A genomic-scale search for regulatory binding sites in the integration host factor regulon of Escherichia coli K12
Genet. mol. res. (Online)
; 4(4): 783-789, 2005. graf
Article
em En
| LILACS
| ID: lil-444843
Biblioteca responsável:
BR1.1
ABSTRACT
We examined general aspects of the DNA-protein interaction between the integration host factor (IHF) global regulator and its regulatory binding sites in the Escherichia coli K12 genome. Two models were developed with distinct weight matrices for the regulatory binding sites recognized by IHF. Using these matrices we performed a genome scale scan and built a set of computationally predicted binding sites for each of the models. The sites found by the model associated with repetitive sequences had a higher score in the sequence to matrix alignment. They were also more rare than the other sites. The sites not associated with repeats rapidly tended to become undistinguishable from the background as statistical stringency was relaxed. We compared our results to the known sites documented in RegulonDB and found new members of the IHF Regulon. The two models exhibit clearly distinct affinity patterns (scores in the sequence to matrix alignments and in the number of regulatory sites), as we vary the stringency of the statistical confidence parameters. We suggest that these differences may play an important role in the dynamics of the network. We concluded that IHF may regulate two genes encoding ATP-dependent RNA helicases. This interaction is not described in RegulonDB, even as a computational prediction. IHF may also regulate RNA modification processes.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
LILACS
Assunto principal:
Genoma Bacteriano
/
Regulon
/
Fatores Hospedeiros de Integração
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
Genet. mol. res. (Online)
Assunto da revista:
BIOLOGIA MOLECULAR
/
GENETICA
Ano de publicação:
2005
Tipo de documento:
Article
País de afiliação:
Brasil
País de publicação:
Brasil