Revisiting Criteria for Plant miRNA Annotation in the Era of Big Data

MicroRNAs (miRNAs) are ~21 nucleotide-long regulatory RNAs that arise from (产生于) endonucleolytic processing (内切酶加工) of hairpin precursors (发夹结构的前体). Many function as essential post-transcriptional regulators (转录后调控子) of target mRNAs and long non-coding RNAs. Alongside miRNAs, plants also produce large numbers of short interfering RNAs (siRNAs), which are distinguished from miRNAs primarily (主要地) by their biogenesis (typically processed from long double-stranded RNA instead of single-stranded hairpins) and functions (typically via roles in transcriptional regulation instead of post-transcriptional regulation). Next-generation DNA sequencing methods have yielded extensive datasets of plant small RNAs, resulting in many miRNA annotations. However, it has become clear that many miRNA annotations are questionable. The sheer number of endogenous siRNAs compared to miRNAs has been a major factor in the erroneous (错误的) annotation of siRNAs as miRNAs. Here, we provide updated criteria for the confident annotation of plant miRNAs, suitable for the era of “big data” from DNA sequencing. The updated criteria emphasize (强调) replication, the minimization of false positives (假阳性), and they require next-generation sequencing of small RNAs. We argue that improved annotation systems are needed for miRNAs and all other classes of plant small RNAs. Finally, to illustrate the complexities (复杂性) of miRNA and siRNA annotation, we review the evolution and functions of miRNAs and siRNAs in plants.

MicroRNAs（miRNAs）是一类长度约在21个碱基长度的调控RNA，其由具有发夹结构前体经过内切酶加工后形成。miRNAs主要作为一些mRNAs和长链非编码RNAs（lncRNAs）的转录后调控子。除了miRNAs，植物同样还会产生数量庞大的短的干扰RNAs（siRNAs），其与miRNAs的区别主要在于生物合成和功能两个方面：siRNAs是来自于长的双链RNA，而miRNAs来自于单链发夹结构前体；siRNAs的功能主要是参与转录调控，而miRNAs主要是参与转录后调控。下一代DNA测序已经产生了数量巨大的植物小RNAs数据，进而有了许多已注释的miRNAs。然而，有越来越多的证据表明许多的miRNA注释结果存在问题。相对于miRNAs的数量，内源的siRNAs数量庞大，因此有很多的siRNAs被错误注释成了miRNAs。本文提供了一个新的植物miRNAs注释标准，比较适合现在DNA测序的大数据时代。这个升级版的注释标准着重于重复和假阳性的最小化，还有，该标准基于的数据是对于小RNAs的下一代高通量测序数据。作者讨论了改良版的注释系统对于miRNAs以及其他所有的植物小RNAs的注释是必需的。最后，出于解释miRNA和siRNA注释工作的复杂性的需要，作者对miRNAs和siRNAs在植物中的演化的功能进行了综述。

通讯：Michael J. Axtell (http://bio.psu.edu/directory/mja18)

个人简介：伊萨卡学院，学士，生物学；加利福尼亚大学，博士，植物生物学。

研究方向：利用高通量测序数据对小RNA进行注释；在陆地植物演化过程中小RNA通路的分化过程；植物中有效小RNA与靶基因互作的序列基础。实验室网址：https://sites.psu.edu/axtell/。

通讯：Blake C. Meyers (https://www.danforthcenter.org/scientists-research/principal-investigators/blake-meyers)

研究方向：RNA沉默通路上的组分元件；植物生殖生物学；植物小RNA的演化；高通量测序等。实验室网址：http://www.meyerslab.org/index.php。

doi: https://doi.org/10.1105/tpc.17.00851

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