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Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia

Title
Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia
Authors
Lee, Seong YeolLee, Ji EonChae, Se HyunMoon, Yun WonLee, Ho YoulPark, Bong JuYang, Eun GyeongHwang, Dae HeePark, Hyun Sung
DGIST Authors
Hwang, Dae Hee
Issue Date
2017-11
Citation
Nucleic acids research, 45(20), 11643-11657
Type
Article
Article Type
Article
Keywords
histonemessenger RNAoxygenadipose tissuecell hypoxiacell linecytologygene expressiongene expression regulationgenetic epigenesisgeneticshistone codehumanmetabolismmethylationphysiologystem cellAdipose TissueCell HypoxiaCell LineEpigenesis, GeneticGene ExpressionGene Expression RegulationHistone CodeHistonesHumansMethylationOxygenRNA, MessengerStem Cells
ISSN
1362-4962
Abstract
Hypoxia increases both active and repressive histone methylation levels via decreased activity of histone demethylases. However, how such increases coordinately regulate induction or repression of hypoxia-responsive genes is largely unknown. Here, we profiled active and repressive histone tri-methylations (H3K4me3, H3K9me3, and H3K27me3) and analyzed gene expression profiles in human adipocyte-derived stem cells under hypoxia. We identified differentially expressed genes (DEGs) and differentially methylated genes (DMGs) by hypoxia and clustered the DEGs and DMGs into four major groups. We found that each group of DEGs was predominantly associated with alterations in only one type among the three histone tri-methylations. Moreover, the four groups of DEGs were associated with different TFs and localization patterns of their predominant types of H3K4me3, H3K9me3 and H3K27me3. Our results suggest that the association of altered gene expression with prominent single-type histone tri-methylations characterized by different localization patterns and with different sets of TFs contributes to regulation of particular sets of genes, which can serve as a model for coordinated epigenetic regulation of gene expression under hypoxia. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
URI
http://hdl.handle.net/20.500.11750/5631
DOI
10.1093/nar/gkx747
Publisher
OXFORD UNIV PRESS
Related Researcher
  • Author Hwang, Dae Hee Systems Biology and Medicine Lab
  • Research Interests Multilayered spatiotemporal networks; Regulatory motifs or pathways; Metabolite-protein networks; Network stochasticity; Proteomics and informatics
Files:
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Collection:
Department of New BiologySystems Biology and Medicine Lab1. Journal Articles


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