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H3K4me3

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https://www.readbyqxmd.com/read/27904655/increased-set1-binding-at-the-promoter-induces-aberrant-epigenetic-alterations-and-up-regulates-cyclic-adenosine-5-monophosphate-response-element-modulator-alpha-in-systemic-lupus-erythematosus
#1
Qing Zhang, Shu Ding, Huilin Zhang, Hai Long, Haijing Wu, Ming Zhao, Vera Chan, Chak-Sing Lau, Qianjin Lu
BACKGROUND: Up-regulated cyclic adenosine 5'-monophosphate response element modulator α (CREMα) which can inhibit IL-2 and induce IL-17A in T cells plays a critical role in the pathogenesis of systemic lupus erythematosus (SLE). This research aimed to investigate the mechanisms regulating CREMα expression in SLE. RESULTS: From the chromatin immunoprecipitation (ChIP) microarray data, we found a sharply increased H3 lysine 4 trimethylation (H3K4me3) amount at the CREMα promoter in SLE CD4+ T cells compared to controls...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27902763/temperature-shift-alters-dna-methylation-and-histone-modification-patterns-in-gonadal-aromatase-cyp19a1-gene-in-species-with-temperature-dependent-sex-determination
#2
Yuiko Matsumoto, Brette Hannigan, David Crews
The environment surrounding the embryos has a profound impact on the developmental process and phenotypic outcomes of the organism. In species with temperature-dependent sex determination, gonadal sex is determined by the incubation temperature of the eggs. A mechanistic link between temperature and transcriptional regulation of developmental genes, however, remains elusive. In this study, we examine the changes in DNA methylation and histone modification patterns of the aromatase (cyp19a1) gene in embryonic gonads of red-eared slider turtles (Trachemys scripta) subjected to a temperature shift during development...
2016: PloS One
https://www.readbyqxmd.com/read/27899639/histone-demethylase-phf8-promotes-epithelial-to-mesenchymal-transition-and-breast-tumorigenesis
#3
Peng Shao, Qi Liu, Peterson Kariuki Maina, Jiayue Cui, Thomas B Bair, Tiandao Li, Shaikamjad Umesalma, Weizhou Zhang, Hank Heng Qi
Histone demethylase PHF8 is upregulated and plays oncogenic roles in various cancers; however, the mechanisms underlying its dysregulation and functions in carcinogenesis remain obscure. Here, we report the novel functions of PHF8 in EMT (epithelial to mesenchymal transition) and breast cancer development. Genome-wide gene expression analysis revealed that PHF8 overexpression induces an EMT-like process, including the upregulation of SNAI1 and ZEB1. PHF8 demethylates H3K9me1, H3K9me2 and sustains H3K4me3 to prime the transcriptional activation of SNAI1 by TGF-β signaling...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899593/the-kdm5-family-is-required-for-activation-of-pro-proliferative-cell-cycle-genes-during-adipocyte-differentiation
#4
Ann-Sofie B Brier, Anne Loft, Jesper G S Madsen, Thomas Rosengren, Ronni Nielsen, Søren F Schmidt, Zongzhi Liu, Qin Yan, Hinrich Gronemeyer, Susanne Mandrup
The KDM5 family of histone demethylases removes the H3K4 tri-methylation (H3K4me3) mark frequently found at promoter regions of actively transcribed genes and is therefore generally considered to contribute to corepression. In this study, we show that knockdown (KD) of all expressed members of the KDM5 family in white and brown preadipocytes leads to deregulated gene expression and blocks differentiation to mature adipocytes. KDM5 KD leads to a considerable increase in H3K4me3 at promoter regions; however, these changes in H3K4me3 have a limited effect on gene expression per se...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899590/different%C3%A2-enhancer-classes-in-drosophila-bind-distinct-architectural-proteins-and-mediate-unique-chromatin-interactions-and-3d-architecture
#5
Caelin Cubeñas-Potts, M Jordan Rowley, Xiaowen Lyu, Ge Li, Elissa P Lei, Victor G Corces
Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and developmental enhancers (dCP). We hypothesized that the two enhancer classes are occupied by distinct architectural proteins, affecting their enhancer-promoter contacts. By evaluating ChIP-seq occupancy of architectural proteins, typical enhancer-associated proteins, and histone modifications, we determine that both enhancer classes are enriched for RNA Polymerase II, CBP, and architectural proteins but there are also distinctions...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899510/identification-and-in-silico-modeling-of-enhancers-reveals-new-features-of-the-cardiac-differentiation-network
#6
Denis Seyres, Yad Ghavi-Helm, Guillaume Junion, Ouarda Taghli-Lamallem, Céline Guichard, Laurence Röder, Charles Girardot, Eileen E M Furlong, Laurent Perrin
Developmental patterning and tissue formation are regulated through complex gene regulatory networks (GRNs) driven through the action of transcription factors (TFs) converging on enhancer elements. Here, as a point of entry to dissect the poorly defined GRN underlying cardiomyocyte differentiation, we apply an integrated approach to identify active enhancers and TFs involved in Drosophila heart development. The Drosophila heart consists of 104 cardiomyocytes, representing less than 0.5% of all cells in the embryo...
December 1, 2016: Development
https://www.readbyqxmd.com/read/27897198/mitochondrial-control-through-nutritionally-regulated-global-histone-h3-lysine-4-demethylation
#7
Maria Soloveychik, Mengshu Xu, Olga Zaslaver, Kwanyin Lee, Ashrut Narula, River Jiang, Adam P Rosebrock, Amy A Caudy, Marc D Meneghini
Histone demethylation by Jumonji-family proteins is coupled with the decarboxylation of α-ketoglutarate (αKG) to yield succinate, prompting hypotheses that their activities are responsive to levels of these metabolites in the cell. Consistent with this paradigm we show here that the Saccharomyces cerevisiae Jumonji demethylase Jhd2 opposes the accumulation of H3K4me3 in fermenting cells only when they are nutritionally manipulated to contain an elevated αKG/succinate ratio. We also find that Jhd2 opposes H3K4me3 in respiratory cells that do not exhibit such an elevated αKG/succinate ratio...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27895308/epigenetic-inhibition-of-mir-663b-by-long-non-coding-rna-hotair-promotes-pancreatic-cancer-cell-proliferation-via-up-regulation-of-insulin-like-growth-factor-2
#8
Huihua Cai, Yong An, Xuemin Chen, Donglin Sun, Tongbing Chen, Yan Peng, Feng Zhu, Yong Jiang, Xiaozhou He
Pancreatic cancer is one of the most deadly cancers with a poor prognosis. Although microRNAs are involving in the carcinogenesis and development of pancreatic cancer, little information is known regarding the role of miR-663b in pancreatic cancer. In this study, the expression of miR-663b in pancreatic cancer cells was down-regulated by hypermethylation in its putative promoter region, and overexpression of miR-663b repressed cell proliferation, invasion and migration, and induced apoptosis in pancreatic cancer cells...
November 22, 2016: Oncotarget
https://www.readbyqxmd.com/read/27877178/an-s-adenosyl-methionine-synthetase-sams-gene-from-andropogon-virginicus-l-confers-aluminum-stress-tolerance-and-facilitates-epigenetic-gene-regulation-in-arabidopsis-thaliana
#9
Bunichi Ezaki, Aiko Higashi, Norie Nanba, Takumi Nishiuchi
Candidate clones which conferred Al tolerance to yeast transformants (TFs) were obtained from a cDNA library derived from a highly Al-tolerant poaceae, Andropogon virginicus L. One such clone, AL3A-4, encoded an S-adenosyl methionine synthetase (SAMS) gene. A full-length cDNA was obtained by 5'-RACE, designated AvSAMS1, and introduced into Arabidopsis thaliana to investigate its biological functions under Al stress. Two TF plant lines both showed higher tolerance than the Col-0 ecotype (non-TF) not only for Al stress, but also for Cu, Pb, Zn and diamide stresses, suggesting the AvSAMS1 was a multiple tolerance gene...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27865928/the-swi2-snf2-chromatin-remodeling-atpase-brahma-regulates-chlorophyll-biosynthesis-in-arabidopsis
#10
Dong Zhang, Yuhong Li, Xinyu Zhang, Ping Zha, Rongcheng Lin
Chlorophyll biosynthesis is critical for chloroplast development and photosynthesis in plants. Although reactions in the biosynthetic pathway are well established, little is known about the regulation of this pathway. In this study, we found that the dark-grown knockout and knockdown mutants and RNA interference transgenic seedlings of BRAHMA (BRM), encoding a SWI2/SNF2 chromatin-remodeling ATPase, had higher greening rates, accumulated less protochlorophyllide, and produced less reactive oxygen species than did Arabidopsis wild-type plants upon light exposure...
November 16, 2016: Molecular Plant
https://www.readbyqxmd.com/read/27863221/the-dual-role-of-epop-and-elongin-bc-in-controlling-transcriptional-activity
#11
Karin Johanna Ferrari, Elisa Lavarone, Diego Pasini
Two studies published in this issue of Molecular Cell (Beringer et al., 2016; Liefke et al., 2016) characterize the novel interaction of EPOP with Elongin BC in regulating gene transcription at both H3K4me3-broad active and H3K27me3 Polycomb-repressed chromatin domains.
