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Epigenetics: Official Journal of the DNA Methylation Society

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https://www.readbyqxmd.com/read/29465290/global-integrated-analysis-of-methylomes-and-transcriptomes-from-laser-capture-microdissected-bronchial-and-alveolar-cells-in-human-lung
#1
Xiao Dong, Miao Shi, Moonsook Lee, Rafael Toro, Silvia Gravina, Weiguo Han, Shoya Yasuda, Tao Wang, Zhengdong Zhang, Jan Vijg, Yousin Suh, Simon D Spivack
Gene regulatory analysis of highly diverse human tissues in vivo is essentially constrained by the challenge of performing genome-wide, integrated epigenetic and transcriptomic analysis in small selected groups of specific cell types. Here we performed genome-wide bisulfite sequencing and RNA-seq from the same small groups of bronchial and alveolar cells isolated by laser capture microdissection from flash-frozen lung tissue of 12 donors and their peripheral blood T cells. Methylation and transcriptome patterns differed between alveolar and bronchial cells, while each of these epithelia showed more differences from mesodermally-derived T cells...
May 10, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29697014/robust-prediction-of-gene-regulation-in-colorectal-cancer-tissues-from-dna-methylation-profiles
#2
Hagen Klett, Yesilda Balavarca, Reka Toth, Biljana Gigic, Nina Habermann, Dominique Scherer, Petra Schrotz-King, Alexis Ulrich, Peter Schirmacher, Esther Herpel, Hermann Brenner, Cornelia M Ulrich, Karin B Michels, Hauke Busch, Melanie Boerries
DNA methylation is recognized as one of several epigenetic regulators of gene expression and as potential driver of carcinogenesis through gene-silencing of tumor suppressors and activation of oncogenes. However, abnormal methylation, even of promoter regions, does not necessarily alter gene expression levels, especially if the gene is already silenced, leaving the exact mechanisms of methylation unanswered. Using a large cohort of matching DNA methylation and gene expression samples of colorectal cancer (CRC; n = 77) and normal adjacent mucosa tissues (n = 108), we investigated the regulatory role of methylation on gene expression...
May 3, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29613829/novel-imprinted-single-cpg-sites-found-by-global-dna-methylation-analysis-in-human-parthenogenetic-induced-pluripotent-stem-cells
#3
Na Young Choi, Jin Seok Bang, Hye Jeong Lee, Yo Seph Park, Minseong Lee, Dahee Jeong, Kisung Ko, Dong Wook Han, Hyung-Min Chung, Gwang Jun Kim, Seung-Hyuk Shim, Han Sung Hwang, Kinarm Ko
Genomic imprinting is the process of epigenetic modification whereby genes are expressed in a parent-of-origin dependent manner; it plays an important role in normal growth and development. Parthenogenetic embryos contain only the maternal genome. Parthenogenetic embryonic stem cells could be useful for studying imprinted genes. In humans, mature cystic ovarian teratomas originate from parthenogenetic activation of oocytes; they are composed of highly differentiated mature tissues containing all three germ layers...
May 3, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29522357/genipin-normalizes-depression-like-behavior-induced-by-prenatal-stress-through-inhibiting-dnmt1
#4
Di Ye, Li Zhang, Weidong Fan, Xianquan Zhang, Erbo Dong
Synthetic antidepressants in current use for the complex etiopathogeneses of depression have slow response and remission as well as various unpleasant side effects. As a result, it is imperative to develop new antidepressants with more effectiveness and less severe side effects. Recent studies demonstrated that genipin, the aglycon of geniposide, extracted from Gardenia jasminoides Ellis has antidepressive effects. However, knowledge regarding the molecular mechanisms of its antidepressant effects remains limited...
May 3, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29527977/droplet-digital-pcr-is-an-accurate-method-to-assess-methylation-status-on-ffpe-samples
#5
Liesbeth Van Wesenbeeck, Leen Janssens, Hanne Meeuws, Ole Lagatie, Lieven Stuyver
Most tissue samples available for cancer research are archived as formalin-fixed paraffin-embedded (FFPE) samples. However, the fixation process and the long storage duration lead to DNA fragmentation and hinder epigenome analysis. The use of droplet digital PCR (ddPCR) to detect DNA methylation has recently emerged. In this study, we compare an optimized ddPCR assay with a conventional qPCR assay by targeting a dilution series of control DNA. In addition, we compare the ddPCR technology with results from Infinium arrays targeting two separate CpG sites on a set of colon adenoma FFPE samples...
April 18, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29513082/maternal-levels-of-endocrine-disrupting-chemicals-in-the-first-trimester-of-pregnancy-are-associated-with-infant-cord-blood-dna-methylation
#6
Luke Montrose, Vasantha Padmanabhan, Jaclyn M Goodrich, Steven E Domino, Marjorie C Treadwell, John D Meeker, Deborah J Watkins, Dana C Dolinoy
Endocrine disrupting chemicals (EDCs) pose a public health risk through disruption of normal biological processes. Identifying toxicoepigenetic mechanisms of developmental exposure-induced effects for EDCs, such as phthalates or bisphenol A (BPA), is essential. Here, we investigate whether maternal exposure to EDCs is predictive of infant DNA methylation at candidate gene regions. In the Michigan Mother-Infant Pairs (MMIP) cohort, DNA was extracted from cord blood leukocytes for methylation analysis by pyrosequencing (n = 116) and methylation changes related to first trimester levels of 9 phthalate metabolites and BPA...
April 18, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29498561/developmentally-linked-human-dna-hypermethylation-is-associated-with-down-modulation-repression-and-upregulation-of-transcription
#7
Carl Baribault, Kenneth C Ehrlich, V K Chaithanya Ponnaluri, Sriharsa Pradhan, Michelle Lacey, Melanie Ehrlich
DNA methylation can affect tissue-specific gene transcription in ways that are difficult to discern from studies focused on genome-wide analyses of differentially methylated regions (DMRs). To elucidate the variety of associations between differentiation-related DNA hypermethylation and transcription, we used available epigenomic and transcriptomic profiles from 38 human cell/tissue types to focus on such relationships in 94 genes linked to hypermethylated DMRs in myoblasts (Mb). For 19 of the genes, promoter-region hypermethylation in Mb (and often a few heterologous cell types) was associated with gene repression but, importantly, DNA hypermethylation was absent in many other repressed samples...
April 18, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29613828/activation-of-class-i-histone-deacetylases-contributes-to-mitochondrial-dysfunction-in-cardiomyocytes-with-altered-complex-activities
#8
Baigalmaa Lkhagva, Yu-Hsun Kao, Ting-I Lee, Ting-Wei Lee, Wan-Li Cheng, Yi-Jen Chen
Histone deacetylases (HDACs) play vital roles in the pathophysiology of heart failure, which is associated with mitochondrial dysfunction. Tumor necrosis factor-α (TNF-α) contributes to the genesis of heart failure and impairs mitochondria. This study evaluated the role of HDACs in TNF-α-induced mitochondrial dysfunction and investigated their therapeutic potential and underlying mechanisms. We measured mitochondrial oxygen consumption rate (OCR) and ATP production using Seahorse XF24 extracellular flux analyzer and bioluminescent assay in control and TNF-α (10 ng/ml, 24 h)-treated HL-1 cells with or without HDAC inhibition...
April 3, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29613827/experience-dependent-neuroplasticity-of-the-developing-hypothalamus-integrative-epigenomic-approaches
#9
Annie Vogel Ciernia, Benjamin I Laufer, Keith W Dunaway, Charles E Mordaunt, Rochelle L Coulson, Theresa S Totah, Danielle S Stolzenberg, Jaime Frahm, Akanksha Singh-Taylor, Tallie Z Baram, Janine M LaSalle, Dag H Yasui
Augmented maternal care during the first postnatal week promotes life-long stress resilience and improved memory compared with the outcome of routine rearing conditions. Recent evidence suggests that this programming commences with altered synaptic connectivity of stress sensitive hypothalamic neurons. However, the epigenomic basis of the long-lived consequences is not well understood. Here, we employed whole-genome bisulfite sequencing (WGBS), RNA-sequencing (RNA-seq), and a multiplex microRNA (miRNA) assay to examine the effects of augmented maternal care on DNA cytosine methylation, gene expression, and miRNA expression...
April 3, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29436922/breast-cancer-family-history-and-allele-specific-dna-methylation-in-the-legacy-girls-study
#10
Hui-Chen Wu, Catherine Do, Irene L Andrulis, Esther M John, Mary B Daly, Saundra S Buys, Wendy K Chung, Julia A Knight, Angela R Bradbury, Theresa H M Keegan, Lisa Schwartz, Izabela Krupska, Rachel L Miller, Regina M Santella, Benjamin Tycko, Mary Beth Terry
Family history, a well-established risk factor for breast cancer, can have both genetic and environmental contributions. Shared environment in families as well as epigenetic changes that also may be influenced by shared genetics and environment may also explain familial clustering of cancers. Epigenetic regulation, such as DNA methylation, can change the activity of a DNA segment without a change in the sequence; environmental exposures experienced across the life course can induce such changes. However, genetic-epigenetic interactions, detected as methylation quantitative trait loci (mQTLs; a...
April 2, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29436261/an-epigenomic-approach-to-identifying-differential-overlapping-and-cis-acting-lncrnas-in-cisplatin-resistant-cancer-cells
#11
Olga Vera, Carlos Rodriguez-Antolin, Javier de Castro, Florian A Karreth, Thomas A Sellers, Inmaculada Ibanez de Caceres
Long noncoding RNAs (lncRNAs) are critical regulators of cell biology whose alteration can lead to the development of diseases such as cancer. The potential role of lncRNAs and their epigenetic regulation in response to platinum treatment are largely unknown. We analyzed four paired cisplatin-sensitive/resistant non-small cell lung cancer and ovarian cancer cell lines. The epigenetic landscape of overlapping and cis-acting lncRNAs was determined by combining human microarray data on 30,586 lncRNAs and 20,109 protein coding mRNAs with whole-genome bisulfite sequencing...
April 2, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29561703/chromium-disrupts-chromatin-organization-and-ctcf-access-to-its-cognate-sites-in-promoters-of-differentially-expressed-genes
#12
Andrew VonHandorf, Francisco Javier Sánchez-Martín, Jacek Biesiada, Hongxia Zhang, Xiang Zhang, Mario Medvedovic, Alvaro Puga
Hexavalent chromium compounds are well-established respiratory carcinogens used in industrial processes. While inhalation exposure constitutes an occupational risk affecting mostly chromium workers, environmental exposure from drinking water is a widespread gastrointestinal cancer risk, affecting millions of people throughout the world. Cr(VI) is genotoxic, forming protein-Cr-DNA adducts and silencing tumor suppressor genes, but its mechanism of action at the molecular level is poorly understood. Our prior work using FAIRE showed that Cr(VI) disrupted the binding of transcription factors CTCF and AP-1 to their cognate chromatin sites...
March 21, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29560787/identification-of-sex-specific-dna-methylation-changes-driven-by-specific-chemicals-in-cord-blood-in-a-faroese-birth-cohort
#13
Yuet-Kin Leung, Bin Ouyang, Liang Niu, Changchun Xie, Jun Ying, Mario Medvedovic, Aimin Chen, Pal Weihe, Damaskini Valvi, Philippe Grandjean, Shuk-Mei Ho
Faroe islanders consume marine foods contaminated with methylmercury (MeHg), polychlorinated biphenyls (PCBs), and other toxicants associated with chronic disease risks. Differential DNA methylation at specific CpG sites in cord blood may serve as a surrogate biomarker of health impacts from chemical exposures. We aimed to identify key environmental chemicals in cord blood associated with DNA methylation changes in a population with elevated exposure to chemical mixtures. We studied 72 participants of a Faroese birth cohort recruited between 1986 and 1987 and followed until adulthood...
March 21, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29384431/epigenetic-mechanisms-in-health-and-disease-bcec-2017
#14
Albert Carbonell, Raquel Fueyo, Andrea Izquierdo-Bouldstridge, Cristina Moreta, Albert Jordan
The Barcelona Conference on Epigenetics and Cancer (BCEC) entitled "Epigenetic Mechanisms in Health and Disease" was held in Barcelona, October 26-26, 2017. The 2017 BCEC was the fifth and last edition of a series of annual conferences organized as a joint effort of five leading Barcelona research institutes together with B-Debate. This edition was organized by Albert Jordan from the Molecular Biology Institute of Barcelona (IBMB-CSIC) and Marcus Bushbeck from the Josep Carreras Leukaemia Research Institute (IJC)...
February 23, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29376485/genome-wide-oxidative-bisulfite-sequencing-identifies-sex-specific-methylation-differences-in-the-human-placenta
#15
Sungsam Gong, Michelle D Johnson, Justyna Dopierala, Francesca Gaccioli, Ulla Sovio, Miguel Constância, Gordon Cs Smith, D Stephen Charnock-Jones
DNA methylation is an important regulator of gene function. Fetal sex is associated with the risk of several specific pregnancy complications related to placental function. However, the association between fetal sex and placental DNA methylation remains poorly understood. We carried out whole-genome oxidative bisulfite sequencing in the placentas of two healthy female and two healthy male pregnancies generating an average genome depth of coverage of 25x. Most highly ranked differentially methylated regions (DMRs) were located on the X chromosome but we identified a 225 kb sex-specific DMR in the body of the CUB and Sushi Multiple Domains 1 (CSMD1) gene on chromosome 8...
February 21, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29451060/cord-blood-buffy-coat-dna-methylation-is-comparable-to-whole-cord-blood-methylation
#16
John Dou, Rebecca J Schmidt, Kelly S Benke, Craig Newschaffer, Irva Hertz-Picciotto, Lisa A Croen, Ana-Maria Iosif, Janine M LaSalle, M Daniele Fallin, Kelly M Bakulski
Cord blood DNA methylation is associated with numerous health outcomes and environmental exposures. Whole cord blood DNA reflects all nucleated blood cell types, while centrifuging whole blood separates red blood cells, generating a white blood cell buffy coat. Both sample types are used in DNA methylation studies. Cell types have unique methylation patterns and processing can impact cell distributions, which may influence comparability. We evaluated differences in cell composition and DNA methylation between cord blood buffy coat and whole cord blood samples...
2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29381404/agreement-in-dna-methylation-levels-from-the-illumina-450k-array-across-batches-tissues-and-time
#17
Marie Forest, Kieran J O'Donnell, Greg Voisin, Helene Gaudreau, Julia L MacIsaac, Lisa M McEwen, Patricia P Silveira, Meir Steiner, Michael S Kobor, Michael J Meaney, Celia M T Greenwood
Epigenome-wide association studies (EWAS) have focused primarily on DNA methylation as a chemically stable and functional epigenetic modification. However, the stability and accuracy of the measurement of methylation in different tissues and extraction types is still being actively studied, and the longitudinal stability of DNA methylation in commonly studied peripheral tissues is of great interest. Here, we used data from two studies, three tissue types, and multiple time points to assess the stability of DNA methylation measured with the Illumina Infinium HumanMethylation450 BeadChip array...
2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29372669/evolutionary-conservation-of-dna-methylation-in-cpg-sites-within-ultraconserved-noncoding-elements
#18
Mathia Colwell, Melissa Drown, Kelly Showel, Chelsea Drown, Amanda Palowski, Christopher Faulk
Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%...
2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29271283/charged-residues-on-the-side-of-the-nucleosome-contribute-to-normal-spt16-gene-interactions-in-budding-yeast
#19
Eugene Nyamugenda, A Brandon Cox, Jacob B Pierce, Ryan C Banning, Michelle L Huynh, Catey May, Sarah Marshall, Claire E Turkal, Andrea A Duina
Previous work in Saccharomyces cerevisiae identified three residues located in close proximity to each other on the side of the nucleosome whose integrity is required for proper association of the Spt16 component of the FACT complex across transcribed genes. In an effort to gain further insights into the parameters that control Spt16 interactions with genes in vivo, we tested the effects of additional histone mutants on Spt16 occupancy across two constitutively transcribed genes. These studies revealed that mutations in several charged residues in the vicinity of the three residues originally identified as important for Spt16-gene interactions also significantly perturb normal association of Spt16 across genes...
2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29235940/slc9b1-methylation-predicts-fetal-intolerance-of-labor
#20
Anna K Knight, Karen N Conneely, Varun Kilaru, Dawayland Cobb, Jennifer L Payne, Samantha Meilman, Elizabeth J Corwin, Zachary A Kaminsky, Anne L Dunlop, Alicia K Smith
Fetal intolerance of labor is a common indication for delivery by Caesarean section. Diagnosis is based on the presence of category III fetal heart rate tracing, which is an abnormal heart tracing associated with increased likelihood of fetal hypoxia and metabolic acidemia. This study analyzed data from 177 unique women who, during their prenatal visits (7-15 weeks and/or 24-32 weeks) to Atlanta area prenatal care clinics, consented to provide blood samples for DNA methylation (HumanMethylation450 BeadChip) and gene expression (Human HT-12 v4 Expression BeadChip) analyses...
2018: Epigenetics: Official Journal of the DNA Methylation Society
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