Using Small RNA-seq Data to Detect siRNA Duplexes Induced by Plant Viruses

文献类型： 外文期刊

第一作者： Niu, Xiaoran

作者： Niu, Xiaoran;Sun, Yu;Gao, Shan;Niu, Xiaoran;Chen, Ze;Niu, Xiaoran;Chen, Ze;Li, Rugang;Padmanabhan, Chellappan;Ling, KaiShu;Ruan, Jishou;Kreuze, Jan F.;Fei, ZhangJun

作者机构：

关键词： siRNA duplex;RNAi;plant virus;small RNA-seq;virus detection

期刊名称：GENES （ 影响因子：4.096； 五年影响因子：4.339 ）

ISSN： 2073-4425

年卷期： 2017 年 8 卷 6 期

页码：

收录情况： SCI

摘要： 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.

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