Localization of NsrR binding sites in the Escherichia coli genome

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. Several other transcription units (including ytfE, ygbA and hcp-hcr) are known to be subject to regulation by NsrR. In this study, chromatin immunoprecipitation and microarray analysis was used to identify NsrR binding sites in the chromosome of Escherichia coli strain MG1655. Keywords: ChIP-chip The nsrR gene was modified by the addition of DNA sequences encoding a C-terminal 3X-Flag tag, and the tagged gene was integrated into the chromosome. Cultures were grown anaerobically in the absence and presence of nitrate, conditions which lead to high and low levels of occupancy of NsrR binding sites, respectively. Chromatin was extracted from the two cultures, labeled with Cy3 and Cy5 (with no PCR amplification step) and hybridized to high density microarrays fabricated by Oxford Gene Technology.