Genetic and Functional Diversification of Small RNA Pathways in Plants

This is an open-access article distributed under the\ud terms of the Creative Commons Attribution License, which permits unrestricted\ud use, distribution, and reproduction in any medium, provided the\ud original work is properly cited.Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types,\ud microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence\ud or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of\ud small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE\ud proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants\ud encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for\ud three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One\ud RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2\ud mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci.\ud Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased\ud virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants\ud contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defens