Wen Jiayu, Ladewig Erik, Shenker Sol, Mohammed Jaaved, Lai Eric C
Department of Developmental Biology, Sloan-Kettering Institute, New York, New York, United States of America.
Department of Developmental Biology, Sloan-Kettering Institute, New York, New York, United States of America; Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York, United States of America.
PLoS Comput Biol. 2015 Sep 1;11(9):e1004441. doi: 10.1371/journal.pcbi.1004441. eCollection 2015 Sep.
Mirtrons are microRNA (miRNA) substrates that utilize the splicing machinery to bypass the necessity of Drosha cleavage for their biogenesis. Expanding our recent efforts for mammalian mirtron annotation, we use meta-analysis of aggregate datasets to identify ~500 novel mouse and human introns that confidently generate diced small RNA duplexes. These comprise nearly 1000 total loci distributed in four splicing-mediated biogenesis subclasses, with 5'-tailed mirtrons as, by far, the dominant subtype. Thus, mirtrons surprisingly comprise a substantial fraction of endogenous Dicer substrates in mammalian genomes. Although mirtron-derived small RNAs exhibit overall expression correlation with their host mRNAs, we observe a subset with substantial differences that suggest regulated processing or accumulation. We identify characteristic sequence, length, and structural features of mirtron loci that distinguish them from bulk introns, and find that mirtrons preferentially emerge from genes with larger numbers of introns. While mirtrons generate miRNA-class regulatory RNAs, we also find that mirtrons exhibit many features that distinguish them from canonical miRNAs. We observe that conventional mirtron hairpins are substantially longer than Drosha-generated pre-miRNAs, indicating that the characteristic length of canonical pre-miRNAs is not a general feature of Dicer substrate hairpins. In addition, mammalian mirtrons exhibit unique patterns of ordered 5' and 3' heterogeneity, which reveal hidden complexity in miRNA processing pathways. These include broad 3'-uridylation of mirtron hairpins, atypically heterogeneous 5' termini that may result from exonucleolytic processing, and occasionally robust decapitation of the 5' guanine (G) of mirtron-5p species defined by splicing. Altogether, this study reveals that this extensive class of non-canonical miRNA bears a multitude of characteristic properties, many of which raise general mechanistic questions regarding the processing of endogenous hairpin transcripts.
镜像微RNA（miRNA）前体是利用剪接机制绕过Drosha切割步骤来完成其生物合成的miRNA底物。为扩展我们近期在哺乳动物镜像微RNA注释方面的工作，我们对汇总数据集进行荟萃分析，以鉴定出约500个新的小鼠和人类内含子，它们能可靠地产生切割后的小RNA双链体。这些内含子总共包含近1000个位点，分布在四个剪接介导的生物合成亚类中，其中5'端带尾的镜像微RNA是迄今为止的主要亚型。因此，令人惊讶的是，镜像微RNA在哺乳动物基因组中占内源性Dicer底物的很大一部分。尽管源自镜像微RNA的小RNA与它们的宿主mRNA总体上呈现表达相关性，但我们观察到一部分存在显著差异，这表明其加工或积累受到调控。我们确定了镜像微RNA位点的特征性序列、长度和结构特征，以将它们与大量内含子区分开来，并发现镜像微RNA优先出现在内含子数量较多的基因中。虽然镜像微RNA产生miRNA类的调控RNA，但我们也发现镜像微RNA具有许多使其与经典miRNA区分开来的特征。我们观察到传统的镜像微RNA发夹结构比Drosha产生的前体miRNA长得多，这表明经典前体miRNA的特征长度并非Dicer底物发夹结构的普遍特征。此外，哺乳动物镜像微RNA呈现出独特的5'和3'端有序异质性模式，这揭示了miRNA加工途径中隐藏的复杂性。这些包括镜像微RNA发夹结构广泛的3'端尿苷化、可能由核酸外切酶加工导致的非典型异质5'端，以及偶尔由剪接定义的镜像微RNA - 5p物种5'端鸟嘌呤（G）的强烈去除。总之，这项研究表明，这类广泛的非经典miRNA具有众多特征属性，其中许多属性引发了关于内源性发夹转录本加工的一般性机制问题。
