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!align=left |Citation | |||
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'''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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!align=left |Abstract | |||
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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/. | |||
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11160901 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC30389 PMC30389] | |||
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!align=left |Keywords | |||
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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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==Significance {{HelpIcon|Help:Literature}} == | |||
{{LitSignificance}} | |||
== Useful Materials and Methods {{HelpIcon|Help:Literature}}== | |||
{{LitMaterials}} | |||
==Annotations {{HelpIcon|Help:Literature}}== | |||
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==EcoliWiki Links {{HelpIcon|Help:Literature}} == | |||
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==See also== | |||
==References== | |||
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Latest revision as of 12:10, 16 June 2014
| 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 |
|---|---|
| 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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