The biogenesis, regulation and functions of transitive siRNA in plants

Abstract

Small RNA (sRNA)-mediated RNA interference (RNAi) is a sequence-specific gene silencing mechanism that modulates gene expression in eukaryotes. As core molecules of RNAi, various sRNAs are encoded in the plant genome or derived from invading RNA molecules, and their biogenesis depends on distinct genetic pathways. Transitive small interfering RNAs (siRNAs), which are sRNAs produced from double-strand RNA (dsRNA) in a process that depends on RNA-dependent RNA polymerases (RDRs), can amplify and spread silencing signals to additional transcripts, thereby enabling a phenomenon termed “transitive RNAi”. Members of this class of siRNAs function in various biological processes ranging from development to stress adaptation. In Arabidopsis thaliana, two RDRs participate in the generation of transitive siRNAs, acting cooperatively with various siRNA generation-related factors, such as the RNA-induced silencing complex (RISC) and aberrant RNAs. Transitive siRNAs are produced in diverse subcellular locations and structures under the control of various mechanisms, highlighting the intricacies of their biogenesis and functions. In this review, we discuss recent advances in understanding the molecular events of transitive siRNA biogenesis and its regulation, with a particular focus on factors involved in RDR recruitment. We aim to provide a comprehensive description of the generalized mechanism governing the biogenesis of transitive siRNAs. Additionally, we present an overview of the diverse biological functions of these siRNAs and raise some pressing questions in this area for further investigation.

1. Introduction

Small RNA-mediated RNAi plays an important role in regulating the expressions of the appropriate genes at the appropriate time and place. This is critical for the development of eukaryotic organisms and their adaptation to environmental stimuli [1,2]. In plants, RNAi is triggered by the presence of double-stranded RNA (dsRNA) or single-stranded RNA (ssRNA) molecules that possess a dsRNA region. These dsRNAs are processed into 21- to 24-nucleotide (nt) small RNA duplexes by DICER-LIKE proteins (DCLs) [1]. The resulting sRNA duplex is 2′-O-methylated at the 3′ end by HUA ENHANCER 1 (HEN1), and is subsequently incorporated into ARGONAUTE (AGO) proteins to form a pre-RNA-induced silencing complex (pre-RISC) [3,4]. After ejection of passenger strand of sRNA, the mature RISC could guide the gene silencing process through complimentary base-pairing [3,4]. Based on the particular AGO proteins found in a RISC and the nature of the target RNA, RNAi can cause either transcriptional gene silencing (TGS) via epigenetic modifications of chromatin or posttranscriptional gene silencing (PTGS) via RNA cleavage or repression of translation [5,6].

An interesting characteristic of sRNA-mediated gene silencing, beyond its ability to silence genes with complementary sequences, is that its silencing effect can be amplified and spread. Gene silencing driven by primary siRNAs, which mostly originate from spontaneously formed dsRNA without amplification by RDRs, is typically restricted to silencing the initiating loci and/or primary targets. In contrast, recruiting RDR to the target RNA via primary siRNAs or miRNAs usually causes the synthesis of dsRNA, which in turn generates secondary siRNAs. This process can lead to the propagation of the silencing signals to target sequences other than the inducer sequence, causing transitive RNAi [7,8]. Thus, secondary siRNAs are also referred to as transitive siRNAs. Recent studies have found that, besides sRNA, many other factors can recruit RDR to given RNAs (discussed below). Once recruited, RDRs extend the RNA to synthesize long dsRNA, thereby producing siRNAs with different sequences. These siRNAs not only silence the cognate genes but also have the potential to target other genes with homologous sequences. Therefore, we also category this class of siRNAs as transitive siRNAs.