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Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups

Authors
  • Giles, Katherine A.1
  • Gould, Cathryn M.1
  • Du, Qian1
  • Skvortsova, Ksenia1
  • Song, Jenny Z.1
  • Maddugoda, Madhavi P.1
  • Achinger-Kawecka, Joanna1, 2
  • Stirzaker, Clare1, 2
  • Clark, Susan J.1, 2
  • Taberlay, Phillippa C.2, 3
  • 1 Garvan Institute of Medical Research, Epigenetics Research, Genomics and Epigenetics Division, Sydney, NSW, 2010, Australia , Sydney (Australia)
  • 2 UNSW Australia, St Vincent’s Clinical School, Sydney, NSW, 2000, Australia , Sydney (Australia)
  • 3 Collage of Health and Medicine, University of Tasmania, School of Medicine, Hobart, TAS, 7000, Australia , Hobart (Australia)
Type
Published Article
Journal
Epigenetics & Chromatin
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Feb 12, 2019
Volume
12
Issue
1
Identifiers
DOI: 10.1186/s13072-019-0258-9
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundATP-dependent chromatin remodelling complexes are responsible for establishing and maintaining the positions of nucleosomes. Chromatin remodellers are targeted to chromatin by transcription factors and non-coding RNA to remodel the chromatin into functional states. However, the influence of chromatin remodelling on shaping the functional epigenome is not well understood. Moreover, chromatin remodellers have not been extensively explored as a collective group across two-dimensional and three-dimensional epigenomic layers.ResultsHere, we have integrated the genome-wide binding profiles of eight chromatin remodellers together with DNA methylation, nucleosome positioning, histone modification and Hi-C chromosomal contacts to reveal that chromatin remodellers can be stratified into two functional groups. Group 1 (BRG1, SNF2H, CHD3 and CHD4) has a clear preference for binding at ‘actively marked’ chromatin and Group 2 (BRM, INO80, SNF2L and CHD1) for ‘repressively marked’ chromatin. We find that histone modifications and chromatin architectural features, but not DNA methylation, stratify the remodellers into these functional groups.ConclusionsOur findings suggest that chromatin remodelling events are synchronous and that chromatin remodellers themselves should be considered simultaneously and not as individual entities in isolation or necessarily by structural similarity, as they are traditionally classified. Their coordinated function should be considered by preference for chromatin features in order to gain a more accurate and comprehensive picture of chromatin regulation.

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