PMID:11160901
| Citation |
McCue, L, Thompson, W, Carmack, C, Ryan, MP, Liu, JS, Derbyshire, V and Lawrence, CE (2001) Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res. 29:774-82 |
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| Abstract |
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/. |
| Links | |
| Keywords |
Base Sequence; Binding Sites/genetics; DNA, Bacterial/genetics; DNA, Bacterial/metabolism; Databases, Factual; 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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