November 17, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27858939/chromatin-remodeling-during-in-vivo-neural-stem-cells-differentiating-to-neurons-in-early-drosophila-embryos
#12
Youqiong Ye, Min Li, Liang Gu, Xiaolong Chen, Jiejun Shi, Xiaobai Zhang, Cizhong Jiang
Neurons are a key component of the nervous system and differentiate from multipotent neural stem cells (NSCs). Chromatin remodeling has a critical role in the differentiation process. However, its in vivo epigenetic regulatory role remains unknown. We show here that nucleosome depletion regions (NDRs) form in both proximal promoters and distal enhancers during NSCs differentiating into neurons in the early Drosophila embryonic development. NDR formation in the regulatory regions involves nucleosome shift and eviction...
November 18, 2016: Cell Death and Differentiation
https://www.readbyqxmd.com/read/27851972/nucleosome-density-chip-seq-identifies-distinct-chromatin-modification-signatures-associated-with-mnase-accessibility
#13
Alireza Lorzadeh, Misha Bilenky, Colin Hammond, David J H F Knapp, Luolan Li, Paul H Miller, Annaick Carles, Alireza Heravi-Moussavi, Sitanshu Gakkhar, Michelle Moksa, Connie J Eaves, Martin Hirst
Nucleosome position, density, and post-translational modification are widely accepted components of mechanisms regulating DNA transcription but still incompletely understood. We present a modified native ChIP-seq method combined with an analytical framework that allows MNase accessibility to be integrated with histone modification profiles. Application of this methodology to the primitive (CD34+) subset of normal human cord blood cells enabled genomic regions enriched in one versus two nucleosomes marked by histone 3 lysine 4 trimethylation (H3K4me3) and/or histone 3 lysine 27 trimethylation (H3K27me3) to be associated with their transcriptional and DNA methylation states...
November 15, 2016: Cell Reports
https://www.readbyqxmd.com/read/27826357/systematic-comparison-of-monoclonal-versus-polyclonal-antibodies-for-mapping-histone-modifications-by-chip-seq
#14
Michele Busby, Catherine Xue, Catherine Li, Yossi Farjoun, Elizabeth Gienger, Ido Yofe, Adrianne Gladden, Charles B Epstein, Evan M Cornett, Scott B Rothbart, Chad Nusbaum, Alon Goren
BACKGROUND: The robustness of ChIP-seq datasets is highly dependent upon the antibodies used. Currently, polyclonal antibodies are the standard despite several limitations: They are non-renewable, vary in performance between lots and need to be validated with each new lot. In contrast, monoclonal antibody lots are renewable and provide consistent performance. To increase ChIP-seq standardization, we investigated whether monoclonal antibodies could replace polyclonal antibodies. We compared monoclonal antibodies that target five key histone modifications (H3K4me1, H3K4me3, H3K9me3, H3K27ac and H3K27me3) to their polyclonal counterparts in both human and mouse cells...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27822470/transcriptional-regulation-of-lncrna-genes-by-histone-modification-in-alzheimer-s-disease
#15
Guoqiang Wan, Wenyang Zhou, Yang Hu, Rui Ma, Shuilin Jin, Guiyou Liu, Qinghua Jiang
Increasing studies have revealed that long noncoding RNAs (lncRNAs) are not transcriptional noise but play important roles in the regulation of a wide range of biological processes, and the dysregulation of lncRNA genes is associated with disease development. Alzheimer's disease (AD) is a chronic neurodegenerative disease that usually starts slowly and gets worse over time. However, little is known about the roles of lncRNA genes in AD and how the lncRNA genes are transcriptionally regulated. Herein, we analyzed RNA-seq data and ChIP-seq histone modification data from CK-p25 AD model and control mice and identified 72 differentially expressed lncRNA genes, 4,917 differential peaks of H3K4me3, and 1,624 differential peaks of H3K27me3 between AD and control samples, respectively...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27822313/quantitative-analysis-of-chip-seq-data-uncovers-dynamic-and-sustained-h3k4me3-and-h3k27me3-modulation-in-cancer-cells-under-hypoxia
#16
Michiel E Adriaens, Peggy Prickaerts, Michelle Chan-Seng-Yue, Twan van den Beucken, Vivian E H Dahlmans, Lars M Eijssen, Timothy Beck, Bradly G Wouters, Jan Willem Voncken, Chris T A Evelo
