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Methylomics

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https://www.readbyqxmd.com/read/29778942/transcriptomic-and-methylomic-analysis-reveal-the-toxicological-effect-of-2-3-7-8-tetrachlorodibenzodioxin-on-human-embryonic-stem-cell
#1
Keng Po Lai, Jing Woei Li, Ting Fung Chan, Andy Chen, Cherie Yin Lau Lee, William Shu Biu Yeung, Chris Kong Chu Wong
Cumulating epidemiological studies demonstrated that environmental exposure to endocrine disrupting chemicals (EDCs) during the early stages of fetal development is associated with the increase in disease susceptibility in later life. The fetal developmental plasticity is considered as a protective mechanism against an undesirable prenatal environment. Dioxin is one of the environmental contaminants and is considered a diabetogenic factor. Experimental animal and human epidemiological studies have revealed that dioxin exposure was associated with insulin resistance and altered beta cell function...
May 10, 2018: Chemosphere
https://www.readbyqxmd.com/read/29775429/genome-wide-dna-methylation-profiles-of-porcine-ovaries-in-estrus-and-proestrus
#2
Xiaolong Zhou, Songbai Yang, Feifei Yan, Ke He, Ayong Zhao
DNA methylation is an important epigenetic modification involved in the estrous cycle and the regulation of reproduction. Here, we investigated the genome-wide profiles of DNA methylation in porcine proestrus and estrus ovaries using methylated DNA immunoprecipitation sequencing (MeDIP-seq). The results showed that DNA methylation was enriched in intergenic and intron regions. The methylation levels of coding regions were higher than those of the 5' and 3' flanking regions of genes. There were 4813 differentially methylated regions (DMRs) of CpG islands in the estrus vs...
May 18, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29764913/mapping-and-characterizing-n6-methyladenine-in-eukaryotic-genomes-using-single-molecule-real-time-sequencing
#3
Shijia Zhu, John Beaulaurier, Gintaras Deikus, Tao Wu, Maya Strahl, Ziyang Hao, Guanzheng Luo, James A Gregory, Andrew Chess, Chuan He, Andrew Xiao, Robert Sebra, Eric E Schadt, Gang Fang
N6-methyladenine (m6dA) has been discovered as a novel form of DNA methylation prevalent in eukaryotes, however, methods for high resolution mapping of m6dA events are still lacking. Single-molecule real-time (SMRT) sequencing has enabled the detection of m6dA events at single-nucleotide resolution in prokaryotic genomes, but its application to detecting m6dA in eukaryotic genomes has not been rigorously examined. Herein, we identified unique characteristics of eukaryotic m6dA methylomes that fundamentally differ from those of prokaryotes...
May 15, 2018: Genome Research
https://www.readbyqxmd.com/read/29759990/epigenetic-targeting-of-adipocytes-inhibits-high-grade-serous-ovarian-cancer-cell-migration-and-invasion
#4
Jessica Tang, Nicholas Pulliam, Ali Ozes, Aaron Buechlein, Ning Ding, Doug Rusch, Harold Keer, Heather O'Hagan, M Sharon Stack, Kenneth P Nephew
Ovarian cancer (OC) cells frequently metastasize to the omentum and adipocytes play a significant role in ovarian tumor progression. Therapeutic interventions targeting aberrant DNA methylation in ovarian tumors have shown promise in the clinic but the effects of epigenetic therapy on the tumor microenvironment are understudied. Here, we examined the effect of adipocytes on OC cell behavior in culture and impact of targeting DNA methylation in adipocytes on OC metastasis. The presence of adipocytes increased OC cell migration and invasion and proximal and direct co-culture of adipocytes increased OC proliferation alone or after treatment with carboplatin...
May 14, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29748167/kdm5b-decommissions-the-h3k4-methylation-landscape-of-self-renewal-genes-during-trophoblast-stem-cell-differentiation
#5
Jian Xu, Benjamin L Kidder
Trophoblast stem (TS) cells derived from the trophectoderm (TE) of mammalian embryos have the ability to self-renew indefinitely or differentiate into fetal lineages of the placenta. Epigenetic control of gene expression plays an instrumental role in dictating the fate of TS cell self-renewal and differentiation. However, the roles of histone demethylases and activating histone modifications such as methylation of histone 3 lysine 4 (H3K4me3/me2) in regulating TS cell expression programs, and in priming the epigenetic landscape for trophoblast differentiation, are largely unknown...
May 10, 2018: Biology Open
https://www.readbyqxmd.com/read/29747401/the-dna-methylome-and-association-of-differentially-methylated-regions-with-differential-gene-expression-during-heat-stress-in-brassica-rapa
#6
Gaofeng Liu, Yudong Xia, Tongkun Liu, Shaojun Dai, Xilin Hou
Cytosine DNA methylation is a critical epigenetic mechanism in the silencing of transposable elements, imprinting and regulating gene expression. However, little is known about the potential role of mC in response to heat stress. To determine and explore the functions of the dynamic DNA methylome during heat stress, we characterized single-base resolution methylome maps of Brassica rapa and assessed the dynamic changes of mC under heat stress using whole genome bisulfite sequencing. On average, the DNA methylation levels of CG, CHG and CHH are 39...
May 9, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29744254/an-integrated-view-of-the-role-of-mir-130b-301b-mirna-cluster-in-prostate-cancer
#7
Rafael Sebastián Fort, Cecilia Mathó, Carolina Oliveira-Rizzo, Beatriz Garat, José Roberto Sotelo-Silveira, María Ana Duhagon
Prostate cancer is a major health problem worldwide due to its high incidence morbidity and mortality. There is currently a need of improved biomarkers, capable to distinguish mild versus aggressive forms of the disease, and thus guide therapeutic decisions. Although miRNAs deregulated in cancer represent exciting candidates as biomarkers, its scientific literature is frequently fragmented in dispersed studies. This problem is aggravated for miRNAs belonging to miRNA gene clusters with shared target genes. The miRNA cluster composed by hsa-mir-130b and hsa-mir-301b precursors was recently involved in prostate cancer pathogenesis, yet different studies assigned it opposite effects on the disease...
2018: Experimental Hematology & Oncology
https://www.readbyqxmd.com/read/29743320/prospective-longitudinal-study-of-the-pregnancy-dna-methylome-the-us-pregnancy-race-environment-genes-preg-study
#8
Dana M Lapato, Sara Moyer, Emily Olivares, Ananda B Amstadter, Patricia A Kinser, Shawn J Latendresse, Colleen Jackson-Cook, Roxann Roberson-Nay, Jerome F Strauss, Timothy P York
PURPOSE: The goal of the Pregnancy, Race, Environment, Genes study was to understand how social and environmental determinants of health (SEDH), pregnancy-specific environments (PSE) and biological processes influence the timing of birth and account for the racial disparity in preterm birth. The study followed a racially diverse longitudinal cohort throughout pregnancy and included repeated measures of PSE and DNA methylation (DNAm) over the course of gestation and up to 1 year into the postpartum period...
May 9, 2018: BMJ Open
https://www.readbyqxmd.com/read/29740169/gain-of-function-mutations-in-dnmt3a-in-patients-with-paraganglioma
#9
Laura Remacha, Maria Currás-Freixes, Raúl Torres-Ruiz, Francesca Schiavi, Rafael Torres-Pérez, Bruna Calsina, Rocío Letón, Iñaki Comino-Méndez, Juan M Roldán-Romero, Cristina Montero-Conde, María Santos, Lucía Inglada Pérez, Guillermo Pita, María R Alonso, Emiliano Honrado, Susana Pedrinaci, Benedicto Crespo-Facorro, Antonio Percesepe, Maurizio Falcioni, Sandra Rodríguez-Perales, Esther Korpershoek, Santiago Ramón-Maiques, Giuseppe Opocher, Cristina Rodríguez-Antona, Mercedes Robledo, Alberto Cascón
PURPOSE: The high percentage of patients carrying germline mutations makes pheochromocytomas/paragangliomas the most heritable of all tumors. However, there are still cases unexplained by mutations in the known genes. We aimed to identify the genetic cause of disease in patients strongly suspected of having hereditary tumors. METHODS: Whole-exome sequencing was applied to the germlines of a parent-proband trio. Genome-wide methylome analysis, RNA-seq, CRISPR/Cas9 gene editing, and targeted sequencing were also performed...
May 8, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29732534/epigenetic-loss-of-heparan-sulfate-3-o-sulfation-sensitizes-ovarian-carcinoma-to-oncogenic-signals-and-predicts-prognosis
#10
Rui-Lan Huang, Hsiang-Ju Chen, Lin-Yu Chen, Tai-Kuang Chao, Wei-Yu Lin, Phui-Ly Liew, Po-Hsuan Su, Yu-Chun Weng, Yu-Chi Wang, Chi-Chun Liao, Yaw-Wen Hsu, Hui- Chen Wang, Hung-Cheng Lai
Precision medicine requires markers for therapeutic guidance. The purpose of this study was to determine whether epithelial ovarian cancer (EOC) epigenetics can lead to the identification of biomarkers for precision medicine. Through integrative methylomics, we discovered and validated the epigenetic signature of NEFH and HS3ST2 as an independent prognostic factor for type II EOC in our dataset (n = 84), two independent methylomics datasets (total n = 467). Integrated transcriptomics dataset (n = 1147) and tissue microarrays (n = 54) of HS3ST2 also related to high-methylation statuses and the EOC prognosis...
May 7, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29728363/increased-hepatic-pdgf-aa-signaling-mediates-liver-insulin-resistance-in-obesity-associated-type-2-diabetes
#11
Amar Abderrahmani, Loïc Yengo, Robert Caiazzo, Mickaël Canouil, Stéphane Cauchi, Violeta Raverdy, Valérie Plaisance, Valérie Pawlowski, Stéphane Lobbens, Julie Maillet, Laure Rolland, Raphael Boutry, Gurvan Queniat, Maxime Kwapich, Mathie Tenenbaum, Julien Bricambert, Sophie Saussenthaler, Elodie Anthony, Pooja Jha, Julien Derop, Olivier Sand, Iandry Rabearivelo, Audrey Leloire, Marie Pigeyre, Martine Daujat-Chavanieu, Sabine Gerbal-Chaloin, Tasnim Dayeh, Guillaume Lassailly, Philippe Mathurin, Bart Staels, Johan Auwerx, Annette Schürmann, Catherine Postic, Clemens Schafmayer, Jochen Hampe, Amélie Bonnefond, François Pattou, Philippe Froguel
In type 2 diabetes (T2D), hepatic insulin resistance is strongly associated with non-alcoholic fatty liver disease (NAFLD). In this study, we hypothesized that DNA methylome of livers from patients with T2D, when compared to livers of individuals with normal plasma glucose levels, can unveil some mechanism of hepatic insulin resistance that could link to NAFLD. Using DNA methylome and transcriptome analyses of livers from obese individuals, we found that both hypomethylation at a CpG site in PDGFA (encoding platelet derived growth factor alpha) and PDGFA overexpression are associated with increased T2D risk, hyperinsulinemia, increased insulin resistance and increased steatohepatitis risk...
May 4, 2018: Diabetes
https://www.readbyqxmd.com/read/29727682/retinoid-sensitive-epigenetic-regulation-of-the-hoxb-cluster-maintains-normal-hematopoiesis-and-inhibits-leukemogenesis
#12
Pengxu Qian, Bony De Kumar, Xi C He, Christof Nolte, Madelaine Gogol, Youngwook Ahn, Shiyuan Chen, Zhenrui Li, Hanzhang Xu, John M Perry, Deqing Hu, Fang Tao, Meng Zhao, Yingli Han, Kate Hall, Allison Peak, Ariel Paulson, Chongbei Zhao, Aparna Venkatraman, Andrew Box, Anoja Perera, Jeffrey S Haug, Tari Parmely, Hua Li, Robb Krumlauf, Linheng Li
Hox genes modulate the properties of hematopoietic stem cells (HSCs) and reacquired Hox expression in progenitors contributes to leukemogenesis. Here, our transcriptome and DNA methylome analyses revealed that Hoxb cluster and retinoid signaling genes are predominantly enriched in LT-HSCs, and this coordinate regulation of Hoxb expression is mediated by a retinoid-dependent cis-regulatory element, distal element RARE (DERARE). Deletion of the DERARE reduced Hoxb expression, resulting in changes to many downstream signaling pathways (e...
May 3, 2018: Cell Stem Cell
https://www.readbyqxmd.com/read/29725341/massive-loss-of-dna-methylation-in-nitrogen-but-not-in-phosphorus-deficient-zea-mays-roots-is-poorly-correlated-with-gene-expression-differences
#13
Svenja Mager, Uwe Ludewig
DNA methylation in plants plays a role in transposon silencing, genome stability and gene expression regulation. Environmental factors alter the methylation pattern of DNA and recently nutrient stresses, such as phosphate starvation, were shown to alter DNA methylation. Furthermore, DNA methylation had been frequently addressed in plants with notably small genomes that are poor in transposons. Here, we compare part of the DNA methylome of nitrogen- and phosphorus-deficient maize roots by reduced representation sequencing and analyze their relationship with gene expression under prolonged stresses...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29723955/the-methylome-of-vertebrate-sex-chromosomes
#14
REVIEW
Shafagh A Waters, Alexander Capraro, Kim L McIntyre, Jennifer A Marshall Graves, Paul D Waters
DNA methylation is a key epigenetic modification in vertebrate genomes known to be involved in the regulation of gene expression, X chromosome inactivation, genomic imprinting, chromatin structure, and control of transposable elements. DNA methylation is common to all eukaryote genomes, but we still lack a complete understanding of the variation in DNA methylation patterns on sex chromosomes and between the sexes in diverse species. To better understand sex chromosome DNA methylation patterns between different amniote vertebrates, we review literature that has analyzed the genome-wide distribution of DNA methylation in mammals and birds...
May 1, 2018: Genes
https://www.readbyqxmd.com/read/29717273/identification-of-an-episignature-of-human-colorectal-cancer-associated-with-obesity-by-genome-wide-dna-methylation-analysis
#15
Ana B Crujeiras, Sonsoles Morcillo, Angel Diaz-Lagares, Juan Sandoval, Daniel Castellano-Castillo, Esperanza Torres, David Hervas, Sebastian Moran, Manel Esteller, Manuel Macias-Gonzalez, Felipe F Casanueva, Francisco J Tinahones
BACKGROUND: Obesity was established as a relevant modifiable risk factor in the onset and progression of colorectal cancer (CRC). This relationship could be mediated by an epigenetic regulation. OBJECTIVES: The current work aimed to explore the effects of excess body weight on the DNA methylation profile of CRC using a genome-wide DNA methylation approach and to identify an epigenetic signature of obesity-related CRC. METHODS: Fifty-six CRC-diagnosed patients (50 years) were included in the study and categorized according to their body mass index (BMI) as non-obese (BMI ≤ 25 kg/m2 ) or overweight/obese (BMI > 25 kg/m2 )...
May 1, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29717022/epigenetic-reprogramming-during-spermatogenesis-and-male-factor-infertility
#16
Hayden M McSwiggin, Alan Mark O'Doherty
Infertility is an often devastating diagnosis encountered by around one in six couples who are trying to conceive. Moving away from the long held belief that infertility is primarily a female issue, it is now recognised that half, if not more, of these cases may be due to male factors. Recent evidence has suggested that epigenetic abnormalities in chromatin dynamics, DNA methylation or sperm-borne RNAs may contribute to male infertility. In light of advances in deep sequencing technologies, researchers have been able to increase the coverage and depth of sequencing results which in turn has allowed more comprehensive analyses of spermatozoa chromatin dynamics and methylomes, and enabled the discovery of new subsets of sperm RNAs...
May 1, 2018: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/29716534/comparative-genomics-of-cocci-shaped-sporosarcina-strains-with-diverse-spatial-isolation
#17
Andrew Oliver, Matthew Kay, Kerry K Cooper
BACKGROUND: Cocci-shaped Sporosarcina strains are currently one of the few known cocci-shaped spore-forming bacteria, yet we know very little about the genomics. The goal of this study is to utilize comparative genomics to investigate the diversity of cocci-shaped Sporosarcina strains that differ in their geographical isolation and show different nutritional requirements. RESULTS: For this study, we sequenced 28 genomes of cocci-shaped Sporosarcina strains isolated from 13 different locations around the world...
May 2, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29707986/gender-specificity-improves-the-early-stage-detection-of-clear-cell-renal-cell-carcinoma-based-on-methylomic-biomarkers
#18
Yanjiao Ren, Xin Feng, Xin Xia, Yexian Zhang, Wenniu Zhang, Jing Su, Zhongyu Wang, Ying Xu, Fengfeng Zhou
AIM: The two genders are different ranging from the molecular to the phenotypic levels. But most studies did not use this important information. We hypothesize that the integration of gender information may improve the overall prediction accuracy. MATERIALS & METHODS: A comprehensive comparative study was carried out to test the hypothesis. The classification of the stages I + II versus III + IV of the clear cell renal cell carcinoma samples was formulated as an example...
April 30, 2018: Biomarkers in Medicine
https://www.readbyqxmd.com/read/29707792/maintenance-of-pre-existing-dna-methylation-states-through-recurring-excess-light-stress
#19
Diep R Ganguly, Peter A Crisp, Steven R Eichten, Barry J Pogson
The capacity for plant stress priming and memory, and the notion of this being underpinned by DNA methylation-mediated memory is an appealing hypothesis for which there is mixed evidence. We previously established a lack of drought-induced methylome variation in Arabidopsis thaliana (Arabidopsis); however, this was tied to only minor observations of physiological memory. There are numerous independent observations demonstrating that photoprotective mechanisms, induced by excess-light (EL) stress, can lead to robust programmable changes in newly developing leaf tissues...
April 29, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29703584/-medulloblastoma-pathology
#20
A Siegfried, M-B Delisle
Medulloblastomas, embryonal neuroepithelial tumors developed in the cerebellum or brain stem, are mainly observed in childhood. The treatment of WHO-Grade IV tumors depends on stratifications that are usually based on postoperative data, histopathological subtype, tumor extension and presence of MYC or NMYC amplifications. Recently, molecular biology studies, based on new technologies (i.e. sequencing, transcriptomic, methylomic) have introduced genetic subtypes integrated into the latest WHO-2016 neuropathological classification...
April 24, 2018: Neuro-Chirurgie
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