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

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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
http://hdl.handle.net/10230/16198
To cite or link this document: http://hdl.handle.net/10230/16198
dc.contributor.author Bellora Pereyra, Nicolás
dc.contributor.author Farré, Domènec
dc.contributor.author Albà Soler, Mar
dc.contributor.other Universitat Pompeu Fabra
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 architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results: We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion: The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.
dc.description.sponsorship We received financial support from Fundación Banco Bilbao Vizcaya Argentaria (FBBVA), Plan Nacional de I+D Ministerio de Educación y Ciencia (BFU2006-07120), Instituto Nacional de Bioinformática (INB), European Commission Infobiomed NoE and, Fundació ICREA.
dc.language.iso eng
dc.publisher BioMed Central
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.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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