RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae

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• dc.contributor.author Plass Pórtulas, Mireya, 1982-ca
• dc.contributor.author Codony Servat, Carlesca
• dc.contributor.author Ferreira, Pedro G.ca
• dc.contributor.author Vilardell, Josepca
• dc.contributor.author Eyras Jiménez, Eduardoca
• dc.date.accessioned 2015-12-14T15:34:34Z
• dc.date.available 2015-12-14T15:34:34Z
• dc.date.issued 2012
• dc.description.abstract Alternative splicing is the mechanism by which different combinations of exons in the pre-mRNA give rise to distinct mature mRNAs. This process is mediated by splicing factors that bind the pre-mRNA and affect the recognition of its splicing signals. Saccharomyces species lack many of the regulatory factors present in metazoans. Accordingly, it is generally assumed that the amount of alternative splicing is limited. However, there is recent compelling evidence that yeast have functional alternative splicing, mainly in response to environmental conditions. We have previously shown that sequence and structure properties of the pre-mRNA could explain the selection of 3' splice sites (ss) in Saccharomyces cerevisiae. In this work, we extend our previous observations to build a computational classifier that explains most of the annotated 3'ss in the CDS and 5' UTR of this organism. Moreover, we show that the same rules can explain the selection of alternative 3'ss. Experimental validation of a number of predicted alternative 3'ss shows that their usage is low compared to annotated 3'ss. The majority of these alternative 3'ss introduce premature termination codons (PTCs), suggesting a role in expression regulation. Furthermore, a genome-wide analysis of the effect of temperature, followed by experimental validation, yields only a small number of changes, indicating that this type of regulation is not widespread. Our results are consistent with the presence of alternative 3'ss selection in yeast mediated by the pre-mRNA structure, which can be responsive to external cues, like temperature, and is possibly related to the control of gene expression.ca
• dc.description.sponsorship E.E. and M.P. were supported by the Spanish Ministry of Science (MICINN) with grants BIO2008-01091, BIO2011-23920, and CSD2009-00080. The work from M.P. was also partly funded by Spanish National Health Institute Carlos III. J.V. and C.C.S. were supported by BIO2008-363 (MICINN) and by CSIC-200920I195. P.G.F. was supported by SFRH/BPD/42003/2007 (FCT-PORTUGAL) and by CSD2007-1500005 (MICINN)
• dc.format.mimetype application/pdfca
• dc.identifier.citation Plass M, Codony-Servat C, Ferreira PG, Vilardell J, Eyras E. RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae. RNA. 2012;18(6):1103-15. DOI: 10.1261/rna.030767.111ca
• dc.identifier.doi http://dx.doi.org/10.1261/rna.030767.111
• dc.identifier.issn 0954-6111
• dc.identifier.uri http://hdl.handle.net/10230/25426
• dc.language.iso engca
• dc.publisher Cold Spring Harbor Laboratory Press (CSHL Press) -- RNAca
• dc.relation.ispartof RNA. 2012;18(6):1103-15
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2008-01091
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2011-23920
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/CSD2009-00080
• dc.rights © 2012 RNA Societyca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.subject.keyword Splicing
• dc.subject.keyword RNA structure
• dc.subject.keyword Yeast
• dc.subject.keyword 3'ss
• dc.subject.other RNAca
• dc.subject.other Saccharomyces cerevisiaeca
• dc.subject.other Biologia computacionalca
• dc.title RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiaeca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca