Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.
Nucleic Acids Res
; 29(3): 774-82, 2001 Feb 01.
Article
en En
| MEDLINE
| ID: mdl-11160901
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/.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Filogenia
/
Sitios de Unión
/
Genoma Bacteriano
/
Gammaproteobacteria
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Nucleic Acids Res
Año:
2001
Tipo del documento:
Article
País de afiliación:
Estados Unidos