Using Small RNA-seq Data to Detect siRNA Duplexes Induced by Plant Viruses.
Using Small RNA-seq Data to Detect siRNA Duplexes Induced by Plant Viruses.
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作者：
Niu X;Sun Y;Chen Z;Li R;Padmanabhan C;Ruan J;Kreuze JF;Ling K;Fei Z;Gao S
小干扰RNA（siRNA）双链体是短的（通常为21 - 24 bp）双链RNA（dsRNA），在5′-和3′-末端具有几个突出的核苷酸。已经发现siRNA双链体结合RNA诱导的沉默复合物（RISC）并用核酸内切酶切割有义链。在这项研究中，我们首次使用下一代测序（NGS）数据大规模检测植物病毒诱导的siRNA双链体。此外，我们使用检测到的21个核苷酸（nt）的siRNA双链体与2个nt的突出端构建数据集，用于未来的数据挖掘。检测到的siRNA双链体的特征分析结果与先前的研究结果一致。siRNA双链体的研究有助于更好地理解RNA干扰（RNAi）机制。这也有助于改进基于小RNA测序（sRNA-seq）技术的病毒检测，并合理设计用于RNAi实验的siRNA。
Small interfering RNA (siRNA) duplexes are short (usually 21 to 24 bp) double-stranded RNAs (dsRNAs) with several overhanging nucleotides at both 5′- and 3′-ends. It has been found that siRNA duplexes bind the RNA-induced silencing complex (RISC) and cleave the sense strands with endonucleases. In this study, for the first time, we detected siRNA duplexes induced by plant viruses on a large scale using next-generation sequencing (NGS) data. In addition, we used the detected 21 nucleotide (nt) siRNA duplexes with 2 nt overhangs to construct a dataset for future data mining. The analytical results of the features in the detected siRNA duplexes were consistent with those from previous studies. The investigation of siRNA duplexes is useful for a better understanding of the RNA interference (RNAi) mechanism. It can also help to improve the virus detection based on the small RNA sequencing (sRNA-seq) technologies and to rationally design siRNAs for RNAi experiments.