Genome-wide identification of binding sites for the nitric oxide-sensitive transcriptional regulator NsrR.
NsrR is a nitric oxide-sensitive regulator of transcription. In Escherichia coli, NsrR is a repressor of the hmp gene encoding the flavohemoglobin that detoxifies nitric oxide. Three other transcription units (ytfE, ygbA, and hcp-hcr) are known to be subject to regulation by NsrR. This chapter describes experimental and statistical protocols used to identify NsrR-binding sites in the E. coli chromosome using chromatin immunoprecipitation and microarray analysis. The methods are applicable, with suitable modifications, to any regulatory protein and any organism.
Efromovich
Sam
S
Department of Mathematical Sciences, University of Texas at Dallas, Richardson, Texas, USA.
Grainger
David
D
Bodenmiller
Diane
D
Spiro
Stephen
S
D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods; D002874:Chromosome Mapping; D019976:Cloning, Organism / Q000379:methods; D004268:DNA-Binding Proteins / Q000378:metabolism* / Q000502:physiology; D001330:Electronic Data Processing / Q000379:methods; D029968:Escherichia coli Proteins / Q000378:metabolism* / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects*; D016680:Genome, Bacterial; D008828:Microbiological Techniques; D008954:Models, Biological; D009569:Nitric Oxide / Q000494:pharmacology*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011485:Protein Binding; D013194:Staining and Labeling / Q000379:methods; D014157:Transcription Factors / Q000378:metabolism* / Q000502:physiology
D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C529899:NsrR protein, E coli; D014157:Transcription Factors; D009569:Nitric Oxide