Dissecting super-enhancer hierarchy based on chromatin interactions

Jialiang Huang, Kailong Li, Wenqing Cai, Xin Liu, Yuannyu Zhang, Stuart H. Orkin, Jian Xu, Guo Cheng Yuan

Research output: Contribution to journalArticle

40 Scopus citations

Abstract

Recent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, here we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants. Genetic ablation of hub enhancers results in profound defects in gene activation and local chromatin landscape. As such, hub enhancers are the major constituents responsible for SE functional and structural organization.

Original languageEnglish (US)
Article number943
JournalNature communications
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2018

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

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    Huang, J., Li, K., Cai, W., Liu, X., Zhang, Y., Orkin, S. H., Xu, J., & Yuan, G. C. (2018). Dissecting super-enhancer hierarchy based on chromatin interactions. Nature communications, 9(1), [943]. https://doi.org/10.1038/s41467-018-03279-9