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Selection upon genome architecture: conservation of functional neighborhoods with changing genes

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dc.contributor.author Al-Shahrour, Fátima
dc.contributor.author Minguez, Pablo
dc.contributor.author Marquès i Bonet, Tomàs, 1975-
dc.contributor.author Gazave, Elodie
dc.contributor.author Navarro i Cuartiellas, Arcadi, 1969-
dc.contributor.author Dopazo, Joaquín
dc.date.accessioned 2015-04-17T07:07:41Z
dc.date.available 2015-04-17T07:07:41Z
dc.date.issued 2010
dc.identifier.citation Al-Shahrour F, Minguez P, Marques-Bonet T, Gazave E, Navarro A, Dopazo J. Selection upon genome architecture: conservation of functional neighborhoods with changing genes. PLoS Computational Biology. 2010; 6(10): e1000953. DOI 10.1371/journal.pcbi.1000953
dc.identifier.issn 1553-734X
dc.identifier.uri http://hdl.handle.net/10230/23431
dc.description.abstract An increasing number of evidences show that genes are not distributed randomly across eukaryotic chromosomes, but rather in functional neighborhoods. Nevertheless, the driving force that originated and maintains such neighborhoods is still a matter of controversy. We present the first detailed multispecies cartography of genome regions enriched in genes with related functions and study the evolutionary implications of such clustering. Our results indicate that the chromosomes of higher eukaryotic genomes contain up to 12% of genes arranged in functional neighborhoods, with a high level of gene co-expression, which are consistently distributed in phylogenies. Unexpectedly, neighborhoods with homologous functions are formed by different (non-orthologous) genes in different species. Actually, instead of being conserved, functional neighborhoods present a higher degree of synteny breaks than the genome average. This scenario is compatible with the existence of selective pressures optimizing the coordinated transcription of blocks of functionally related genes. If these neighborhoods were broken by chromosomal rearrangements, selection would favor further rearrangements reconstructing other neighborhoods of similar function. The picture arising from this study is a dynamic genomic landscape with a high level of functional organization.
dc.description.sponsorship This work is supported by grants BIO2008-04212, BFU2009-13409-C02-02, and BFU2006-15413-C02-01 from the Spanish Ministry of Science and Innovation, and PROMETEO/2010/001 from the GVA-FEDER. The National Institute of Bioinformatics (www.inab.org) and The CIBER de Enfermedades Raras are initiatives of the ISCIII. This work is also partially supported by a grant (RD06/0020/1019) from Red Tematica de Investigacion Cooperativa en Cancer (RTICC), Instituto de Salud Carlos III (ISCIII), and the Spanish Ministry of Science and Innovation. The funders had no role in study design, data collection and analysis,decision to publish, or preparation of the manuscript
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Public Library of Science (PLoS)
dc.relation.ispartof PLoS Computational Biology. 2010; 6(10): e1000953
dc.rights © 2010 Al-Shahrour et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
dc.subject.other Saccharomyces cerevisiae -- Metabolisme
dc.subject.other Factors de transcripció
dc.subject.other Genètica animal
dc.title Selection upon genome architecture: conservation of functional neighborhoods with changing genes
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1371/journal.pcbi.1000953
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2008-04212
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2009-13409
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BFU2006-15413
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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