Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion

Abstract Up to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the appearance of genome-wide accessibility sites and triggers an interf...

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Veröffentlicht in:Nucleic acids research 2022-04, Vol.50 (7), p.3892-3910
Hauptverfasser: Serna-Pujol, Núria, Salinas-Pena, Mónica, Mugianesi, Francesca, Le Dily, François, Marti-Renom, Marc A, Jordan, Albert
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container_issue 7
container_start_page 3892
container_title Nucleic acids research
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creator Serna-Pujol, Núria
Salinas-Pena, Mónica
Mugianesi, Francesca
Le Dily, François
Marti-Renom, Marc A
Jordan, Albert
description Abstract Up to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the appearance of genome-wide accessibility sites and triggers an interferon response via activation of heterochromatic repeats. However, how these changes in the expression profile relate to the re-distribution of H1 variants as well as to genome conformational changes have not been yet studied. Here, we combined ChIP-seq of five endogenous H1 variants with Chromosome Conformation Capture analysis in wild-type and H1.2/H1.4 knock-down T47D cells. The results indicate that H1 variants coexist in the genome in two large groups depending on the local GC content and that their distribution is robust with respect to H1 depletion. Despite the small changes in H1 variants distribution, knock-down of H1 translated into more isolated but de-compacted chromatin structures at the scale of topologically associating domains (TADs). Such changes in TAD structure correlated with a coordinated gene expression response of their resident genes. This is the first report describing simultaneous profiling of five endogenous H1 variants and giving functional evidence of genome topology alterations upon H1 depletion in human cancer cells.
doi_str_mv 10.1093/nar/gkac226
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subjects Base Composition
Chromatin - genetics
Chromatin Assembly and Disassembly
Gene Expression
Gene regulation, Chromatin and Epigenetics
Histones - genetics
Histones - metabolism
Humans
title Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion
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