Bellora Pereyra, NicolásFarré, DomènecAlbà Soler, Mar2012-02-092012-02-092007Bellora 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 10.1186/1471-2164-8-4591471-2164http://hdl.handle.net/10230/16198Background: 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.application/pdfeng© 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.GenèticaÀcids nucleicsinfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1186/1471-2164-8-459Promoter regionsMiceDNAGene expressioninfo:eu-repo/semantics/openAccess