatory regions, gene enhancers and the epigenetic mechanisms by which they are regulated is opening up new opportunities for the treatment of immune-mediated diseases, focusing particularly on the BET family of epigenetic reader proteins as potential therapeutic targets...
December 7, 2016: Epigenomics
https://www.readbyqxmd.com/read/27919171/cpg-methylation-participates-in-regulation-of-hepatitis-b-virus-gene-expression-in-host-sperm-and-sperm-derived-embryos
#10
ChengYao Zhong, Hui Lu, TingTing Han, XiaoFang Tan, PengHao Li, JiHua Huang, QingDong Xie, ZhiWei Hou, Ting Qu, Yang Jiang, Sheng Wang, Lan Xu, Ying Zhong, TianHua Huang
AIM: This study was undertaken to investigate relationship between hepatitis B virus (HBV) CpG methylation and HBV gene transcription in sperm and sperm-derived embryos. METHODS: HBV-infected patient sperm and HBV plasmid-transfected donor sperm were subjected to interspecific in vitro fertilization, methylation-specific PCR, bisulfite sequencing PCR, reverse transcription PCR and real-time quantitative PCR. RESULTS: Positive methylation bands for CpG islands II and III in the HBV genome were observed in patient sperm but not in controls, and methylation percentages of CpG sites varied among different patient sperm samples...
December 6, 2016: Epigenomics
https://www.readbyqxmd.com/read/27911095/epigenetic-alterations-in-blood-mirror-age-associated-dna-methylation-and-gene-expression-changes-in-human-liver
#11
Madhusudhan Bysani, Alexander Perfilyev, Vanessa D de Mello, Tina Rönn, Emma Nilsson, Jussi Pihlajamäki, Charlotte Ling
AIM: To study the impact of aging on DNA methylation and mRNA expression in human liver. EXPERIMENTAL PROCEDURES: We analysed genome-wide DNA methylation and gene expression in human liver samples using Illumina 450K and HumanHT12 expression BeadChip arrays. RESULTS: DNA methylation analysis of ∼455,000 CpG sites in human liver revealed that age was significantly associated with altered DNA methylation of 20,396 CpG sites. Comparison of liver methylation data with published methylation data in other tissues showed that vast majority of the age-associated significant CpG sites overlapped between liver and blood, whereas a smaller overlap was found between liver and pancreatic islets or adipose tissue, respectively...
December 2, 2016: Epigenomics
https://www.readbyqxmd.com/read/27911079/trans-acting-epigenetic-effects-of-chromosomal-aneuploidies-lessons-from-down-syndrome-and-mouse-models
#12
Catherine Do, Zhuo Xing, Y Eugene Yu, Benjamin Tycko
An important line of postgenomic research seeks to understand how genetic factors can influence epigenetic patterning. Here we review epigenetic effects of chromosomal aneuploidies, focusing on findings in Down syndrome (DS, trisomy 21). Recent work in human DS and mouse models has shown that the extra chromosome 21 acts in trans to produce epigenetic changes, including differential CpG methylation (DS-DM), in specific sets of downstream target genes, mostly on other chromosomes. Mechanistic hypotheses emerging from these data include roles of chromosome 21-linked methylation pathway genes (DNMT3L and others) and transcription factor genes (RUNX1, OLIG2, GABPA, ERG and ETS2) in shaping the patterns of DS-DM...
December 2, 2016: Epigenomics
https://www.readbyqxmd.com/read/27908198/tet-proteins-master-regulators-of-vertebrate-body-plan-formation
#13
Ozren Bogdanović
No abstract text is available yet for this article.
December 2, 2016: Epigenomics
https://www.readbyqxmd.com/read/27894195/accelerated-placental-aging-in-early-onset-preeclampsia-pregnancies-identified-by-dna-methylation
#14
Benjamin T Mayne, Shalem Y Leemaqz, Alicia K Smith, James Breen, Claire T Roberts, Tina Bianco-Miotto
AIM: To determine whether dynamic DNA methylation changes in the human placenta can be used to predict gestational age. MATERIALS & METHODS: Publicly available placental DNA methylation data from 12 studies, together with our own dataset, using Illumina Infinium Human Methylation BeadChip arrays. RESULTS & CONCLUSION: We developed an accurate tool for predicting gestational age of placentas using 62 CpG sites. There was a higher predicted gestational age for placentas from early onset preeclampsia cases, but not term preeclampsia, compared with their chronological age...
