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Evidence for transcript networks composed of chimeric RNAs in human cells

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dc.contributor.author Djebali, Sarah
dc.contributor.author Lagarde, Julien
dc.contributor.author Lacroix, Vincent
dc.contributor.author Foissac, Sylvain
dc.contributor.author Ribeca, Paolo
dc.contributor.author Martin, David
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author Gingeras, Thomas R.
dc.date.accessioned 2014-06-20T08:18:12Z
dc.date.available 2014-06-20T08:18:12Z
dc.date.issued 2012
dc.identifier.citation Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM et al. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012; 7(1): e28213. DOI: 10.1371/journal.pone.0028213
dc.identifier.issn 1932-6203
dc.identifier.uri http://hdl.handle.net/10230/22591
dc.description.abstract The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes. Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22. Analyses of the locations of the 5' and 3' transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes. The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs. The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network.
dc.description.sponsorship This work has been supported by grants U01HG003150 and U01HG003147 from the National Human Genome Research for the ENCODE project. RG was also supported by a grant from the Spanish Ministry of Education and Science. In addition, KS-A, RM, XY, CL, LG and MV were supported by a grant from the Ellison Foundation and as Institute Sponsored Research from the Dana Farber Cancer Institute Strategic Initiative. The laboratories of SA and AR were supported by grants from the Swiss National Science Foundation and the European Commission AnEUploidy Integrated Project. SA was also supported by the National Center of Excellence ‘‘Frontiers in Genetics’’, ChildCare Foundation and an ERC grant from the European Union. AF, TH and JM acknowledge support from the Wellcome Trust. The work of JLG and MO has been supported by the Spanish Ministry of Science (CTQ2005-09365-C02-02, BIO2009-10964), Instituto Nacional de Bioinformática, the Consolider E-science project (CSD2007-00050), COMBIOMED RETICS and the Fundación Marcelino Botin. JD is supported by a grant from the National Institutes of Health (HG003143) and a W. M. Keck Foundation Distinguished Young Scholar Award. JS is supported by a grant from the National Institutes of Health (U54 HG004592). The work of MT and AV was supported by Consolider E-Science (CSD2007-00050) and the Instituto Nacional de Bioinformática. MV (Center for Cancer Systems Biology, CCSB) is a ‘‘Chercheur Qualifié Honoraire’’ from the Fonds de la Recherche Scientifique (FRS-FNRS, French Community of Belgium). This work has also been funded by grant to TG by NHGRI (U54HG004557) and partially byAffymetirix, Corp
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Public Library of Science (PLoS)
dc.rights © 2012 Sarah Djebali et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution
dc.rights.uri http://creativecommons.org/licenses/by/2.5/
dc.subject.other Metabolisme cel·lular
dc.subject.other Genètica
dc.subject.other RNA
dc.title Evidence for transcript networks composed of chimeric RNAs in human cells
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1371/journal.pone.0028213
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2009-10964
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/CTQ2005-09365
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/CSD2007-00050
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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