Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1

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• dc.contributor.author Vivori, Claudia, 1989-
• dc.contributor.author Papasaikas, Panagiotis
• dc.contributor.author Stadhouders, Ralph
• dc.contributor.author Di Stefano, Bruno, 1984-
• dc.contributor.author Ribó Rubio, Anna
• dc.contributor.author Berenguer, Clara
• dc.contributor.author Generoso, Serena Francesca, 1988-
• dc.contributor.author Mallol, Anna
• dc.contributor.author Sardina, Jose Luis
• dc.contributor.author Payer, Bernhard
• dc.contributor.author Graf, T. (Thomas)
• dc.contributor.author Valcárcel, J. (Juan)
• dc.date.accessioned 2021-11-22T07:50:12Z
• dc.date.available 2021-11-22T07:50:12Z
• dc.date.issued 2021
• dc.description.abstract Background: Somatic cell reprogramming is the process that allows differentiated cells to revert to a pluripotent state. In contrast to the extensively studied rewiring of epigenetic and transcriptional programs required for reprogramming, the dynamics of post-transcriptional changes and their associated regulatory mechanisms remain poorly understood. Here we study the dynamics of alternative splicing changes occurring during efficient reprogramming of mouse B cells into induced pluripotent stem (iPS) cells and compare them to those occurring during reprogramming of mouse embryonic fibroblasts. Results: We observe a significant overlap between alternative splicing changes detected in the two reprogramming systems, which are generally uncoupled from changes in transcriptional levels. Correlation between gene expression of potential regulators and specific clusters of alternative splicing changes enables the identification and subsequent validation of CPSF3 and hnRNP UL1 as facilitators, and TIA1 as repressor of mouse embryonic fibroblasts reprogramming. We further find that these RNA-binding proteins control partially overlapping programs of splicing regulation, involving genes relevant for developmental and morphogenetic processes. Conclusions: Our results reveal common programs of splicing regulation during reprogramming of different cell types and identify three novel regulators of this process and their targets.
• dc.description.sponsorship C.V. was recipient of an FPI-Severo Ochoa Fellowship from the Spanish Ministry of Economy and Competitiveness. Work in J.V. laboratory is supported by the European Research Council (ERC AdvG 670146), AGAUR, Spanish Ministry of Economy and Competitiveness (BFU 2017 89308-P) and the Centre of Excellence Severo Ochoa. Work in T.G.’s laboratory was supported by the European Research Council FP7/2007-2013 (ERC Synergy Grant 4D-Genome) the Ministerio de Educación y Ciencia (SAF.2012-37167) and AGAUR. We acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership and the CERCA Programme / Generalitat de Catalunya.
• dc.format.mimetype application/pdf
• dc.identifier.citation Vivori C, Papasaikas P, Stadhouders R, Di Stefano B, Rubio AR, Balaguer CB, Generoso S, Mallol A, Sardina JL, Payer B, Graf T, Valcárcel J. Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1. Genome Biol. 2021;22(1):171. DOI: 10.1186/s13059-021-02372-5
• dc.identifier.doi http://dx.doi.org/10.1186/s13059-021-02372-5
• dc.identifier.issn 1474-7596
• dc.identifier.uri http://hdl.handle.net/10230/49031
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof Genome Biol. 2021;22(1):171
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/670146
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-89308-P
• dc.rights © The Author(s). 2021 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
• 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 CPSF3
• dc.subject.keyword Pluripotency
• dc.subject.keyword Somatic cell reprogramming
• dc.subject.keyword TIA1
• dc.subject.keyword hnRNP UL1
• dc.title Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion