title: The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting.
abstract: We perform a genome-wide analysis of the transition between transcriptional initiation and elongation in Escherichia coli by determining the association of core RNA polymerase (RNAP) and the promoter-recognition factor sigma70 with respect to RNA transcripts. We identify 1286 sigma70-associated promoters, including many internal to known operons, and demonstrate that sigma70 is usually released very rapidly from elongating RNAP complexes. On average, RNAP density is higher at the promoter than in the coding sequence, although the ratio is highly variable among different transcribed regions. Strikingly, a significant fraction of RNAP-bound promoters is not associated with transcriptional activity, perhaps due to an intrinsic energetic barrier to promoter escape. Thus, the transition from transcriptional initiation to elongation is highly variable, often rate limiting, and in some cases is essentially blocked such that RNAP is effectively "poised" to transcribe only under the appropriate environmental conditions. The genomic pattern of RNAP density in E. coli differs from that in yeast and mammalian cells.
authors.affiliation: Harvard University Biophysics Program, Harvard Medical School, Boston, Massachusetts 02115; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115.
authors.forename: Nikos B
authors.initials: NB
authors.lastname: Reppas
authors.affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.
authors.forename: Joseph T
authors.initials: JT
authors.lastname: Wade
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115.
authors.forename: George M
authors.initials: GM
authors.lastname: Church
authors.affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115. Electronic address: kevin@hms.harvard.edu.
authors.forename: Kevin
authors.initials: K
authors.lastname: Struhl
mesh_terms: D047369:Chromatin Immunoprecipitation; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D016680:Genome, Bacterial; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D012808:Sigma Factor / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger; D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases