ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies

ATP-dependent nucleosome remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, Saccharomyces cerevisiae ISWI and CHD remodelers require ∼30–85 bp of extranucleosomal DNA to reposition nucleosomes, but linker DNA in S. cerevisiae averages <...

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Main Authors:	Zentner, Gabriel E., Tsukiyama, Toshio, Henikoff, Steven
Format:	Online
Language:	English
Published:	Public Library of Science 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585014/

id	pubmed-3585014
recordtype	oai_dc
spelling	pubmed-35850142013-03-06 ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies Zentner, Gabriel E. Tsukiyama, Toshio Henikoff, Steven Research Article ATP-dependent nucleosome remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, Saccharomyces cerevisiae ISWI and CHD remodelers require ∼30–85 bp of extranucleosomal DNA to reposition nucleosomes, but linker DNA in S. cerevisiae averages <20 bp. To address this discrepancy between in vitro and in vivo observations, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution on native chromatin. Although these remodelers act in gene bodies, we find that they are also highly enriched at nucleosome-depleted regions (NDRs), where they bind to extended regions of DNA adjacent to particular transcription factors. Surprisingly, catalytically inactive remodelers show similar binding patterns. We find that remodeler occupancy at NDRs and gene bodies is associated with nucleosome turnover and transcriptional elongation rate, suggesting that remodelers act on regions of transient nucleosome unwrapping or depletion within gene bodies subsequent to transcriptional elongation. Public Library of Science 2013-02-28 /pmc/articles/PMC3585014/ /pubmed/23468649 http://dx.doi.org/10.1371/journal.pgen.1003317 Text en © 2013 Zentner et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Zentner, Gabriel E. Tsukiyama, Toshio Henikoff, Steven
spellingShingle	Zentner, Gabriel E. Tsukiyama, Toshio Henikoff, Steven ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies
author_facet	Zentner, Gabriel E. Tsukiyama, Toshio Henikoff, Steven
author_sort	Zentner, Gabriel E.
title	ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies
title_short	ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies
title_full	ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies
title_fullStr	ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies
title_full_unstemmed	ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies
title_sort	iswi and chd chromatin remodelers bind promoters but act in gene bodies
description	ATP-dependent nucleosome remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, Saccharomyces cerevisiae ISWI and CHD remodelers require ∼30–85 bp of extranucleosomal DNA to reposition nucleosomes, but linker DNA in S. cerevisiae averages <20 bp. To address this discrepancy between in vitro and in vivo observations, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution on native chromatin. Although these remodelers act in gene bodies, we find that they are also highly enriched at nucleosome-depleted regions (NDRs), where they bind to extended regions of DNA adjacent to particular transcription factors. Surprisingly, catalytically inactive remodelers show similar binding patterns. We find that remodeler occupancy at NDRs and gene bodies is associated with nucleosome turnover and transcriptional elongation rate, suggesting that remodelers act on regions of transient nucleosome unwrapping or depletion within gene bodies subsequent to transcriptional elongation.
publisher	Public Library of Science
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585014/
_version_	1611958434653011968

ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies

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