Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome

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• dc.contributor.author Reixachs i Solé, Marina
• dc.contributor.author Ruiz Orera, Jorge, 1988-
• dc.contributor.author Albà Soler, Mar
• dc.contributor.author Eyras Jiménez, Eduardo
• dc.date.accessioned 2020-05-06T07:10:33Z
• dc.date.available 2020-05-06T07:10:33Z
• dc.date.issued 2020
• dc.description.abstract The differential production of transcript isoforms from gene loci is a key cellular mechanism. Yet, its impact in protein production remains an open question. Here, we describe ORQAS (ORF quantification pipeline for alternative splicing), a pipeline for the translation quantification of individual transcript isoforms using ribosome-protected mRNA fragments (ribosome profiling). We find evidence of translation for 40-50% of the expressed isoforms in human and mouse, with 53% of the expressed genes having more than one translated isoform in human, and 33% in mouse. Differential splicing analysis revealed that about 40% of the splicing changes at RNA level are concordant with changes in translation. Furthermore, orthologous cassette exons between human and mouse preserve the directionality of the change, and are enriched in microexons in a comparison between glia and glioma. ORQAS leverages ribosome profiling to uncover a widespread and evolutionarily conserved impact of differential splicing on translation, particularly of microexon-containing isoforms.
• dc.description.sponsorship We acknowledge funding from the Spanish Government and FEDER with grants BFU2015-65235-P, BIO2017-85364-R, and MDM-2014-0370, and by Catalan Government (AGAUR) with grant SGR2017-1020. MR-S had funding from an FI grant from the Catalan Government with reference 2018FI_B1_00126 for part of this work.
• dc.format.mimetype application/pdf
• dc.identifier.citation Reixachs-Solé M, Ruiz-Orera J, Albà MM, Eyras E. Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome. Nat Commun. 2020; 11(1):1768. DOI: 10.1038/s41467-020-15634-w
• dc.identifier.doi http://dx.doi.org/10.1038/s41467-020-15634-w
• dc.identifier.issn 2041-1723
• dc.identifier.uri http://hdl.handle.net/10230/44421
• dc.language.iso eng
• dc.publisher Nature Research
• dc.relation.ispartof Nat Commun. 2020; 11(1):1768
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-65235-P
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BIO2017-85364-R
• dc.rights © The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Alternative splicing
• dc.subject.keyword Computational biology and bioinformatics
• dc.subject.keyword Ribosome
• dc.subject.keyword RNA
• dc.subject.keyword Transcriptomics
• dc.title Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion