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Epigenetics: Official Journal of the DNA Methylation Society

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https://www.readbyqxmd.com/read/28621618/placental-imprinting-variation-associated-with-assisted-reproductive-technologies-and-subfertility
#1
Julia F Litzky, Maya A Deyssenroth, Todd M Everson, David A Armstrong, Luca Lambertini, Jia Chen, Carmen J Marsit
Infertility affects one in six couples in developed nations, resulting in an increasing use of assisted reproductive technologies (ART). Both ART and subfertility appear to be linked to lower birth weight outcomes, setting infants up for poor long-term health. Prenatal growth is, in part, regulated via epigenetically controlled imprinted genes in the placenta. Although differences in DNA methylation between ART and control infants have been found, it remains unclear whether these differences are due to the ART procedures or to the underlying parental subfertility and how these methylation differences affect imprinted gene expression...
June 16, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28621576/tethering-of-lsh-at-the-oct4-locus-promotes-gene-repression-associated-with-epigenetic-changes
#2
Jianke Ren, Nathaniel A Hathaway, Gerald R Crabtree, Kathrin Muegge
Lsh is a chromatin remodeling factor that regulates DNA methylation and chromatin function in mammals. The dynamics of these chromatin changes and whether they are directly controlled by Lsh remain unclear. To understand the molecular mechanisms of Lsh chromatin controlled regulation of gene expression, we established a tethering system that recruits a Gal4-Lsh fusion protein to an engineered Oct4 locus through Gal4 binding sites in murine embryonic stem (ES) cells. We examined the molecular epigenetic events induced by Lsh binding including: histone modification, DNA methylation and chromatin accessibility to determine nucleosome occupancy before and after embryonic stem cell differentiation...
June 16, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28557629/comparative-analysis-of-12-different-kits-for-bisulfite-conversion-of-circulating-cell-free-dna
#3
Mai-Britt Worm Ørntoft, Sarah Østrup Jensen, Thomas Birkballe Hansen, Jesper Bertram Bramsen, Claus Lindbjerg Andersen
Blood circulating cell-free DNA (cfDNA) is becoming popular in the search of promising predictive and prognostic biomarkers. Among these biomarkers, cfDNA methylation markers have especially gained considerable attention. A significant challenge in the utilization of cfDNA methylation markers is the limited amount of cfDNA available for analyses; reportedly, bisulfite conversion (BSC) reduce cfDNA amounts even further. Nevertheless, few efforts have focused on ensuring high cfDNA conversion efficiency and recovery after BSC...
May 30, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28557603/genome-wide-methyl-seq-analysis-of-blood-brain-targets-of-glucocorticoid-exposure
#4
Fayaz Seifuddin, Gary Wand, Olivia Cox, Mehdi Pirooznia, Laura Moody, Xiaoju Yang, Jonathan Tai, Gretha Boersma, Kellie Tamashiro, Peter Zandi, Richard Lee
Chronic exposure to glucocorticoids (GCs) can lead to psychiatric complications through epigenetic mechanisms such as DNA methylation (DNAm). We sought to determine whether epigenetic changes in a peripheral tissue can serve as a surrogate for those in a relatively inaccessible tissue such as the brain. DNA extracted from the hippocampus and blood of mice treated with GCs or vehicle solution was assayed using a genome-wide DNAm platform (Methyl-Seq) to identify differentially methylated regions (DMRs) induced by GC treatment...
May 30, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28557546/inflammation-associated-dna-methylation-patterns-in-epithelium-of-ulcerative-colitis
#5
Alan Barnicle, Cathal Seoighe, John M Greally, Aaron Golden, Laurence J Egan
Aberrant DNA methylation patterns have been reported in inflamed tissues and may play a role in disease. We studied DNA methylation and gene expression profiles of purified intestinal epithelial cells from ulcerative colitis patients, comparing inflamed and non-inflamed areas of the colon. We identified 577 differentially methylated sites (false discovery rate <0.2) mapping to 210 genes. From gene expression data from the same epithelial cells, we identified 62 differentially expressed genes with increased expression in the presence of inflammation at prostate cancer susceptibility genes PRAC1 and PRAC2...
May 30, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28548590/prenatal-exposure-to-neurotoxic-metals-is-associated-with-increased-placental-glucocorticoid-receptor-dna-methylation
#6
Allison A Appleton, Brian P Jackson, Margaret Karagas, Carmen J Marsit
Epigenetic alterations related to prenatal neurotoxic metals exposure may be key in understanding the origins of cognitive and neurobehavioral problems in children. Placental glucocorticoid receptor (NR3C1) methylation has been linked to neurobehavioral risk in early life, but has not been examined in response to neurotoxic metals exposure despite parallel lines of research showing metals exposure and NR3C1 methylation each contribute to a similar set of neurobehavioral phenotypes. Thus, we conducted a study of prenatal neurotoxic metals exposure and placental NR3C1 methylation in a cohort of healthy term singleton pregnancies from Rhode Island, USA (n = 222)...
May 26, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28524769/machine-learning-for-epigenetics-and-future-medical-applications
#7
Lawrence B Holder, M Muksitul Haque, Michael K Skinner
Understanding epigenetic processes holds immense promise for medical applications. Advances in Machine Learning (ML) are critical to realize this promise. Previous studies used epigenetic data sets associated with the germline transmission of epigenetic transgenerational inheritance of disease and novel ML approaches to predict genome-wide locations of critical epimutations. A combination of Active Learning (ACL) and Imbalanced Class Learning (ICL) was used to address past problems with ML to develop a more efficient feature selection process and address the imbalance problem in all genomic data sets...
May 19, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28494218/maternal-cigarette-smoking-during-pregnancy-and-offspring-dna-methylation-in-midlife
#8
Parisa Tehranifar, Hui-Chen Wu, Jasmine A McDonald, Farzana Jasmine, Regina M Santella, Irina Gurvich, Julie D Flom, Mary Beth Terry
Maternal smoking in pregnancy (MSP) has been associated with DNA methylation in specific CpG sites in infants and children. We investigated whether MSP, independent of own personal active smoking, was associated with midlife DNA methylation in CpGs that were previously identified in studies of MSP-DNA methylation in children. We used data on MSP collected from pregnant mothers of 89 adult women born in 1959-1964 and measured DNA methylation measured in blood (granulocytes) collected in 2001-2007 (mean age: 43 years)...
May 11, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28486003/placental-lipoprotein-lipase-dna-methylation-alterations-are-associated-with-gestational-diabetes-and-body-composition-at-5%C3%A2-years-of-age
#9
Valérie Gagné-Ouellet, Andrée-Anne Houde, Simon-Pierre Guay, Patrice Perron, Daniel Gaudet, Renée Guérin, Jean-Patrice Baillargeon, Marie-France Hivert, Diane Brisson, Luigi Bouchard
Gestational diabetes mellitus (GDM) is associated with obesity in childhood. This suggests that consequences of in utero exposure to maternal hyperglycemia extend beyond the fetal development, possibly through epigenetic programming. The aims of this study were to assess whether placental DNA methylation (DNAm) marks were associated with maternal GDM status and to offspring body composition at 5 years old in a prospective birth cohort. DNAm levels were measured in the fetal side of the placenta in 66 samples (24 from GDM mothers) using bisDNA-pyrosequencing...
May 9, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28448736/orphan-cpg-islands-define-a-novel-class-of-highly-active-enhancers
#10
Joshua S K Bell, Paula M Vertino
CpG islands (CGI) are critical genomic regulatory elements that support transcriptional initiation and are associated with the promoters of most human genes. CGI are distinguished from the bulk genome by their high CpG density, lack of DNA methylation, and euchromatic features. While CGI are canonically known as strong promoters, thousands of 'orphan' CGI lie far from any known transcript, leaving their function an open question. We undertook a comprehensive analysis of the epigenetic state of orphan CGI across over 100 cell types...
April 27, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28426282/emerging-roles-of-macrosatellite-repeats-in-genome-organization-and-disease-development
#11
Gabrijela Dumbovic, Sonia-V Forcales, Manuel Perucho
Abundant repetitive DNA sequences are an enigmatic part of the human genome. Despite increasing evidence on the functionality of DNA repeats, their biologic role is still elusive and under frequent debate. Macrosatellites are the largest of the tandem DNA repeats, located on one or multiple chromosomes. The contribution of macrosatellites to genome regulation and human health was demonstrated for the D4Z4 macrosatellite repeat array on chromosome 4q35. Reduced copy number of D4Z4 repeats is associated with local euchromatinization and the onset of facioscapulohumeral muscular dystrophy...
April 20, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28426276/integrative-epigenetic-and-genetic-pan-cancer-somatic-alteration-portraits
#12
Lucas A Salas, Kevin C Johnson, Devin C Koestler, Dylan E O'Sullivan, Brock C Christensen
Genetic and epigenetic alterations are required for carcinogenesis and the mutation burden across tumor types has been investigated. Here, we investigate epigenetic alterations with a novel measure of global DNA methylation dysregulation, the methylation dysregulation index (MDI), across 14 cancer types in The Cancer Genome Atlas (TCGA) database. DNA methylation data-obtained using Illumina HumanMethylation450 BeadChip-was accessed from TCGA. We calculated the MDI in 14 tumor types (n = 5,592 tumors), using adjacent normal tissues (n = 701) from each tumor site...
April 20, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28402695/uhrf2-regulates-local-5-methylcytosine-and-suppresses-spontaneous-seizures
#13
Yidan Liu, Bin Zhang, Xiaoyu Meng, Matthew J Korn, Jack M Parent, Lin-Yu Lu, Xiaochun Yu
The 5-methylcytosine (5mC) modification regulates multiple cellular processes and is faithfully maintained following DNA replication. In addition to DNA methyltransferase (DNMT) family proteins, ubiquitin-like PHD and ring finger domain-containing protein 1 (UHRF1) plays an important role in the maintenance of 5 mC levels. Loss of UHRF1 abolishes 5 mC in cells and leads to embryonic lethality in mice. Interestingly, UHRF1 has a paralog, UHRF2, that has similar sequence and domain architecture, but its biological function is not clear...
April 12, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28387599/novel-insights-into-systemic-autoimmune-rheumatic-diseases-using-shared-molecular-signatures-and-an-integrative-analysis
#14
Marie Hudson, Sasha Bernatsky, Ines Colmegna, Maximilien Lora, Tomi Pastinen, Kathleen Klein Oros, Celia M T Greenwood
We undertook this study to identify DNA methylation signatures of three systemic autoimmune rheumatic diseases (SARDs), namely rheumatoid arthritis, systemic lupus erythematosus, and systemic sclerosis, compared to healthy controls. Using a careful design to minimize confounding, we restricted our study to subjects with incident disease and performed our analyses on purified CD4(+) T cells, key effector cells in SARD. We identified differentially methylated (using the Illumina Infinium HumanMethylation450 BeadChip array) and expressed (using the Illumina TruSeq stranded RNA-seq protocol) sites between cases and controls, and investigated the biological significance of this SARD signature using gene annotation databases...
April 7, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28387569/associations-between-post-translational-histone-modifications-myelomeningocele-risk-environmental-arsenic-exposure-and-folate-deficiency-among-participants-in-a-case-control-study-in-bangladesh
#15
Jannah Tauheed, Marco Sanchez-Guerra, Jane J Lee, Ligi Paul, Md Omar Sharif Ibne Hasan, Quazi Quamruzzaman, Jacob Selhub, Robert O Wright, David C Christiani, Brent A Coull, Andrea A Baccarelli, Maitreyi Mazumdar
Arsenic exposure may contribute to disease risk in humans through alterations in the epigenome. Previous studies reported that arsenic exposure is associated with changes in plasma histone concentrations. Posttranslational histone modifications have been found to differ between the brain tissue of human embryos with neural tube defects and that of controls. Our objectives were to investigate the relationships between plasma histone 3 levels, history of having an infant with myelomeningocele, biomarkers of arsenic exposure, and maternal folate deficiency...
April 7, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28387568/non-linear-patterns-in-age-related-dna-methylation-may-reflect-cd4-t-cell-differentiation
#16
Nicholas D Johnson, Howard W Wiener, Alicia K Smith, Shota Nishitani, Devin M Absher, Donna K Arnett, Stella Aslibekyan, Karen N Conneely
DNA methylation (DNAm) is an important epigenetic process involved in the regulation of gene expression. While many studies have identified thousands of loci associated with age, few have differentiated between linear and non-linear DNAm trends with age. Non-linear trends could indicate early- or late-life gene regulatory processes. Using data from the Illumina 450K array on 336 human peripheral blood samples, we identified 21 CpG sites that associated with age (P<1.03E-7) and exhibited changing rates of DNAm change with age (P<1...
April 7, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28362134/estrogen-signaling-through-estrogen-receptor-%C3%AE-regulates-dna-methylation-and-its-machinery-in-male-germ-line-in-adult-rats
#17
Kushaan Dumasia, Anita Kumar, Sharvari Deshpande, Nafisa H Balasinor
Estrogen, through its receptors, regulates various aspects of spermatogenesis and male fertility. To understand the roles of estrogen receptors (ERα and ERβ) in male fertility, we have developed in vivo selective ER agonist administration models. Treatment of adult male rats with ERα or ERβ agonist for 60 d decreases fertility and litter size mainly due to increased pre- and post-implantation embryo loss. Since epigenetic mechanisms like DNA methylation play a crucial role in male fertility, we investigated the effects of the ER agonists on DNA methylation in spermatozoa...
March 31, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28358281/dna-methylation-aberrancies-as-a-guide-for-surveillance-and-treatment-of-human-cancers
#18
Gangning Liang, Daniel J Weisenberger
DNA methylation aberrancies are hallmarks of human cancers and are characterized by global DNA hypomethylation of repetitive elements and non-CpG rich regions concomitant with locus-specific DNA hypermethylation. DNA methylation changes may result in altered gene expression profiles, most notably the silencing of tumor suppressors, microRNAs, endogenous retorviruses and tumor antigens due to promoter DNA hypermethylation, as well as oncogene upregulation due to gene-body DNA hypermethylation. Here, we review DNA methylation aberrancies in human cancers, their use in cancer surveillance and the interplay between DNA methylation and histone modifications in gene regulation...
March 30, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28541128/epigenetic-drugs-more-than-meets-the-eye
#19
Manel Esteller
No abstract text is available yet for this article.
May 4, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28277979/structural-insight-into-inhibitors-of-flavin-adenine-dinucleotide-dependent-lysine-demethylases
#20
Hideaki Niwa, Takashi Umehara
Until 2004, many researchers believed that protein methylation in eukaryotic cells was an irreversible reaction. However, the discovery of lysine-specific demethylase 1 in 2004 drastically changed this view and the concept of chromatin regulation. Since then, the enzymes responsible for lysine demethylation and their cellular substrates, biological significance, and selective regulation have become major research topics in epigenetics and chromatin biology. Many cell-permeable inhibitors for lysine demethylases have been developed, including both target-specific and nonspecific inhibitors...
May 4, 2017: Epigenetics: Official Journal of the DNA Methylation Society
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