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

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dc.contributor.author Plass Pórtulas, Mireya, 1982-
dc.contributor.author Codony Servat, Carles
dc.contributor.author Ferreira, Pedro G.
dc.contributor.author Vilardell, Josep
dc.contributor.author Eyras Jiménez, Eduardo
dc.date.accessioned 2015-12-14T15:34:34Z
dc.date.available 2015-12-14T15:34:34Z
dc.date.issued 2012
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.030767.111
dc.identifier.issn 0954-6111
dc.identifier.uri http://hdl.handle.net/10230/25426
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.
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/pdf
dc.language.iso eng
dc.publisher Cold Spring Harbor Laboratory Press (CSHL Press) -- RNA
dc.relation.ispartof RNA. 2012;18(6):1103-15
dc.rights © 2012 RNA Society
dc.subject.other RNA
dc.subject.other Saccharomyces cerevisiae
dc.subject.other Biologia computacional
dc.title RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1261/rna.030767.111
dc.subject.keyword Splicing
dc.subject.keyword RNA structure
dc.subject.keyword Yeast
dc.subject.keyword 3'ss
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.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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