Cleavage and polyadenylation is necessary for the formation of mature mRNA molecules. The rate at which this process occurs can determine the temporal availability of mRNA for subsequent function throughout the cell and is likely tightly regulated. Despite advances in high-throughput approaches for global kinetic profiling of RNA maturation, genome-wide 3′ end cleavage rates have never been measured. Here, we describe a novel approach to estimate the rates of cleavage, using metabolic labeling of nascent RNA, high-throughput sequencing, and mathematical modeling. Using in silico simulations of nascent RNA-seq data, we show that our approach can accurately and precisely estimate cleavage half-lives for both constitutive and alternative sites. We find that 3′ end cleavage is fast on average, with half-lives under a minute, but highly variable across individual sites. Rapid cleavage is promoted by the presence of canonical sequence elements and an increased density of polyadenylation signals near a cleavage site. Finally, we find that cleavage rates are associated with the localization of RNA polymerase II at the end of a gene, and faster cleavage leads to quicker degradation of downstream readthrough RNA. Our findings shed light on the features important for efficient 3′ end cleavage and the regulation of transcription termination.

中文翻译：

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前体 mRNA 3' 末端切割的全基因组动力学分析

切割和聚腺苷酸化对于成熟 mRNA 分子的形成是必要的。这一过程发生的速率可以决定 mRNA 在整个细胞中的后续功能的时间可用性，并且可能受到严格调控。尽管用于 RNA 成熟全局动力学分析的高通量方法取得了进展，但从未测量过全基因组 3' 末端切割率。在这里，我们描述了一种利用新生 RNA 的代谢标记、高通量测序和数学模型来估计切割率的新方法。使用新生 RNA-seq 数据的计算机模拟，我们表明我们的方法可以准确且精确地估计本构位点和替代位点的切割半衰期。我们发现 3' 末端裂解平均速度很快，半衰期不到一分钟，但各个位点之间差异很大。规范序列元件的存在和切割位点附近多腺苷酸化信号密度的增加促进了快速切割。最后，我们发现切割速率与基因末端 RNA 聚合酶 II 的定位有关，更快的切割会导致下游通读 RNA 更快的降解。我们的研究结果揭示了对于有效 3' 末端切割和转录终止调控的重要特征。