Small RNAs and their roles in plant development

Abstract

Small RNAs of 20-30 nucleotides guide regulatory processes at the DNA or RNA level in a wide range of eukaryotic organisms. Many, although not all, small RNAs are processed from double-stranded RNAs or single-stranded RNAs with local hairpin structures by RNase III enzymes and are loaded into argonaute-protein-containing effector complexes. Many eukaryotic organisms have evolved multiple members of RNase III and the argonaute family of proteins to accommodate different classes of small RNAs with specialized molecular functions. Some small RNAs cause transcriptional gene silencing by guiding heterochromatin formation at homologous loci, whereas others lead to posttranscriptional gene silencing through mRNA degradation or translational inhibition. Small RNAs are not only made from and target foreign nucleic acids such as viruses and transgenes, but are also derived from endogenous loci and regulate a multitude of developmental and physiological processes. Here I review the biogenesis and function of three major classes of endogenous small RNAs in plants: microRNAs, trans-acting siRNAs, and heterochromatic siRNAs, with an emphasis on the roles of these small RNAs in developmental regulation.

Figure 1

miRNA biogenesis and degradation. A plant microRNA gene (MIR) is located between two protein-coding genes. The MIR gene is transcribed into a pri-miRNA, which is capped and polyadenylated. The pri-miRNA is processed into the pre-miRNA, which is further processed into the miRNA/miRNA* duplex. The duplex is methylated by HEN1 and the miRNA is loaded into an AGO1 complex. The heterodimeric cap-binding complex (CBP) and the RNA binding protein DDL promote miRNA biogenesis but are not essential. (See text for a more detailed description of the major steps in miRNA metabolism.) DDL, DAWDLE; DCL1, DICER-LIKE1; SE, SERRATE; HYL1, HYPONASTIC LEAVES1; AGO1, ARGONAUTE1; SDN, SMALL RNA DEGRADING NUCLEASE.

Figure 2

Modes of action of plant miRNAs at the tissue level. (a) A miRNA restricts the domain of expression of its target gene. The target gene is transcribed in two adjacent domains, but the miRNA restricts the products of the target gene to one of them. (b) A miRNA reduces target gene expression in its native domain. (c) miRNA serves as an insurance mechanism to limit target gene expression to a domain conferred largely by transcriptional regulation. The rectangles represent two adjacent tissue domains; the ones with the miRNA are shaded red.

Figure 3

Biogenesis of ta-siRNAs. (a) At the TAS1 locus, long noncoding transcripts are cleaved by miR173/AGO1, and the 3′ cleavage products are presumably bound by SGS3 and copied into dsRNAs by RDR6. The dsRNAs are processed into siRNAs by DCL4 in a step-wise manner from the end defined by the initial cleavage. (b) At the TAS3 locus, long noncoding transcripts are recognized at two sites by miR390/AGO7, which cleaves the transcripts only at the 3′ site. The 5′ cleavage products are channeled into ta-siRNA production by SGS3, RDR6, and DCL4. TAS1, trans-acting siRNA locus 1; TAS3, trans-acting siRNA locus 3; AGO1, ARGONAUTE1; AGO7, ARGONAUTE7; SGS3, SUPPRESSOR OF GENE SILENCING 3; RDR6, RNA-DEPENDENT RNA POLYMERASE6; dsRNAs, double-stranded RNAs; siRNAs, small interfering RNAs; DCL4, DICER-LIKE4; HEN1, HUA ENHANCER1; ta-siRNA, trans-acting siRNA; miR173, microRNA173; miR390, microRNA390.

Figure 4

Biogenesis and function of heterochromatic siRNAs. Heterochromatic loci are presumably transcribed by Pol IV into single-stranded noncoding transcripts that are copied into dsRNAs by RDR2. Twenty-four–nt siRNAs are processed from the dsRNAs by DCL3, methylated by HEN1, and loaded into AGO4-containing RISCs. The siRNAs are recruited to the source loci by transcripts generated by Pol V and perhaps by interaction between Pol V and AGO4. Through unknown mechanisms, DNA and/or histone methyltransferases are recruited by the RISCs to effect heterochromatin formation and subsequent siRNA production in a feed-forward loop. The transcription activities of Pol IV and Pol V are aided by chromatin remodeling proteins CLASSY1 and DRD1, respectively. Pol IV, DNA-dependent RNA polymerase IV; Pol V, DNA-dependent RNA polymerase V; CLASSY, a protein similar to chromatin remodeling proteins; AGO4, ARGONAUTE4; RDR2, RNA-DEPENDENT RNA POLYMERASE2; DCL3, DICER-LIKE3; HEN1, HUA ENHANCER1; dsRNAs, double-stranded RNAs; siRNAs, small interfering RNAs, RISCs, RNA-induced silencing complexes; DRD1, DEFECTIVE IN RNA-DIRECTED DNA METHYLATION1; DMS3, DEFECTIVE IN MERISTEM SILENCING3.