Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes

Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks, we present a phylogenetic footprinting method for identifying these sites. Probable transcription regu...

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Bibliographic Details
Published in:Nucleic acids research 2001-02, Vol.29 (3), p.774-782
Main Authors: McCue, L, Thompson, W, Carmack, C, Ryan, M P, Liu, J S, Derbyshire, V, Lawrence, C E
Format: Article
Language:English
Subjects:
Base Sequence
Binding Sites - genetics
Databases, Factual
DNA, Bacterial - genetics
DNA, Bacterial - metabolism
Escherichia coli - genetics
Gammaproteobacteria - genetics
Genes, Bacterial - genetics
Genome, Bacterial
Phylogeny
Protein Binding
Sequence Alignment
Sequence Homology, Nucleic Acid
Transcription Factors - metabolism
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Summary:Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks, we present a phylogenetic footprinting method for identifying these sites. Probable transcription regulatory sites upstream of Escherichia coli genes were identified by cross-species comparison using an extended Gibbs sampling algorithm. Close examination of a study set of 184 genes with documented transcription regulatory sites revealed that when orthologous data were available from at least two other gamma proteobacterial species, 81% of our predictions corresponded with the documented sites, and 67% corresponded when data from only one other species were available. That the remaining predictions included bona fide TF-binding sites was proven by affinity purification of a putative transcription factor (YijC) bound to such a site upstream of the fabA gene. Predicted regulatory sites for 2097 E.coli genes are available at http://www.wadsworth.org/resnres/bioinfo/.
ISSN:1362-4962
0305-1048
1362-4962
DOI:10.1093/nar/29.3.774