Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes

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Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes

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Title: Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
Author: McCue, L. A.; Thompson, William; Carmack, C. Steven; Ryan, Michael P.; Liu, Jun; Derbyshire, Victoria; Lawrence, Charles E.

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Citation: McCue, 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.
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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/.
Published Version: doi:10.1093/nar/29.3.774
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC30389/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:27002732
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