One recently identified mechanism that regulates mRNA abundance is RNA silencing, and pioneering work in Arabidopsis thaliana and other genetic model organisms helped define this process. RNA silencing pathways are triggered by either self-complementary fold-back structures or the production of double-stranded RNA (dsRNA) that gives rise to small RNAs (smRNAs) known as microRNAs (miRNAs) or small-interfering RNAs (siRNAs). These smRNAs direct sequence-specific regulation of various gene transcripts, repetitive sequences, viruses, and mobile elements via RNA cleavage, translational inhibition, or transcriptional silencing through DNA methylation and heterochromatin formation. Early genetic screens in Arabidopsis were instrumental in uncovering numerous proteins required for these important regulatory pathways. Among the factors identified by these studies were RNA-dependent RNA polymerases (RDRs), which are proteins that synthesize siRNA-producing dsRNA molecules using a single-stranded RNA (ssRNA) molecule as a template. Recently, a growing body of evidence has implicated RDR-dependent RNA silencing in many different aspects of plant biology ranging from reproductive development to pathogen resistance. Here, we focus on the specific functions of the six Arabidopsis RDRs in RNA silencing, their ssRNA substrates and resulting RDR-dependent smRNAs, and the numerous biological functions of these proteins in plant development and stress responses.
How eukaryotic organisms regulate mRNA levels is a fundamental question in biology. It is clear that the steady-state concentration of RNA in a cell is determined by both the rate of its synthesis and turnover. Most of the early attention was focused on the study of gene transcription, while only recently posttranscriptional mechanisms have gained recognition for their regulatory importance. Posttranscriptional control of RNA levels is mediated by a number of pathways, including general RNA degradation and the more recently identified mechanism of RNA silencing (Belostotsky and Sieburth, Curr Opin Plant Biol 12:96-102, 2009; Garneau et al., Nat Rev Mol Cell Biol 8:113-126, 2007; Ramachandran and Chen, Trends Plant Sci 13:368-374, 2008; Xie and Qi, Biochim Biophys Acta 1779:720-724, 2008). Intriguingly, the regulatory RNA targets of both pathways can be identified by the distinguishing characteristic of a 5' monophosphate. Specifically, removal of the 7-methyl guanosine cap attached to the 5' end of mRNA molecules is an initiating signal for subsequent 5'-3' RNA degradation. In RNA silencing, small RNA-directed, protein-mediated cleavage of an mRNA target generates a free 5' monophosphate on the resulting 3' RNA fragment (Belostotsky and Sieburth, Curr Opin Plant Biol 12:96-102, 2009; Garneau et al., Nat Rev Mol Cell Biol 8:113-126, 2007). Taking advantage of this chemical property (free 5' monophosphate), a genome-wide approach for mapping all uncapped and cleaved transcripts in eukaryotic transcriptomes has been developed that we have termed "genome-wide mapping of uncapped and cleaved transcripts" (Gregory et al., Developmental Cell 14:854-866, 2008), which others have called degradome sequencing (Addo-Quaye et al., Curr Biol 18:758-762, 2008) or "parallel analysis of RNA ends" (German et al., Nat Biotechnol 26:941-946, 2008).
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