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 Escherichia coli 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/σ⁷⁰, RpoH/σ³², and RpoN/σ⁵⁴), 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 sigma factors occupy active cognate promoters, RpoH and RpoN can occupy quiescent promoters without the presence of RNAP. Thus, promoter-bound sigma factors can be triggered to recruit RNAP by a mechanism that is distinct from an obligatory cycle of free sigma binding RNAP followed by promoter binding. These findings add new dimensions to how sigma factors achieve promoter specificity through DNA sequence and shape, and further define mechanistic steps in regulated genome-wide assembly of RNAP at promoters in E. coli.

中文翻译：

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以单碱基分辨率测量大肠杆菌中的全基因组启动子组装

当以单碱基对分辨率检测时，DNA 结合蛋白的全基因组位置、占据水平和结构组织为基因组调控提供了机制见解。在这里，我们使用 ChIP-exo 提供细胞呈指数级生长和快速重编程（急性热休克）时大肠杆菌转录机制和类核结构蛋白的表观基因组组织的近碱基对分辨率视图。我们检查了三个西格玛因子（RpoD/σ ⁷⁰、RpoH/σ ³²和 RpoN/σ ⁵⁴）、RNA 聚合酶（RNAP 或 RpoA、-B、-C）和两种核蛋白（Fis 和 IHF）。我们认为同源基序侧面的 DNA 形状有助于驱动位点特异性。我们发现，虽然 RNAP 和 sigma 因子占据活性同源启动子，但 RpoH 和 RpoN 可以在不存在 RNAP 的情况下占据静止启动子。因此，启动子结合的σ因子可以通过与游离σ结合RNAP随后启动子结合的强制性循环不同的机制来触发募集RNAP。这些发现为 sigma 因子如何通过 DNA 序列和形状实现启动子特异性增加了新的维度，并进一步定义了大肠杆菌启动子上受调控的全基因组 RNAP 组装的机制步骤。