Characterization of the escherichia coli δS core regulon by chromatin immunoprecipitation-sequencing (ChIP-seq) analysis

Abstract

In bacteria, selective promoter recognition by RNA polymerase is achieved by its association with δfactors, accessory subunits able to direct RNA polymerase â €œ core enzymeâ €(E) to different promoter sequences. Using Chromatin Immunoprecipitation-sequencing (ChIP-seq), we searched for promoters bound by the δS -associated RNA polymerase form (EδS) during transition from exponential to stationary phase. We identified 63 binding sites for EδS 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 δS -encoding rpoS gene. EδS binding did not always correlate with an increase in transcription level, suggesting that, at some δS -dependent promoters, EδS might remain poised in a pre-initiation state upon binding. A large fraction of EδS -binding sites corresponded to promoters recognized by RNA polymerase associated with δ70 or other δfactors, suggesting a considerable overlap in promoter recognition between different forms of RNA polymerase. In particular, EδS 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 EδS in the regulation of non coding RNAs, such as OmrA/B, RyeA/B and SibC.