Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells
File(s)
Published version
Author(s)
Type
Journal Article
Abstract
Accessibility of the genomic regulatory information is largely controlled by the nucleosome-organizing activity of transcription factors (TFs). While stimulus-induced TFs bind to genomic regions that are maintained accessible by lineage-determining TFs, they also increase accessibility of thousands of cis-regulatory elements. Nucleosome remodeling events underlying such changes and their interplay with basal positioning are unknown. Here, we devised a novel quantitative framework discriminating different types of nucleosome remodeling events in micrococcal nuclease ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) data sets and used it to analyze nucleosome dynamics at stimulus-regulated cis-regulatory elements. At enhancers, remodeling preferentially affected poorly positioned nucleosomes while sparing well-positioned nucleosomes flanking the enhancer core, indicating that inducible TFs do not suffice to overrule basal nucleosomal organization maintained by lineage-determining TFs. Remodeling events appeared to be combinatorially driven by multiple TFs, with distinct TFs showing, however, different remodeling efficiencies. Overall, these data provide a systematic view of the impact of stimulation on nucleosome organization and genome accessibility in mammalian cells.
Date Issued
2019-09-01
Date Acceptance
2019-07-03
Citation
Genes and Development, 2019, 33 (17-18), pp.1159-1174
ISSN
0890-9369
Publisher
Cold Spring Harbor Laboratory Press
Start Page
1159
End Page
1174
Journal / Book Title
Genes and Development
Volume
33
Issue
17-18
Copyright Statement
© 2019 Comoglio et al. This article, published in Genes & Development,
is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/
licenses/by-nc/4.0/.
is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/
licenses/by-nc/4.0/.
License URL
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000484361100005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Subjects
Science & Technology
Life Sciences & Biomedicine
Cell Biology
Developmental Biology
Genetics & Heredity
chromatin
macrophages
nucleosome
CIS-REGULATORY ELEMENTS
GENE-EXPRESSION
ENHANCER LANDSCAPE
OPEN CHROMATIN
CPG ISLANDS
DNA SHAPE
TRANSCRIPTION
OCCUPANCY
MACROPHAGE
DYNAMICS
Publication Status
Published
Date Publish Online
2019-08-01