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Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia
- Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia
- Lee, Seong Yeol; Lee, Ji Eon; Chae, Se Hyun; Moon, Yun Won; Lee, Ho Youl; Park, Bong Ju; Yang, Eun Gyeong; Hwang, Dae Hee; Park, Hyun Sung
- DGIST Authors
- Hwang, Dae Hee
- Issue Date
- Nucleic acids research, 45(20), 11643-11657
- Article Type
- histone; messenger RNA; oxygen; adipose tissue; cell hypoxia; cell line; cytology; gene expression; gene expression regulation; genetic epigenesis; genetics; histone code; human; metabolism; methylation; physiology; stem cell; Adipose Tissue; Cell Hypoxia; Cell Line; Epigenesis, Genetic; Gene Expression; Gene Expression Regulation; Histone Code; Histones; Humans; Methylation; Oxygen; RNA, Messenger; Stem Cells
- 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.
- OXFORD UNIV PRESS
- Related Researcher
Hwang, Dae Hee
Systems Biology and Medicine Lab
Multilayered spatiotemporal networks; Regulatory motifs or pathways; Metabolite-protein networks; Network stochasticity; Proteomics and informatics
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