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Methods Enzymol. 2008;437:211-33. doi: 10.1016/S0076-6879(07)37012-2.

Genome-wide identification of binding sites for the nitric oxide-sensitive transcriptional regulator NsrR.

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  • 1Department of Mathematical Sciences, University of Texas at Dallas, Richardson, Texas, USA.


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.

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