title: Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis.
abstract: In bacteria, selective promoter recognition by RNA polymerase is achieved by its association with σ factors, accessory subunits able to direct RNA polymerase "core enzyme" (E) to different promoter sequences. Using Chromatin Immunoprecipitation-sequencing (ChIP-seq), we searched for promoters bound by the σ(S)-associated RNA polymerase form (Eσ(S)) during transition from exponential to stationary phase. We identified 63 binding sites for Eσ(S) 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 σ(S)-encoding rpoS gene. Eσ(S) binding did not always correlate with an increase in transcription level, suggesting that, at some σ(S)-dependent promoters, Eσ(S) might remain poised in a pre-initiation state upon binding. A large fraction of Eσ(S)-binding sites corresponded to promoters recognized by RNA polymerase associated with σ(70) or other σ factors, suggesting a considerable overlap in promoter recognition between different forms of RNA polymerase. In particular, Eσ(S) 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 Eσ(S) in the regulation of non coding RNAs, such as OmrA/B, RyeA/B and SibC.
authors.affiliation: Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy.
authors.forename: Clelia
authors.initials: C
authors.lastname: Peano
authors.affiliation: EAWAG, Swiss Federal Institute for Environmental Science and Technology, Dübendorf, Switzerland.
authors.forename: Johannes
authors.initials: J
authors.lastname: Wolf
authors.affiliation: Lab. Adaptation et Pathogénie des Micro-organismes (LAPM), Univ. Grenoble Alpes, F-38000 Grenoble, France.|UMR 5163, Centre National de Recherche Scientifique (CNRS), Grenoble, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Demol
authors.affiliation: Department of Biosciences, Università degli Studi di Milano, Milan, Italy.
authors.forename: Elio
authors.initials: E
authors.lastname: Rossi
authors.affiliation: Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Petiti
authors.affiliation: Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy.
authors.forename: Gianluca
authors.initials: G
authors.lastname: De Bellis
authors.affiliation: Lab. Adaptation et Pathogénie des Micro-organismes (LAPM), Univ. Grenoble Alpes, F-38000 Grenoble, France.|UMR 5163, Centre National de Recherche Scientifique (CNRS), Grenoble, France.
authors.forename: Johannes
authors.initials: J
authors.lastname: Geiselmann
authors.affiliation: EAWAG, Swiss Federal Institute for Environmental Science and Technology, Dübendorf, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Egli
authors.affiliation: Lab. Adaptation et Pathogénie des Micro-organismes (LAPM), Univ. Grenoble Alpes, F-38000 Grenoble, France.|UMR 5163, Centre National de Recherche Scientifique (CNRS), Grenoble, France.
authors.forename: Stephan
authors.initials: S
authors.lastname: Lacour
authors.affiliation: Department of Biosciences, Università degli Studi di Milano, Milan, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Landini
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D011401:Promoter Regions, Genetic; D022661:RNA, Untranslated / Q000235:genetics; D012808:Sigma Factor / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D022661:RNA, Untranslated; D012808:Sigma Factor