scholarly journals Bisphenol A-associated alterations in genome-wide DNA methylation and gene expression patterns reveal sequence-dependent and non-monotonic effects in human fetal liver

2015 ◽  
Vol 1 (1) ◽  
pp. dvv006 ◽  
Author(s):  
Christopher Faulk ◽  
Jung H. Kim ◽  
Tamara R. Jones ◽  
Richard C. McEachin ◽  
Muna S. Nahar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Bisphenol A ◽  
Fetal Liver ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Human Fetal Liver ◽  
Sequence Dependent ◽  
Genome Wide

scholarly journals Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago

PLoS Genetics ◽  
2020 ◽  
Vol 16 (5) ◽  
pp. e1008749 ◽  
Author(s):  
Heini M. Natri ◽  
Katalina S. Bobowik ◽  
Pradiptajati Kusuma ◽  
Chelzie Crenna Darusallam ◽  
Guy S. Jacobs ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Expression Patterns ◽  
Genetic Ancestry ◽  
Gene Expression Patterns ◽  
Indonesian Archipelago ◽  
Genome Wide

scholarly journals Genome-wide DNA methylation and gene expression patterns provide insight into polycystic ovary syndrome development

Oncotarget ◽  
2014 ◽  
Vol 5 (16) ◽  
pp. 6603-6610 ◽  
Author(s):  
Xiu-Xia Wang ◽  
Jing-Zan Wei ◽  
Jiao Jiao ◽  
Shu-Yi Jiang ◽  
Da-Hai Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Polycystic Ovary Syndrome ◽  
Polycystic Ovary ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Ovary Syndrome ◽  
Genome Wide ◽  
Insight Into

scholarly journals Genome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells

Oncotarget ◽  
2015 ◽  
Vol 6 (29) ◽  
pp. 26729-26745 ◽  
Author(s):  
Adil El Taghdouini ◽  
Anita L. Sørensen ◽  
Andrew H. Reiner ◽  
Mar Coll ◽  
Stefaan Verhulst ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Hepatic Stellate Cells ◽  
Human Liver ◽  
Expression Patterns ◽  
Stellate Cells ◽  
Gene Expression Patterns ◽  
Genome Wide Analysis ◽  
Human Liver Cells ◽  
Genome Wide

scholarly journals Gene expression profiling of epigenetic chromatin modification enzymes and histone marks by cigarette smoke: implications for COPD and lung cancer

2016 ◽  
Vol 311 (6) ◽  
pp. L1245-L1258 ◽  
Author(s):  
Isaac K. Sundar ◽  
Irfan Rahman
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Dna Methylation ◽  
Cigarette Smoke ◽  
Histone Modifications ◽  
Expression Patterns ◽  
Chromatin Modification ◽  
Gene Expression Patterns ◽  
Validation Data ◽  
Histone Marks

Chromatin-modifying enzymes mediate DNA methylation and histone modifications on recruitment to specific target gene loci in response to various stimuli. The key enzymes that regulate chromatin accessibility for maintenance of modifications in DNA and histones, and for modulation of gene expression patterns in response to cigarette smoke (CS), are not known. We hypothesize that CS exposure alters the gene expression patterns of chromatin-modifying enzymes, which then affects multiple downstream pathways involved in the response to CS. We have, therefore, analyzed chromatin-modifying enzyme profiles and validated by quantitative real-time PCR (qPCR). We also performed immunoblot analysis of targeted histone marks in C57BL/6J mice exposed to acute and subchronic CS, and of lungs from nonsmokers, smokers, and patients with chronic obstructive pulmonary disease (COPD). We found a significant increase in expression of several chromatin modification enzymes, including DNA methyltransferases, histone acetyltransferases, histone methyltransferases, and SET domain proteins, histone kinases, and ubiquitinases. Our qPCR validation data revealed a significant downregulation of Dnmt1, Dnmt3a, Dnmt3b, Hdac2, Hdac4, Hat1, Prmt1, and Aurkb. We identified targeted chromatin histone marks (H3K56ac and H4K12ac), which are induced by CS. Thus CS-induced genotoxic stress differentially affects the expression of epigenetic modulators that regulate transcription of target genes via DNA methylation and site-specific histone modifications. This may have implications in devising epigenetic-based therapies for COPD and lung cancer.

