Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβ

Differential splicing efficiency of specific introns is a mechanism that dramatically increases protein diversity, based on selection of alternative exons for the final mature mRNA. However, it is unclear whether splicing efficiency of introns within the same gene is coordinated and eventually regul...

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Autores: Sánchez-Escabias, Elena, Guerrero-Martínez, José A., Reyes, José C.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/282992
Acceso en línea:http://hdl.handle.net/10261/282992
Access Level:acceso abierto
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spelling Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβSánchez-Escabias, ElenaGuerrero-Martínez, José A.Reyes, José C.Differential splicing efficiency of specific introns is a mechanism that dramatically increases protein diversity, based on selection of alternative exons for the final mature mRNA. However, it is unclear whether splicing efficiency of introns within the same gene is coordinated and eventually regulated as a mechanism to control mature mRNA levels. Based on nascent chromatin-associated RNA-sequencing data, we now find that co-transcriptional splicing (CTS) efficiency tends to be similar between the different introns of a gene. We establish that two well-differentiated strategies for CTS efficiency exist, at the extremes of a gradient: short genes that produce high levels of pre-mRNA undergo inefficient splicing, while long genes with relatively low levels of pre-mRNA have an efficient splicing. Notably, we observe that genes with efficient CTS display a higher level of mature mRNA relative to their pre-mRNA levels. Further, we show that the TGFβ signal transduction pathway regulates the general CTS efficiency, causing changes in mature mRNA levels. Taken together, our data indicate that CTS efficiency is a gene-specific characteristic that can be regulated to control gene expression.This work was funded by the Spanish Ministry of Economy and Competitiveness MCIN/AEI/10.13039/501100011033/ (grant numbers BFU2017-85420-R and PID2020-118516GB-I00), the Junta de Andalucía (grant P18-FR-1962 and BIO-321), “Fundación Vencer El Cancer” (VEC) and the European Union FEDER “A way to build Europe”. CABIMER is a Center partially funded by the Junta de Andalucía.Nature Publishing GroupAgencia Estatal de Investigación (España)Ministerio de Ciencia, Innovación y Universidades (España)Junta de AndalucíaFundación Vencer el CancerEuropean CommissionConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2022202220222022info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/282992reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2017-85420-Rinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-118516GB-I00Guerrero-Martínez, José A.; Ceballos-Chávez, María; Koehler, Florian; Peiró, Sandra; Reyes, José C.; Sánchez-Escabias, Elena; 2020; Characterization of epigenomic and transcriptomic changes upon TGF-beta treatment in NMuMG cells [Dataset]; Gene Expression Omnibus; GSE140552http://dx.doi.org/10.1038/s42003-022-03224-zSíinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2829922026-05-22T06:33:51Z
dc.title.none.fl_str_mv Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβ
title Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβ
spellingShingle Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβ
Sánchez-Escabias, Elena
title_short Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβ
title_full Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβ
title_fullStr Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβ
title_full_unstemmed Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβ
title_sort Co-transcriptional splicing efficiency is a gene-specific feature that can be regulated by TGFβ
dc.creator.none.fl_str_mv Sánchez-Escabias, Elena
Guerrero-Martínez, José A.
Reyes, José C.
author Sánchez-Escabias, Elena
author_facet Sánchez-Escabias, Elena
Guerrero-Martínez, José A.
Reyes, José C.
author_role author
author2 Guerrero-Martínez, José A.
Reyes, José C.
author2_role 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
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
description Differential splicing efficiency of specific introns is a mechanism that dramatically increases protein diversity, based on selection of alternative exons for the final mature mRNA. However, it is unclear whether splicing efficiency of introns within the same gene is coordinated and eventually regulated as a mechanism to control mature mRNA levels. Based on nascent chromatin-associated RNA-sequencing data, we now find that co-transcriptional splicing (CTS) efficiency tends to be similar between the different introns of a gene. We establish that two well-differentiated strategies for CTS efficiency exist, at the extremes of a gradient: short genes that produce high levels of pre-mRNA undergo inefficient splicing, while long genes with relatively low levels of pre-mRNA have an efficient splicing. Notably, we observe that genes with efficient CTS display a higher level of mature mRNA relative to their pre-mRNA levels. Further, we show that the TGFβ signal transduction pathway regulates the general CTS efficiency, causing changes in mature mRNA levels. Taken together, our data indicate that CTS efficiency is a gene-specific characteristic that can be regulated to control gene expression.
publishDate 2022
dc.date.none.fl_str_mv 2022
2022
2022
2022
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/10261/282992
url http://hdl.handle.net/10261/282992
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2017-85420-R
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-118516GB-I00
Guerrero-Martínez, José A.; Ceballos-Chávez, María; Koehler, Florian; Peiró, Sandra; Reyes, José C.; Sánchez-Escabias, Elena; 2020; Characterization of epigenomic and transcriptomic changes upon TGF-beta treatment in NMuMG cells [Dataset]; Gene Expression Omnibus; GSE140552
http://dx.doi.org/10.1038/s42003-022-03224-z
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 Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
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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