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Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

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dc.contributor.author Bellora Pereyra, Nicolás
dc.contributor.author Farré, Domènec
dc.contributor.author Albà Soler, Mar
dc.date.accessioned 2012-02-09T09:45:28Z
dc.date.available 2012-02-09T09:45:28Z
dc.date.issued 2007
dc.identifier.citation Bellora N, Farré D, Albà M M. Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters. BMC Genomics. 2007;8:459. DOI 10.1186/1471-2164-8-459
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10230/16198
dc.description.abstract Background: The arrangement of regulatory motifs in gene promoters, or promoter/narchitecture, is the result of mutation and selection processes that have operated over many/nmillions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of/nspecific protein-interacting DNA motifs in gene promoters. However, little is known about the/nrelative location and spacing of these motifs. To fill this gap, we have performed a systematic search/nfor motifs that show significant bias at specific promoter locations in a large collection of/nhousekeeping and tissue-specific genes./nResults: We observe that promoters driving housekeeping gene expression are enriched in/nparticular motifs with strong positional bias, such as YY1, which are of little relevance in promoters/ndriving tissue-specific expression. We also identify a large number of motifs that show positional/nbias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific/nmotifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis,/nas well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions/nfor 559 tissue-specific motifs in mouse gene promoters./nConclusion: The study shows that motif positional bias is an important feature of mammalian/nproximal promoters and that it affects both general and tissue-specific motifs. Motif positional/nconstraints define very distinct promoter architectures depending on breadth of expression and/ntype of tissue.
dc.description.sponsorship We received financial support from Fundación/nBanco Bilbao Vizcaya Argentaria (FBBVA), Plan Nacional de I+D Ministerio/nde Educación y Ciencia (BFU2006-07120), Instituto Nacional de Bioinformática/n(INB), European Commission Infobiomed NoE and, Fundació/nICREA.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof BMC Genomics. 2007;8:459
dc.rights © 2007 Bellora et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.uri http://creativecommons.org/licenses/by/2.0/
dc.subject.other Genètica
dc.subject.other Àcids nucleics
dc.title Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/1471-2164-8-459
dc.subject.keyword Promoter regions
dc.subject.keyword Mice
dc.subject.keyword DNA
dc.subject.keyword Gene expression
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BFU2006-07120
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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