scholarly journals Genome-wide gene-expression patterns of donor kidney biopsies distinguish primary allograft function

2003 ◽  
Vol 84 (3) ◽  
pp. 353-361 ◽  
Author(s):  
Peter Hauser ◽  
Christoph Schwarz ◽  
Christa Mitterbauer ◽  
Heinz M Regele ◽  
Ferdinand Mühlbacher ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Donor Kidney ◽  
Genome Wide ◽  
Allograft Function ◽  
Genome Wide Gene Expression

scholarly journals In utero Bisphenol A Exposure Is Linked with Sex Specific Changes in the Transcriptome and Methylome of Human Amniocytes

2019 ◽  
Vol 105 (2) ◽  
pp. 453-467
Author(s):  
Amita Bansal ◽  
Nicole Robles-Matos ◽  
Paul Zhiping Wang ◽  
David E Condon ◽  
Apoorva Joshi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Bisphenol A ◽  
Gestational Age ◽  
Molecular Mechanisms ◽  
In Utero ◽  
Metabolic Dysfunction ◽  
Altered Expression ◽  
Obesity And Diabetes ◽  
Genome Wide

Abstract Context Prenatal exposure to bisphenol A (BPA) is linked to obesity and diabetes but the molecular mechanisms driving these phenomena are not known. Alterations in deoxyribonucleic acid (DNA) methylation in amniocytes exposed to BPA in utero represent a potential mechanism leading to metabolic dysfunction later in life. Objective To profile changes in genome-wide DNA methylation and expression in second trimester human amniocytes exposed to BPA in utero. Design A nested case-control study was performed in amniocytes matched for offspring sex, maternal race/ethnicity, maternal age, gestational age at amniocentesis, and gestational age at birth. Cases had amniotic fluid BPA measuring 0.251 to 23.74 ng/mL. Sex-specific genome-wide DNA methylation analysis and RNA-sequencing (RNA-seq) were performed to determine differentially methylated regions (DMRs) and gene expression changes associated with BPA exposure. Ingenuity pathway analysis was performed to identify biologically relevant pathways enriched after BPA exposure. In silico Hi-C analysis identified potential chromatin interactions with DMRs. Results There were 101 genes with altered expression in male amniocytes exposed to BPA (q < 0.05) in utero, with enrichment of pathways critical to hepatic dysfunction, collagen signaling and adipogenesis. Thirty-six DMRs were identified in male BPA-exposed amniocytes and 14 in female amniocyte analysis (q < 0.05). Hi-C analysis identified interactions between DMRs and 24 genes with expression changes in male amniocytes and 12 in female amniocytes (P < 0.05). Conclusion In a unique repository of human amniocytes exposed to BPA in utero, sex-specific analyses identified gene expression changes in pathways associated with metabolic disease and novel DMRs with potential distal regulatory functions.

scholarly journals Genome-wide gene expression patterns in dikaryon of the basidiomycete fungus Pleurotus ostreatus

2017 ◽  
Vol 48 (2) ◽  
pp. 380-390 ◽  
Author(s):  
Tianxiang Liu ◽  
Huiru Li ◽  
Yatong Ding ◽  
Yuancheng Qi ◽  
Yuqian Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pleurotus Ostreatus ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Genome Wide ◽  
Genome Wide Gene Expression ◽  
Basidiomycete Fungus

Microarray data uncover the genome-wide gene expression patterns in response to heat stress in rice post-meiosis panicle

2014 ◽  
Vol 57 (6) ◽  
pp. 327-336 ◽  
Author(s):  
Xianwen Zhang ◽  
Hairong Xiong ◽  
Ailing Liu ◽  
Xiaoyun Zhou ◽  
Yan Peng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Microarray Data ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Genome Wide ◽  
Genome Wide Gene Expression
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