Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis

In bacteria, selective promoter recognition by RNA polymerase is achieved by its association with \u3c3 factors, accessory subunits able to direct RNA polymerase \u201ccore enzyme\u201d (E) to different promoter sequences. Using Chromatin Immunoprecipitation-sequencing (ChIP-seq), we searched for promoters bound by the \u3c3S-associated RNA polymerase form (E\u3c3S) during transition from exponential to stationary phase. We identified 63 binding sites for E\u3c3S overlapping known or putative promoters, often located upstream of genes (encoding either ORFs or non-coding RNAs) showing at least some degree of dependence on the \u3c3S-encoding rpoS gene. E\u3c3S binding did not always correlate with an increase in transcription level, suggesting that, at some \u3c3S-dependent promoters, E\u3c3S might remain poised in a pre-initiation state upon binding. A large fraction of E\u3c3S-binding sites corresponded to promoters recognized by RNA polymerase associated with \u3c370 or other \u3c3 factors, suggesting a considerable overlap in promoter recognition between different forms of RNA polymerase. In particular, E\u3c3S appears to contribute significantly to transcription of genes encoding proteins involved in LPS biosynthesis and in cell surface composition. Finally, our results highlight a direct role of E\u3c3S in the regulation of non coding RNAs, such as OmrA/B, RyeA/B and SibC