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Open Access Research article

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

Nicolás Bellora12, Domènec Farré2 and M Mar Albà134*

Author Affiliations

1 Research Unit on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain

2 Centre for Genomic Regulation, Barcelona, Spain

3 Fundació Institut Municipal d'Investigació Mèdica, Barcelona, Spain

4 Catalan Institution for Research and Advanced Studies, Barcelona, Spain

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BMC Genomics 2007, 8:459  doi:10.1186/1471-2164-8-459

Published: 13 December 2007

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.