Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data
Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data
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DOI：
10.1105/tpc.17.00851
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发表时间：
2018-02-01
期刊：
影响因子：
11.6
通讯作者：
Meyers, Blake C.
中科院分区：
文献类型：
--
作者：
Axtell, Michael J.;Meyers, Blake C.
MicroRNAs （miRNAs）类似于发夹前体核内溶解过程中产生的21核苷酸长的调控rna。许多功能是靶mrna和长链非编码rna的基本转录后调节因子。除了mirna，植物还产生大量的短干扰RNA (sirna)，它们与mirna的区别主要在于它们的生物发生（通常由长双链RNA而不是单链发夹加工而成）和功能（通常通过转录调控而不是转录后调控）。下一代DNA测序方法已经产生了广泛的植物小rna数据集，导致许多miRNA注释。然而，很明显，许多miRNA注释是有问题的。与miRNAs相比，内源性sirna的绝对数量一直是sirna被错误注释为miRNAs的主要因素。在这里，我们为植物mirna的自信标注提供了更新的标准，适用于DNA测序的“大数据”时代。更新的标准强调复制和最小化假阳性，并要求对小rna进行下一代测序。我们认为需要改进的mirna和所有其他类型的植物小rna的注释系统。最后，为了说明miRNA和siRNA注释的复杂性，我们回顾了miRNA和siRNA在植物中的进化和功能。
MicroRNAs (miRNAs) are similar to 21-nucleotide-long regulatory RNAs that arise from endonucleolytic processing of hairpin precursors. Many function as essential posttranscriptional regulators of target mRNAs and long noncoding RNAs. Alongside miRNAs, plants also produce large numbers of short interfering RNAs (siRNAs), which are distinguished from miRNAs primarily 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 posttranscriptional regulation). Next-generation DNA sequencing methods have yielded extensive data sets 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 with miRNAs has been a major factor in the erroneous 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 replication and the minimization of false positives, 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 of miRNA and siRNA annotation, we review the evolution and functions of miRNAs and siRNAs in plants.