November 29, 2016: Epigenomics
https://www.readbyqxmd.com/read/28112569/epigenetic-regulation-of-noncoding-rna-transcription-by-mammalian-rna-polymerase-iii
#15
Jong-Lyul Park, Yeon-Su Lee, Nawapol Kunkeaw, Seon-Young Kim, In-Hoo Kim, Yong Sun Lee
RNA polymerase III (Pol III) synthesizes a range of medium-sized noncoding RNAs (collectively 'Pol III genes') whose early established biological roles were so essential that they were considered 'housekeeping genes'. Besides these fundamental functions, diverse unconventional roles of mammalian Pol III genes have recently been recognized and their expression must be exquisitely controlled. In this review, we summarize the epigenetic regulation of Pol III genes by chromatin structure, histone modification and CpG DNA methylation...
February 2017: Epigenomics
https://www.readbyqxmd.com/read/27981856/distinct-cellular-and-molecular-environments-support-aging-related-dna-methylation-changes-in-the-substantia-nigra
#16
Maria Fasolino, Shuo Liu, Yinsheng Wang, Zhaolan Zhou
AIM: We aimed to couple brain region-specific changes in global DNA methylation over aging to underlying cellular and molecular environments. MATERIALS & METHODS: We measured two major forms of DNA methylation and analyzed Dnmt, Tet and metabolite levels in the striatum and substantia nigra (SN) over aging in healthy male mice. RESULTS: The ratio of 5-hydroxymethylcytosine to 5-methylcytosine increases over aging in the SN, and 5-hydroxymethylcytosine increases preferentially in dopaminergic neurons...
January 2017: Epigenomics
https://www.readbyqxmd.com/read/27981852/epigenetics-obesity-and-early-life-cadmium-or-lead-exposure
#17
Sarah S Park, David A Skaar, Randy L Jirtle, Cathrine Hoyo
Obesity is a complex and multifactorial disease, which likely comprises multiple subtypes. Emerging data have linked chemical exposures to obesity. As organismal response to environmental exposures includes altered gene expression, identifying the regulatory epigenetic changes involved would be key to understanding the path from exposure to phenotype and provide new tools for exposure detection and risk assessment. In this report, we summarize published data linking early-life exposure to the heavy metals, cadmium and lead, to obesity...
January 2017: Epigenomics
https://www.readbyqxmd.com/read/27936932/disruption-of-the-3d-cancer-genome-blueprint
#18
Joanna Achinger-Kawecka, Susan J Clark
Recent advances in chromosome conformation capture technologies are improving the current appreciation of how 3D genome architecture affects its function in different cell types and disease. Long-range chromatin interactions are organized into topologically associated domains, which are known to play a role in constraining gene expression patterns. However, in cancer cells there are alterations in the 3D genome structure, which impacts on gene regulation. Disruption of topologically associated domains architecture can result in alterations in chromatin interactions that bring new regulatory elements and genes together, leading to altered expression of oncogenes and tumor suppressor genes...
January 2017: Epigenomics
https://www.readbyqxmd.com/read/27936926/the-application-of-genome-wide-5-hydroxymethylcytosine-studies-in-cancer-research
#19
John P Thomson, Richard R Meehan
Early detection and characterization of molecular events associated with tumorgenesis remain high priorities. Genome-wide epigenetic assays are promising diagnostic tools, as aberrant epigenetic events are frequent and often cancer specific. The deposition and analysis of multiple patient-derived cancer epigenomic profiles contributes to our appreciation of the underlying biology; aiding the detection of novel identifiers for cancer subtypes. Modifying enzymes and co-factors regulating these epigenetic marks are frequently mutated in cancers, and as epigenetic modifications themselves are reversible, this makes their study very attractive with respect to pharmaceutical intervention...
January 2017: Epigenomics
https://www.readbyqxmd.com/read/27936916/identical-twins-doubly-exchanged-at-birth-a-case-report-of-genetic-and-environmental-influences-on-the-adult-epigenome
#20
Nancy L Segal, Yesika S Montoya, Yuk J Loke, Jeffrey M Craig
AIM: Epigenetic comparisons within monozygotic twin pairs have enhanced our understanding of nongenetic mechanisms underlying disease etiology. We present epigenetic findings for a unique case of doubly exchanged Colombian male monozygotic twins raised in extremely different environments. RESULTS: Using genome-wide DNA methylation data from cheek swabs from which blood-specific differentially methylated probes had been removed, the individuals grouped by shared genetics rather than shared environment, except for one twin who presented as an outlier...
January 2017: Epigenomics
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