Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). More than 1,800 miRNA loci are annotated in humans, but it remains largely unknown whether and at which sites pri-miRNAs are cleaved by DROSHA. Here, we performed in vitro processing on a full set of human pri-miRNAs (miRBase version 21) followed by sequencing. This comprehensive profiling enabled us to classify miRNAs on the basis of DROSHA dependence and map their cleavage sites with respective processing efficiency measures. Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing. We observe widespread alternative processing and unproductive cleavage events such as “nick” or “inverse” processing. SRSF3 is a broad-acting auxiliary factor modulating alternative processing and suppressing unproductive processing. The profiling data and methods developed in this study will allow systematic analyses of miRNA regulation.

规范 microRNA (miRNA) 的成熟由切割初级转录物 (pri-miRNA) 的 DROSHA 启动。人类中有超过 1,800 个 miRNA 位点被注释，但在很大程度上仍不清楚 pri-miRNA 是否以及在哪些位点被 DROSHA 切割。在这里，我们对全套人类 pri-miRNA（miRBase 版本 21）进行了体外处理，然后进行了测序。这种全面的分析使我们能够根据 DROSHA 依赖性对 miRNA 进行分类，并用各自的处理效率措施绘制它们的切割位点。只有 758 个 pri-miRNA 被 DROSHA 自信地处理，而大多数可能是非规范的或错误的条目。DROSHA 依赖性 pri-miRNA 的分析显示了关键的顺式- 用于处理的元素。我们观察到广泛的替代加工和非生产性切割事件，例如“缺口”或“反向”加工。SRSF3 是一种广泛作用的辅助因子，可调节替代加工和抑制非生产加工。本研究中开发的分析数据和方法将允许对 miRNA 调控进行系统分析。