Evidence for transcript networks composed of chimeric RNAs in human cells

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...

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Autores: Djebali, Sarah, Lagarde, Julien, Lacroix, Vincent, Foissac, Sylvain, Ribeca, Paolo, Martin, David, Guigó Serra, Roderic, Gingeras, Thomas R.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2012
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/22591
Acceso en línea:http://hdl.handle.net/10230/22591
http://dx.doi.org/10.1371/journal.pone.0028213
Access Level:acceso abierto
Palabra clave:Metabolisme cel·lular
Genètica
RNA
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spelling Evidence for transcript networks composed of chimeric RNAs in human cellsDjebali, SarahLagarde, JulienLacroix, VincentFoissac, SylvainRibeca, PaoloMartin, DavidGuigó Serra, RodericGingeras, Thomas R.Metabolisme cel·lularGenèticaRNAThe 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.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, CorpPublic Library of Science (PLoS)201420142012info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/22591http://dx.doi.org/10.1371/journal.pone.0028213reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésPLoS One. 2012;7(1):e28213info:eu-repo/grantAgreement/ES/3PN/BIO2009-10964info:eu-repo/grantAgreement/ES/2PN/CTQ2005-09365info:eu-repo/grantAgreement/ES/2PN/CSD2007-00050© 2012 Sarah Djebali et al. This is an Open Access article distributed under the terms of the Creative Commons Attributionhttp://creativecommons.org/licenses/by/2.5/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/225912026-06-12T07:21:37Z
dc.title.none.fl_str_mv Evidence for transcript networks composed of chimeric RNAs in human cells
title Evidence for transcript networks composed of chimeric RNAs in human cells
spellingShingle Evidence for transcript networks composed of chimeric RNAs in human cells
Djebali, Sarah
Metabolisme cel·lular
Genètica
RNA
title_short Evidence for transcript networks composed of chimeric RNAs in human cells
title_full Evidence for transcript networks composed of chimeric RNAs in human cells
title_fullStr Evidence for transcript networks composed of chimeric RNAs in human cells
title_full_unstemmed Evidence for transcript networks composed of chimeric RNAs in human cells
title_sort Evidence for transcript networks composed of chimeric RNAs in human cells
dc.creator.none.fl_str_mv Djebali, Sarah
Lagarde, Julien
Lacroix, Vincent
Foissac, Sylvain
Ribeca, Paolo
Martin, David
Guigó Serra, Roderic
Gingeras, Thomas R.
author Djebali, Sarah
author_facet Djebali, Sarah
Lagarde, Julien
Lacroix, Vincent
Foissac, Sylvain
Ribeca, Paolo
Martin, David
Guigó Serra, Roderic
Gingeras, Thomas R.
author_role author
author2 Lagarde, Julien
Lacroix, Vincent
Foissac, Sylvain
Ribeca, Paolo
Martin, David
Guigó Serra, Roderic
Gingeras, Thomas R.
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Metabolisme cel·lular
Genètica
RNA
topic Metabolisme cel·lular
Genètica
RNA
description 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.
publishDate 2012
dc.date.none.fl_str_mv 2012
2014
2014
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/22591
http://dx.doi.org/10.1371/journal.pone.0028213
url http://hdl.handle.net/10230/22591
http://dx.doi.org/10.1371/journal.pone.0028213
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv PLoS One. 2012;7(1):e28213
info:eu-repo/grantAgreement/ES/3PN/BIO2009-10964
info:eu-repo/grantAgreement/ES/2PN/CTQ2005-09365
info:eu-repo/grantAgreement/ES/2PN/CSD2007-00050
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/2.5/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/2.5/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science (PLoS)
publisher.none.fl_str_mv Public Library of Science (PLoS)
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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