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Epigenetics: Official Journal of the DNA Methylation Society

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https://www.readbyqxmd.com/read/27911668/association-of-5-hydroxymethylation-and-5-methylation-of-dna-cytosine-with-tissue-specific-gene-expression
#1
V K Chaithanya Ponnaluri, Kenneth C Ehrlich, Guoqiang Zhang, Michelle Lacey, Douglas Johnston, Sriharsa Pradhan, Melanie Ehrlich
Differentially methylated or hydroxymethylated regions (DMRs) in mammalian DNA are often associated with tissue-specific gene expression but the functional relationships are still being unraveled. To elucidate these relationships, we studied 16 human genes containing myogenic DMRs by analyzing profiles of their epigenetics and transcription and quantitatively assaying 5-hydroxymethylcytosine (5 hmC) and 5-methylcytosine (5 mC) at specific sites in these genes in skeletal muscle (SkM), myoblasts, heart, brain, and diverse other samples...
December 2, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27911230/bromodomain-inhibitors-and-cancer-therapy-from-structures-to-applications
#2
Montserrat Pérez-Salvia, Manel Esteller
Aberrations in the epigenetic landscape are a hallmark of cancer. Alterations in enzymes that are "writers", "erasers", or "readers" of histone modification marks are common. Bromodomains are "readers" that bind acetylated lysines in histone tails. Their most important function is the regulation of gene transcription by the recruitment of different molecular partners. Moreover, proteins containing bromodomains are also epigenetic regulators, although little is known about the specific function of these domains...
December 2, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27911222/the-histone-methyltransferases-set5-and-set1-have-overlapping-functions-in-gene-silencing-and-telomere-maintenance
#3
Meagan Jezek, Alison Gast, Grace Choi, Rushmie Kulkarni, Jeremiah Quijote, Andrew Graham-Yooll, DoHwan Park, Erin M Green
Genes adjacent to telomeres are subject to transcriptional repression mediated by an integrated set of chromatin modifying and remodeling factors. The telomeres of Saccharomyces cerevisiae have served as a model for dissecting the function of diverse chromatin proteins in gene silencing, and their study has revealed overlapping roles for many chromatin proteins in either promoting or antagonizing gene repression. The H3K4 methyltransferase Set1, which is commonly linked to transcriptional activation, has been implicated in telomere silencing...
December 2, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27911167/recommendations-for-a-nomenclature-system-for-reporting-methylation-aberrations-in-imprinted-domains
#4
David Monk, Joannella Morales, Johan T den Dunnen, Silvia Russo, Franck Court, Dirk Prawitt, Thomas Eggermann, Jasmin Beygo, Karin Buiting, Zeynep Tümer
The analysis of DNA methylation has become routine in the pipeline for diagnosis of imprinting disorders, with many publications reporting aberrant methylation associated with imprinted differentially methylated regions (DMRs). However, comparisons between these studies are routinely hampered by the lack of consistency in reporting sites of methylation evaluated. To avoid confusion surrounding nomenclature, special care is needed to communicate results accurately, especially between scientists and other health care professionals...
December 2, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27892790/line-1-methylation-status-in-prostate-cancer-and-non-neoplastic-tissue-adjacent-to-tumor-in-association-with-mortality
#5
Valentina Fiano, Daniela Zugna, Chiara Grasso, Morena Trevisan, Luisa Delsedime, Luca Molinaro, Anna Gillio-Tos, Franco Merletti, Lorenzo Richiardi
Aberrant DNA methylation seems to be associated with prostate cancer behavior. We investigated LINE-1 methylation in prostate cancer and non-neoplastic tissue adjacent to tumor (NTAT) in association with mortality from prostate cancer. We selected 157 prostate cancer patients with available NTAT from two cohorts of patients diagnosed between 1982-1988 and 1993-1996, followed up until 2010. An association between LINE-1 hypomethylation and prostate cancer mortality in tumor was suggested [hazard ratio per 5% decrease in LINE-1 methylation levels: 1...
November 28, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27874289/epigenetic-changes-as-prognostic-predictors-in-endometrial-carcinomas
#6
Sanja A Farkas, Bengt G Sorbe, Torbjörn K Nilsson
Endometrial carcinoma is one of the most frequent gynecological malignancies of the female. The diagnostic and prognostic markers for the high-risk subgroups with unfavorable prognosis are under intense debate worldwide, and, therefore, the aim of this study was to identify new potential DNA methylation markers for the high-risk groups. We used the Illumina Infinium HumanMethylation450 BeadChip to analyze the DNA methylation pattern and investigated its association with clinicopathological features important for defining the high-risk (FIGO-grade 3) and low-risk (FIGO-grade 1) groups of patients with endometrial cancer (n = 31 and n = 39, respectively)...
November 22, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27858532/tracking-the-evolution-of-epialleles-during-neural-differentiation-and-brain-development-d-aspartate-oxidase-as-a-model-gene
#7
Ermanno Florio, Simona Keller, Lorena Coretti, Ornella Affinito, Giovanni Scala, Francesco Errico, Annalisa Fico, Francesca Boscia, Maria Josè Sisalli, Mafalda Giovanna Reccia, Gennaro Miele, Antonella Monticelli, Antonella Scorziello, Francesca Lembo, Luca Colucci-D'Amato, Gabriella Minchiotti, Vittorio Enrico Avvedimento, Alessandro Usiello, Sergio Cocozza, Lorenzo Chiariotti
We performed ultra-deep methylation analysis at single molecule level of the promoter region of developmentally regulated D-Aspartate oxidase (Ddo), as a model gene, during brain development and embryonic stem cell neural differentiation. Single molecule methylation analysis enabled us to establish the effective epiallele composition within mixed or pure brain cell populations. In this framework, an epiallele is defined as a specific combination of methylated CpG within Ddo locus and can represent the epigenetic haplotype revealing a cell-to-cell methylation heterogeneity...
November 18, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27858497/high-fat-diet-and-exercise-lead-to-a-disrupted-and-pathogenic-dna-methylome-in-mouse-liver
#8
Dan Zhou, Ryan A Hlady, Marissa J Schafer, Thomas A White, Chen Liu, Jeong-Hyeon Choi, Jordan D Miller, Lewis R Roberts, Nathan K LeBrasseur, Keith D Robertson
High-fat diet consumption and sedentary life style elevates risk for obesity, non-alcoholic fatty liver disease, and cancer. Exercise training conveys health benefits in populations with or without these chronic conditions. Diet and exercise regulate gene expression by mediating epigenetic mechanisms in many tissues; however, such effects are poorly documented in the liver, a central metabolic organ. To dissect the consequences of diet and exercise on the liver epigenome, we measured DNA methylation, using reduced representation bisulfite sequencing, and transcription, using RNA-seq, in mice maintained on a fast food diet with sedentary lifestyle or exercise, compared to control diet with and without exercise...
November 18, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27846368/epigenetic-therapy-approaches-in-non-small-cell-lung-cancer-update-and-perspectives
#9
Insa Schiffmann, Gabriele Greve, Manfred Jung, Michael Lübbert
Non-small cell lung cancer (NSCLC) still constitutes the most common cancer-related cause of death worldwide. All efforts to introduce suitable treatment options using chemotherapeutics or targeted therapies have, up to this point, failed to exhibit a substantial effect on the 5-year-survival rate. The involvement of epigenetic alterations in the evolution of different cancers has led to the development of epigenetics-based therapies, mainly targeting DNA methyltransferases (DNMTs) and histone-modifying enzymes...
November 15, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27830979/dietary-and-supplemental-maternal-methyl-group-donor-intake-and-cord-blood-dna-methylation
#10
Sara Pauwels, Manosij Ghosh, Radu Corneliu Duca, Bram Bekaert, Kathleen Freson, Inge Huybrechts, Sabine Langie, Gudrun Koppen, Roland Devlieger, Lode Godderis
Maternal nutrition is critically involved in the development and health of the fetus. We evaluated maternal methyl-group donor intake through diet (methionine, betaine, choline, folate) and supplementation (folic acid) before and during pregnancy in relation to global DNA methylation and hydroxymethylation and gene specific (IGF2 DMR, DNMT1, LEP, RXRA) cord blood methylation. A total of 115 mother-infant pairs were enrolled in the MAternal Nutrition and Offspring's Epigenome (MANOE) study. The intake of methyl-group donors was assessed using a food-frequency questionnaire...
November 10, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27824296/lens-development-requires-dnmt1-but-takes-place-normally-in-the-absence-of-both-dnmt3a-and-dnmt3b-activity
#11
Thanh V Hoang, Evan R Horowitz, Blake R Chaffee, Peipei Qi, Rachel E Flake, Devin G Bruney, Blake J Rasor, Savana E Rosalez, Brad D Wagner, Michael L Robinson
Despite the wealth of knowledge of transcription factors involved in lens development, little information exists about the role of DNA methylation in this process. Here, we investigated the role of DNA methylation in lens development and fiber cell differentiation using mice conditionally lacking maintenance or de novo methyltransferases in the lens lineage. We found that while Dnmt1 inactivation at the lens placode stage (via the Le-Cre transgene) led to lens DNA hypomethylation and severe lens epithelial apoptosis, lens fiber cell differentiation remained largely unaffected...
November 8, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27824289/peg3-binds-to-h19-icr-as-a-transcriptional-repressor
#12
An Ye, Hongzhi He, Joomyeong Kim
Paternally expressed gene 3 (Peg3) encodes a DNA-binding protein with twelve C2H2 zinc finger motifs. In the current study, we performed ChIP-seq using mouse embryonic fibroblast (MEF) cells. This experiment identified a set of 16 PEG3 genomic targets, the majority of which overlapped with the promoter regions of genes with oocyte expression. These potential downstream genes were upregulated in MEF cells lacking PEG3 protein, suggesting a potential repressor role for PEG3. Our study also identified the imprinting control region (ICR) of H19 as a genomic target...
November 8, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27801613/12th-conference-on-transcription-and-chromatin-august-27-30-2016-heidelberg-germany
#13
Sascha H C Duttke
A pleasant atmosphere and outstanding science certainly made the 12th EMBL Conference on Transcription and Chromatin an event to remember. With 62 talks and over 200 posters, there was no shortage of cutting edge research to catch on.
November 1, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27786608/de-novo-methylation-in-male-germ-cells-of-the-common-marmoset-monkey-occurs-during-postnatal-development-and-is-maintained-in-vitro
#14
Daniel Langenstroth-Röwer, Jörg Gromoll, Joachim Wistuba, Ina Tröndle, Sandra Laurentino, Stefan Schlatt, Nina Neuhaus
The timing of de novo DNA methylation in male germ cells during human testicular development is yet unsolved. Apart from that, the stability of established imprinting patterns in vitro is controversially discussed. This study aimed at determining the timing of DNA de novo methylation and at assessing the stability of the methylation status in vitro. We employed the marmoset monkey (Callithrix jacchus) as it is considered the best non-human primate model for human testicular development. We selected neonatal, pre-pubertal, pubertal, and adult animals (n = 3, each) and assessed germ cell global DNA methylation levels by 5-methyl cytosine staining, and Alu elements and gene-specific methylation (H19, LIT1, SNRPN, MEST, OCT4, MAGE-A4, and DDX-4) by pyrosequencing...
October 27, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27786595/cocaine-mediated-downregulation-of-microglial-mir-124-expression-involves-promoter-dna-methylation
#15
Ming-Lei Guo, Palsamy Periyasamy, Ke Liao, Yeon Hee Kook, Fang Niu, Shannon E Callen, Shilpa Buch
Neuroinflammation plays a critical role in the development of reward-related behavior in cocaine self-administration rodents. Cocaine, one of most commonly abused drugs, has been shown to activate microglia both in vitro and in vivo. Detailed molecular mechanisms underlying cocaine-mediated microglial activation remain poorly understood. microRNAs (miRs), belonging to a class of small noncoding RNA superfamily have been shown to modulate the activation status of microglia. miR-124, one of the microglia-enriched miRs, functions as an anti-inflammatory regulator that maintains microglia in a quiescent state...
October 27, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27767379/identification-and-characterization-of-pkf118-310-as-a-kdm4a-inhibitor
#16
Gianluigi Franci, Federica Sarno, Angela Nebbioso, Lucia Altucci
Epigenetic modifications are functionally involved in gene expression regulation. In particular, histone posttranslational modifications play a crucial role in functional chromatin organization. Several drugs able to inhibit or stimulate some families of proteins involved in epigenetic histone regulation have been found, a number of which are FDA-approved for the treatment of cutaneous T-cell lymphoma or are in phase I/II/III clinical trials for solid tumors. Although some protein families, such as histone deacetylases and their inhibitors, are well characterized, our understanding of histone lysine demethylases is still incomplete...
October 21, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27748645/modelling-dna-methylation-by-analyzing-the-individual-configurations-of-single-molecules
#17
Ornella Affinito, Giovanni Scala, Domenico Palumbo, Ermanno Florio, Antonella Monticelli, Gennaro Miele, Vittorio Enrico Avvedimento, Alessandro Usiello, Lorenzo Chiariotti, Sergio Cocozza
DNA methylation is often analyzed by reporting the average methylation degree of each cytosine. In this study, we used a single molecule methylation analysis in order to look at the methylation conformation of individual molecules. Using D-aspartate oxidase as a model gene, we performed an in-depth methylation analysis through the developmental stages of three different mouse tissues (brain, lung, and gut), where this gene undergoes opposite methylation destiny. This approach allowed us to track both methylation and demethylation processes at high resolution...
October 17, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27689695/epigenetic-regulation-of-glycosylation-and-the-impact-on-chemo-resistance-in-breast-and-ovarian-cancer
#18
Gordon Greville, Amanda McCann, Pauline M Rudd, Radka Saldova
Glycosylation is one of the most fundamental posttranslational modifications in cellular biology and has been shown to be epigenetically regulated. Understanding this process is important as the clinical use of epigenetic therapies such as DNA methyltransferase inhibitors are undergoing clinical trials for the treatment of ovarian and breast cancer. Previous work has demonstrated that altered glycosylation patterns are associated with aggressive disease in women presenting with breast and ovarian cancer. Moreover, the tumor microenvironment of hypoxia results in globally altered DNA methylation and is associated with aggressive cancer phenotypes and chemo-resistance, a feature integral to many cancers...
September 30, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27689475/cdo1-promoter-methylation-is-associated-with-gene-silencing-and-is-a-prognostic-biomarker-for-biochemical-recurrence-free-survival-in-prostate-cancer-patients
#19
Sebastian Meller, Lisa Zipfel, Heidrun Gevensleben, Jörn Dietrich, Jörg Ellinger, Michael Majores, Johannes Stein, Verena Sailer, Maria Jung, Glen Kristiansen, Dimo Dietrich
Molecular biomarkers may facilitate the distinction between aggressive and clinically insignificant prostate cancer (PCa), thereby potentially aiding individualized treatment. We analyzed cysteine dioxygenase 1 (CDO1) promoter methylation and mRNA expression in order to evaluate its potential as prognostic biomarker. CDO1 methylation and mRNA expression were determined in cell lines and formalin-fixed paraffin-embedded prostatectomy specimens from a first cohort of 300 PCa patients using methylation-specific qPCR and qRT-PCR...
September 30, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27668573/validation-of-a-dna-methylation-reference-panel-for-the-estimation-of-nucleated-cells-types-in-cord-blood
#20
Andres Cardenas, Catherine Allard, Myriam Doyon, E Andres Houseman, Kelly M Bakulski, Patrice Perron, Luigi Bouchard, Marie-France Hivert
Cord blood is widely used as surrogate tissue in epigenome-wide association studies of prenatal conditions. Cell type composition variation across samples can be an important confounder of epigenome-wide association studies in blood that constitute a mixture of cells. We evaluated a newly developed cord blood reference panel to impute cell type composition from DNA methylation levels, including nucleated red blood cells (nRBCs). We estimated cell type composition from 154 unique cord blood samples with available DNA methylation data as well as direct measurements of nucleated cell types...
September 26, 2016: Epigenetics: Official Journal of the DNA Methylation Society
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