BACKGROUND: A comprehensive assessment of the epigenetic dynamics in cancer cells is the key to understanding the molecular mechanisms underlying cancer and to improving cancer diagnostics, prognostics and treatment. By combining genome-wide ChIP-seq epigenomics and microarray transcriptomics, we studied the effects of oxygen deprivation and subsequent reoxygenation on histone 3 trimethylation of lysine 4 (H3K4me3) and lysine 27 (H3K27me3) in a breast cancer cell line, serving as a model for abnormal oxygenation in solid tumors...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27821479/functional-roles-of-acetylated-histone-marks-at-mouse-meiotic-recombination-hotspots
#17
Irina V Getun, Zhen Wu, Mohammad Fallahi, Souad Ouizem, Qin Liu, Weimin Li, Roberta Costi, William R Roush, John L Cleveland, Philippe R J Bois
Meiotic recombination initiates following the formation of DNA double strand breaks (DSBs) by the Spo11 endonuclease early in prophase I at discrete regions in the genome coined hotspots. In mammals, meiotic DSB site selection is directed in part by sequence specific binding of PRDM9, a polymorphic histone H3 (H3K4Me3) methyltransferase. However, other chromatin features needed for meiotic hotspot specification are largely unknown. Here, we show that the recombinogenic cores of active hotspots in mice harbor several histone H3 and H4 acetylation and methylation marks that are typical of open, active chromatin...
November 7, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27821436/histone-h3-lysine-4-trimethylation-h3k4me3-lysine-27-trimethylation-h3k27me3-and-lysine-27-acetylation-h3k27ac-contribute-to-the-transcriptional-repression-of-solute-carrier-family-47-member-2-in-renal-cell-carcinoma
#18
Qinqin Yu, Yanqing Liu, Xiaoli Zheng, Qianying Zhu, Zhuowei Shen, Hua Wang, Huadong He, Nengming Lin, Huidi Jiang, Lushan Yu, Su Zeng
In recent years, finding effective biomarkers for identifying early stage cancer and predicating prognosis is crucial for renal cell carcinoma (RCC) diagnosis and treatment. In this study, a dramatic decrease of the solute carrier family 47 member 2 (SLC47A2) mRNA in RCC comparing with the paired adjacent non-tumor tissues from patients at low TNM stage was observed. Thus, patients with SLC47A2 transcriptional repression are susceptible to RCC. Little is known about the regulation mechanism of SLC47A2. We found that it was a bivalent gene which was enriched with both histone H3 lysine 4 trimethylation (H3K4me3) and lysine 27 trimethylation (H3K27me3)...
November 7, 2016: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/27819326/insights-into-a-novel-nuclear-function-for-fascin-in-the-regulation-of-the-amino-acid-transporter-slc3a2
#19
Amine Saad, Krikor Bijian, Dinghong Qiu, Sabrina Daniela da Silva, Maud Marques, Chia-Hao Chang, Hassan Nassour, Dindial Ramotar, Sambasivarao Damaraju, John Mackey, Tarek Bismar, Michael Witcher, Moulay A Alaoui-Jamali
Fascin 1 (FSCN1) is a cytoskeleton-associated protein recognized to function primarily in the regulation of cytoskeleton structure and formation of plasma membrane protrusions. Here we report a novel nuclear function for Fascin 1. Biochemical studies and genome wide localization using ChIP-seq identified phosphorylated Fascin 1 (pFascin) in complexes associated with transcription and that it co-localizes with histone H3 Lys4 trimethylation (H3K4me3) on chromatin. Gene expression profiling identified genes affected by Fascin 1 including SLC3A2, a gene encoding for a plasma membrane transporter that regulates intracellular amino acid levels...
November 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27818691/osteogenic-differentiation-of-human-amniotic-fluid-mesenchymal-stem-cells-is-determined-by-epigenetic-changes
#20
Monika Glemžaitė, Rūta Navakauskienė
Osteogenic differentiation of human amniotic fluid derived mesenchymal stem cells (AF-MSCs) has been widely studied in vitro and in vivo as a potential tool for regenerative medicine and tissue engineering. While most of the studies analyze changes in transcriptional profile during differentiation to date there is not much information regarding epigenetic changes in AF-MSCs during differentiation. The aim of our study was to evaluate epigenetic changes during osteogenic differentiation of AF-MS cells. Isolated AF-MSCs were characterized morphologically and osteogenic differentiation was confirmed by cell staining and determining expression of alkaline phosphatase and osteopontin by RT-qPCR...
2016: Stem Cells International
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