Pausing by RNA polymerase (RNAP) during transcription elongation, in which a translocating RNAP uses a “stepping” mechanism, has been studied extensively, but pausing by RNAP during initial transcription, in which a promoter-anchored RNAP uses a “scrunching” mechanism, has not. We report a method that directly defines the RNAP-active-center position relative to DNA with single-nucleotide resolution (XACT-seq; “crosslink-between-active-center-and-template sequencing”). We apply this method to detect and quantify pausing in initial transcription at 4¹¹ (∼4,000,000) promoter sequences in vivo in Escherichia coli. The results show initial-transcription pausing can occur in each nucleotide addition during initial transcription, particularly the first 4 to 5 nucleotide additions. The results further show initial-transcription pausing occurs at sequences that resemble the consensus sequence element for transcription-elongation pausing. Our findings define the positional and sequence determinants for initial-transcription pausing and establish initial-transcription pausing is hard coded by sequence elements similar to those for transcription-elongation pausing.

在转录延伸期间由 RNA 聚合酶 (RNAP) 暂停，其中易位 RNAP 使用“步进”机制，已被广泛研究，但在初始转录期间由 RNAP 暂停，其中启动子锚定的 RNAP 使用“压缩”机制，没有。我们报告了一种以单核苷酸分辨率直接定义 RNAP 活性中心相对于 DNA 的位置的方法（XACT-seq；“活性中心和模板之间的交联测序”）。我们应用此方法来检测和量化在4在初始转录暂停¹¹（~4,000,000）启动子序列在体内在大肠杆菌. 结果表明，在初始转录过程中，每次添加核苷酸都会发生初始转录暂停，尤其是前 4 到 5 个核苷酸添加。结果进一步显示初始转录暂停发生在类似于转录-延伸暂停的共有序列元件的序列处。我们的发现定义了初始转录暂停的位置和序列决定因素，并确定初始转录暂停是由类似于转录延伸暂停的序列元素硬编码的。