{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["John J"],"funding":["NIEHS NIH HHS","National Institutes of Health"],"pagination":["878-892"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9104697"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["32(5)"],"pubmed_abstract":["When detected at single-base-pair resolution, the genome-wide location, occupancy level, and structural organization of DNA-binding proteins provide mechanistic insights into genome regulation. Here we use ChIP-exo to provide a near-base-pair resolution view of the epigenomic organization of the <i>Escherichia coli</i> transcription machinery and nucleoid structural proteins at the time when cells are growing exponentially and upon rapid reprogramming (acute heat shock). We examined the site specificity of three sigma factors (RpoD/σ<sup>70</sup>, RpoH/σ<sup>32</sup>, and RpoN/σ<sup>54</sup>), RNA polymerase (RNAP or RpoA, -B, -C), and two nucleoid proteins (Fis and IHF). We suggest that DNA shape at the flanks of cognate motifs helps drive site specificity. We find that although RNAP and "],"journal":["Genome research"],"pubmed_title":["Genome-wide promoter assembly in <i>E. coli</i> measured at single-base resolution."],"pmcid":["PMC9104697"],"funding_grant_id":["R01 ES013768","ES013768"],"pubmed_authors":["Jabbar J","John J","Rossi MJ","Lai WKM","Pugh BF","Badjatia N"],"additional_accession":[]},"is_claimable":false,"name":"Genome-wide promoter assembly in <i>E. coli</i> measured at single-base resolution.","description":"When detected at single-base-pair resolution, the genome-wide location, occupancy level, and structural organization of DNA-binding proteins provide mechanistic insights into genome regulation. Here we use ChIP-exo to provide a near-base-pair resolution view of the epigenomic organization of the <i>Escherichia coli</i> transcription machinery and nucleoid structural proteins at the time when cells are growing exponentially and upon rapid reprogramming (acute heat shock). We examined the site specificity of three sigma factors (RpoD/σ<sup>70</sup>, RpoH/σ<sup>32</sup>, and RpoN/σ<sup>54</sup>), RNA polymerase (RNAP or RpoA, -B, -C), and two nucleoid proteins (Fis and IHF). We suggest that DNA shape at the flanks of cognate motifs helps drive site specificity. We find that although RNAP and ","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 May","modification":"2026-05-09T13:31:37.585Z","creation":"2025-02-19T04:03:02.593Z"},"accession":"S-EPMC9104697","cross_references":{"pubmed":["35483960"],"doi":["10.1101/gr.276544.121"]}}