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Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups

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Giles, KA, Gould, CM, Du, Q, Skvortsova, K, Song, JZ, Maddugoda, MP, Achinger-Kawecka, J, Stirzaker, C, Clark, SJ and Taberlay, PC ORCID: 0000-0002-5298-8730 2019 , 'Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups' , Epigenetics and Chromatin, vol. 12, no. 1 , pp. 1-19 , doi: 10.1186/s13072-019-0258-9.

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Abstract

Background: ATP-dependent chromatin remodelling complexes are responsible for establishing and maintainingthe positions of nucleosomes. Chromatin remodellers are targeted to chromatin by transcription factors and noncoding RNA to remodel the chromatin into functional states. However, the infuence of chromatin remodelling onshaping the functional epigenome is not well understood. Moreover, chromatin remodellers have not been exten‑sively explored as a collective group across two-dimensional and three-dimensional epigenomic layers.Results: Here, we have integrated the genome-wide binding profles of eight chromatin remodellers together withDNA methylation, nucleosome positioning, histone modifcation and Hi-C chromosomal contacts to reveal that chro‑matin remodellers can be stratifed into two functional groups. Group 1 (BRG1, SNF2H, CHD3 and CHD4) has a clearpreference for binding at ‘actively marked’ chromatin and Group 2 (BRM, INO80, SNF2L and CHD1) for ‘repressivelymarked’ chromatin. We fnd that histone modifcations and chromatin architectural features, but not DNA methyla‑tion, stratify the remodellers into these functional groups.Conclusions: Our fndings suggest that chromatin remodelling events are synchronous and that chromatin remod‑ellers themselves should be considered simultaneously and not as individual entities in isolation or necessarily bystructural similarity, as they are traditionally classifed. Their coordinated function should be considered by preferencefor chromatin features in order to gain a more accurate and comprehensive picture of chromatin regulation.

Item Type: Article
Authors/Creators:Giles, KA and Gould, CM and Du, Q and Skvortsova, K and Song, JZ and Maddugoda, MP and Achinger-Kawecka, J and Stirzaker, C and Clark, SJ and Taberlay, PC
Keywords: chromatin, nucleosome, chromatin remodelling, enhancer, promoter, gene regulation, epigenetics, CHD, SWI/SNF, INO80, ISWI
Journal or Publication Title: Epigenetics and Chromatin
Publisher: BioMed Central
ISSN: 1756-8935
DOI / ID Number: 10.1186/s13072-019-0258-9
Copyright Information:

Copyright 2019 The Authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/

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