SWI/SNF-dependent genes are defined by their chromatin landscape

SWI/SNF complexes are evolutionarily conserved, ATP-dependent chromatin remodeling machines. Here, we characterize the features of SWI/SNF-dependent genes using BRM014, an inhibitor of the ATPase activity of the complexes. We find that SWI/SNF activity is required to maintain chromatin accessibility...

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Detalhes bibliográficos
Autores: Basurto-Cayuela, Laura, Guerrero-Martínez, José A., Gómez-Marín, Elena, Sánchez-Escabias, Elena, Escaño-Maestre, María, Ceballos-Chávez, María, Reyes, José C.
Tipo de documento: artigo
Estado:Versão publicada
Data de publicação:2024
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositório:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/358902
Acesso em linha:http://hdl.handle.net/10261/358902
Access Level:Acceso aberto
Palavra-chave:BRG1/SMARCA4
BRM/SMARCA2
Alternative TSS
Alternative splicing
PBAF
Antisense transcription
cBAF
Chromatin remodeling
Nucleosome occupancy
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network_name_str España
repository_id_str
spelling SWI/SNF-dependent genes are defined by their chromatin landscapeBasurto-Cayuela, LauraGuerrero-Martínez, José A.Gómez-Marín, ElenaSánchez-Escabias, ElenaEscaño-Maestre, MaríaCeballos-Chávez, MaríaReyes, José C.BRG1/SMARCA4BRM/SMARCA2Alternative TSSAlternative splicingPBAFAntisense transcriptioncBAFChromatin remodelingNucleosome occupancySWI/SNF complexes are evolutionarily conserved, ATP-dependent chromatin remodeling machines. Here, we characterize the features of SWI/SNF-dependent genes using BRM014, an inhibitor of the ATPase activity of the complexes. We find that SWI/SNF activity is required to maintain chromatin accessibility and nucleosome occupancy for most enhancers but not for most promoters. SWI/SNF activity is needed for expression of genes with low to medium levels of expression that have promoters with (1) low chromatin accessibility, (2) low levels of active histone marks, (3) high H3K4me1/H3K4me3 ratio, (4) low nucleosomal phasing, and (5) enrichment in TATA-box motifs. These promoters are mostly occupied by the canonical Brahma-related gene 1/Brahma-associated factor (BAF) complex. These genes are surrounded by SWI/SNF-dependent enhancers and mainly encode signal transduction, developmental, and cell identity genes (with almost no housekeeping genes). Machine-learning models trained with different chromatin characteristics of promoters and their surrounding regulatory regions indicate that the chromatin landscape is a determinant for establishing SWI/SNF dependency.Research in the J.C.R. lab was funded by the Spanish Ministry of Science and Innovation MCIN/AEI/10.13039/501100011033/grant PID2020-118516GB-I00, the Junta de Andalucía (grants P18-FR-1962 and BIO-321), “Fundación Vencer El Cancer” (VEC), and the European Union FEDER “A Way to Build Europe” program. CABIMER is a center partially funded by the Junta de Andalucía. L.B.-C. and E.S.-E. are recipients of FPU fellowships from the Spanish Ministry of Education. E.G.-M. is the recipient of an FPI fellowship from the Spanish Ministry of Science and Innovation.Peer reviewedElsevierAgencia Estatal de Investigación (España)Ministerio de Ciencia, Innovación y Universidades (España)Junta de AndalucíaFundación Vencer el CancerEuropean CommissionMinisterio de Ciencia e Innovación (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202420242024info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/358902reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-118516GB-I00The underlying dataset has been published as supplementary material of the article in the publisher platform at https://doi.org/10.1016/j.celrep.2024.113855https://doi.org/10.1016/j.celrep.2024.113855Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3589022026-05-22T06:33:51Z
dc.title.none.fl_str_mv SWI/SNF-dependent genes are defined by their chromatin landscape
title SWI/SNF-dependent genes are defined by their chromatin landscape
spellingShingle SWI/SNF-dependent genes are defined by their chromatin landscape
Basurto-Cayuela, Laura
BRG1/SMARCA4
BRM/SMARCA2
Alternative TSS
Alternative splicing
PBAF
Antisense transcription
cBAF
Chromatin remodeling
Nucleosome occupancy
title_short SWI/SNF-dependent genes are defined by their chromatin landscape
title_full SWI/SNF-dependent genes are defined by their chromatin landscape
title_fullStr SWI/SNF-dependent genes are defined by their chromatin landscape
title_full_unstemmed SWI/SNF-dependent genes are defined by their chromatin landscape
title_sort SWI/SNF-dependent genes are defined by their chromatin landscape
dc.creator.none.fl_str_mv Basurto-Cayuela, Laura
Guerrero-Martínez, José A.
Gómez-Marín, Elena
Sánchez-Escabias, Elena
Escaño-Maestre, María
Ceballos-Chávez, María
Reyes, José C.
author Basurto-Cayuela, Laura
author_facet Basurto-Cayuela, Laura
Guerrero-Martínez, José A.
Gómez-Marín, Elena
Sánchez-Escabias, Elena
Escaño-Maestre, María
Ceballos-Chávez, María
Reyes, José C.
author_role author
author2 Guerrero-Martínez, José A.
Gómez-Marín, Elena
Sánchez-Escabias, Elena
Escaño-Maestre, María
Ceballos-Chávez, María
Reyes, José C.
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Agencia Estatal de Investigación (España)
Ministerio de Ciencia, Innovación y Universidades (España)
Junta de Andalucía
Fundación Vencer el Cancer
European Commission
Ministerio de Ciencia e Innovación (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv BRG1/SMARCA4
BRM/SMARCA2
Alternative TSS
Alternative splicing
PBAF
Antisense transcription
cBAF
Chromatin remodeling
Nucleosome occupancy
topic BRG1/SMARCA4
BRM/SMARCA2
Alternative TSS
Alternative splicing
PBAF
Antisense transcription
cBAF
Chromatin remodeling
Nucleosome occupancy
description SWI/SNF complexes are evolutionarily conserved, ATP-dependent chromatin remodeling machines. Here, we characterize the features of SWI/SNF-dependent genes using BRM014, an inhibitor of the ATPase activity of the complexes. We find that SWI/SNF activity is required to maintain chromatin accessibility and nucleosome occupancy for most enhancers but not for most promoters. SWI/SNF activity is needed for expression of genes with low to medium levels of expression that have promoters with (1) low chromatin accessibility, (2) low levels of active histone marks, (3) high H3K4me1/H3K4me3 ratio, (4) low nucleosomal phasing, and (5) enrichment in TATA-box motifs. These promoters are mostly occupied by the canonical Brahma-related gene 1/Brahma-associated factor (BAF) complex. These genes are surrounded by SWI/SNF-dependent enhancers and mainly encode signal transduction, developmental, and cell identity genes (with almost no housekeeping genes). Machine-learning models trained with different chromatin characteristics of promoters and their surrounding regulatory regions indicate that the chromatin landscape is a determinant for establishing SWI/SNF dependency.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/358902
url http://hdl.handle.net/10261/358902
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-118516GB-I00
The underlying dataset has been published as supplementary material of the article in the publisher platform at https://doi.org/10.1016/j.celrep.2024.113855
https://doi.org/10.1016/j.celrep.2024.113855
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,81155

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