Comparative analyses of bidirectional promoters in vertebrates.
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.


CONCLUSIONS
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.
Genome Technology Branch, NHGRI, NIH, MD, USA. yangma@mail.nih.gov
Mary Qu
MQ
Yang
James
J
Taylor
Laura
L
Elnitski
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D002874:Chromosome Mapping / Q000379:methods*; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D014714:Vertebrates / Q000235:genetics*