Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
McCue, L. A.
Carmack, C. Steven
Ryan, Michael P.
Lawrence, Charles E.Note: Order does not necessarily reflect citation order of authors.
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CitationMcCue, L. A. 2001. “Phylogenetic Footprinting of Transcription Factor Binding Sites in Proteobacterial Genomes.” Nucleic Acids Research 29 (3) (February 1): 774–782. doi:10.1093/nar/29.3.774. http://dx.doi.org/10.1093/nar/29.3.774.
AbstractToward 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/.
Citable link to this pagehttp://nrs.harvard.edu/urn-3:HUL.InstRepos:27002732
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