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This article is part of the supplement: Symposium of Computations in Bioinformatics and Bioscience (SCBB07)

Open Access Research

Comparative analyses of bidirectional promoters in vertebrates

Mary Qu Yang1, James Taylor2 and Laura Elnitski1*

Author Affiliations

1 Genome Technology Branch, NHGRI, NIH, MD, USA

2 Courant Institute of Mathematical Sciences, New York University, NY, USA

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BMC Bioinformatics 2008, 9(Suppl 6):S9  doi:10.1186/1471-2105-9-S6-S9

Published: 28 May 2008

Abstract

Background

Orthologous genes with deep phylogenetic histories are likely to retain similar regulatory features. In this report we utilize orthology assignments for pairs of genes co-regulated by bidirectional promoters to map the ancestral history of the promoter regions.

Results

Our mapping of bidirectional promoters from humans to fish shows that many such promoters emerged after the divergence of chickens and fish. Furthermore, annotations of promoters in deep phylogenies enable detection of missing data or assembly problems present in higher vertebrates. The functional importance of bidirectional promoters is indicated by selective pressure to maintain the arrangement of genes regulated by the promoter over long evolutionary time spans. Characteristics unique to bidirectional promoters are further elucidated using a technique for unsupervised classification, known as ESPERR.

Conclusion

Results of these analyses will aid in our understanding of the evolution of bidirectional promoters, including whether the regulation of two genes evolved as a consequence of their proximity or if function dictated their co-regulation.