Abstract:

Small RNA（sRNA）-mediated RNA silencing（or RNA interference）is a conserved mechanism for regulating gene expression in eukaryotes. Endogenous or exogenous double-stranded RNAs（dsRNAs）are processed into sRNAs, which recognize complementary mRNAs or DNAs in a sequence-specific manner, and regulate gene expression at either the posttranscriptional level or the transcriptional level by degrading mRNAs, inhibiting translation and DNA methylation. Owing to the target-specific actions of dsRNAs, RNAi-based strategies have become ubiquitous tools in the study of gene function, the development of RNA drugs, the design of molecular breeding methods, and the exploitation of biopesticides. The discovery of the bidirectional transfer among species and function of sRNAs provides a theoretical basis for exploiting RNAi-based technologies. Previous studies have shown that several factors affect the efficiency of dsRNA-induced RNAi, such as the size and dose of dsRNAs, as well as the application method. The complex structure of RNA leads to its functional diversity in vivo. Here, we described the principles of RNAi-based strategies for crop protection, including host-induced gene silencing（HIGS）, spray-induced gene silencing（SIGS）and microbe-induced gene silencing（MIGS）. We summarized the experimental evidence that the structures of target mRNAs and sRNAs affect RNAi efficiency, aiming to deepen the understanding of the RNA structure affecting RNAi efficiency, to provide experience for target screening and dsRNA design, and provide reference for the development of efficient RNAi technology. We also reviewed the representative methods and computational tools for detecting and predicting RNA structures, thereby providing approaches in establishing efficient RNAi-based techniques.

Key words: small RNA, RNA silencing, double-stranded RNA, RNA structure