Functions and applications of RNA interference and small regulatory RNAs

Abstract

Small regulatory RNAs play a variety of crucial roles in eukaryotes, influencing gene regulation, developmental timing, antiviral defense, and genome integrity via a process termed RNA interference (RNAi). This process involves Argonaute/small RNA (AGO/sRNA) complexes that target transcripts via sequence complementarity and modulate gene expression and epigenetic modifications. RNAi is a highly conserved gene regulatory phenomenon that recognizes self- and non-self nucleic acids, thereby defending against invasive sequences. Since its discovery, RNAi has been widely applied in functional genomic studies and a range of practical applications. In this review, we focus on the current understanding of the biological roles of the RNAi pathway in transposon silencing, fertility, developmental regulation, immunity, stress responses, and acquired transgenerational inheritance. Additionally, we provide an overview of the applications of RNAi technology in biomedical research, agriculture, and therapeutics.

1. Introduction

Small regulatory RNAs direct sequence-specific regulation of gene expression via a mechanism termed RNA interference (RNAi), which was first described in nematodes in 1998 [1]. In a range of eukaryotic organisms, small regulatory RNAs and their associated Argonaute proteins play essential roles in RNAi-mediated gene silencing, whereby small regulatory RNAs guide the Argonaute-containing protein complexes to targeted nucleic acids with sequence complementarity [2‒7]. Small RNA/Argonaute complexes modulate gene expression via several mechanisms, including degrading targeted RNAs, inhibiting translation, inducing epigenetic modifications and heterochromatin formation, and inhibiting transcription elongation or triggering alternative splicing [8‒14].

There are three main classes of small regulatory RNAs: microRNAs (miRNAs), small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) [15‒18]. Additional classes of small regulatory RNAs, such as antisense ribosomal siRNAs (risiRNAs) [19‒21], tRNA-derived small RNAs (tsRNAs), and phased secondary small interfering RNAs (phasiRNAs), have also been shown to act through the RNAi pathway (Table 1) [22‒25]. Notably, recent developments in novel RNA-sequencing techniques have significantly expanded our knowledge of small regulatory RNAs by overcoming sequencing obstacles, which are caused either by specific modifications or by terminus multiplicities of small RNAs. More importantly, many of these newly detected small RNAs have important functions in different biological processes, such as reprogramming, lineage specification and apoptosis [26‒28].