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Abstract
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.
Highlights
RNA interference (RNAi) is a cytoplasmic cell surveillance system that recognizes double strandedRNAs and destroys single and double stranded RNA molecules homologous to the double-stranded RNAs (dsRNAs) inducers, using small interfering RNAs as guides [1]
The abundant Small interfering RNA (siRNA) accumulated during the RNAi process can be captured by the small RNA sequencing technology that has been used for virus detection in plants [2,3,4] and invertebrates [5,6]
The detection of viruses in somatic mammalian cells using sRNA-seq is hampered by the presence of a number of dsRNA-triggered nonspecific responses such as the type I interferon (IFN) synthesis [7], it is well known that antiviral RNAi functions in mammalian germ cells and embryonic stem cells (ESCs), as well as some carcinoma cell lines [8]
Summary
RNA interference (RNAi) is a cytoplasmic cell surveillance system that recognizes double strandedRNAs (dsRNAs) and destroys single and double stranded RNA molecules homologous to the dsRNA inducers, using small interfering RNAs (siRNAs) as guides [1]. The abundant siRNAs accumulated during the RNAi process can be captured by the small RNA sequencing (sRNA-seq) technology that has been used for virus detection in plants [2,3,4] and invertebrates [5,6]. In 2016, Wang et al first used big data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to prove that sRNA-seq can be used to detect and identify human viruses [1], but the detection results were not as good as those of plant viruses. The study of RNA fragments related to RNAi could help to find some featured RNA fragments to improve the virus detection in mammals
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