Despite the critical regulatory function of promoter-proximal pausing, the influence of pausing kinetics on transcriptional control remains an active area of investigation. Here, we present Start-TimeLapse-seq (STL-seq), a method that captures the genome-wide kinetics of short, capped RNA turnover and reveals principles of regulation at the pause site. By measuring the rates of release into elongation and premature termination through the inhibition of pause release, we determine that pause-release rates are highly variable, and most promoter-proximal paused RNA polymerase II molecules prematurely terminate (∼80%). The preferred regulatory mechanism upon a hormonal stimulus (20-hydroxyecdysone) is to influence pause-release rather than termination rates. Transcriptional shutdown occurs concurrently with the induction of promoter-proximal termination under hyperosmotic stress, but paused transcripts from TATA box-containing promoters remain stable, demonstrating an important role for cis-acting DNA elements in pausing. STL-seq dissects the kinetics of pause release and termination, providing an opportunity to identify mechanisms of transcriptional regulation.

尽管启动子近端暂停具有关键的调节功能，但暂停动力学对转录控制的影响仍然是一个活跃的研究领域。在这里，我们提出了 Start-TimeLapse-seq (STL-seq)，这是一种捕获短、有帽 RNA 周转的全基因组动力学并揭示暂停位点的调控原理的方法。通过测量释放到延长的速率以及通过抑制暂停释放而提前终止，我们确定暂停释放速率是高度可变的，并且大多数启动子近端暂停的RNA聚合酶II分子过早终止（~80%）。激素刺激（20-羟基蜕皮激素）的首选调节机制是影响暂停释放而不是终止率。在高渗胁迫下，转录关闭与启动子近端终止的诱导同时发生，但来自含有 TATA 盒的启动子的暂停转录物保持稳定，这证明了顺式作用 DNA 元件在暂停中的重要作用。 STL-seq 剖析了暂停释放和终止的动力学，为识别转录调控机制提供了机会。