Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis (original) (raw)

• Kim, V.N., Han, J. & Siomi, M.C. Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol. 10, 126–139 (2009).
  Article CAS Google Scholar
• Ghildiyal, M. & Zamore, P.D. Small silencing RNAs: an expanding universe. Nat. Rev. Genet. 10, 94–108 (2009).
  Article CAS Google Scholar
• Guang, S. et al. An Argonaute transports siRNAs from the cytoplasm to the nucleus. Science 321, 537–541 (2008).
  Article CAS Google Scholar
• Gu, W. et al. Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol. Cell 36, 231–244 (2009).
  Article CAS Google Scholar
• Claycomb, J.M. et al. The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell 139, 123–134 (2009).
  Article CAS Google Scholar
• Carthew, R.W. & Sontheimer, E.J. Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642–655 (2009).
  Article CAS Google Scholar
• Meister, G. & Tuschl, T. Mechanisms of gene silencing by double-stranded RNA. Nature 431, 343–349 (2004).
  Article CAS Google Scholar
• Makeyev, E.V. & Bamford, D.H. Cellular RNA-dependent RNA polymerase involved in posttranscriptional gene silencing has two distinct activity modes. Mol. Cell 10, 1417–1427 (2002).
  Article CAS Google Scholar
• Sijen, T., Steiner, F.A., Thijssen, K.L. & Plasterk, R.H. Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 315, 244–247 (2007).
  Article CAS Google Scholar
• Pak, J. & Fire, A. Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315, 241–244 (2007).
  Article CAS Google Scholar
• Motamedi, M.R. et al. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119, 789–802 (2004).
  Article CAS Google Scholar
• Correa, R.L., Steiner, F.A., Berezikov, E. & Ketting, R.F. MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans. PLoS Genet. 6, e1000903 (2010).
  Article Google Scholar
• Voinnet, O. Use, tolerance and avoidance of amplified RNA silencing by plants. Trends Plant Sci. 13, 317–328 (2008).
  Article CAS Google Scholar
• Mallory, A.C., Elmayan, T. & Vaucheret, H. MicroRNA maturation and action–the expanding roles of ARGONAUTEs. Curr. Opin. Plant Biol. 11, 560–566 (2008).
  Article CAS Google Scholar
• Howell, M.D. et al. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell 19, 926–942 (2007).
  Article CAS Google Scholar
• Peragine, A., Yoshikawa, M., Wu, G., Albrecht, H.L. & Poethig, R.S. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of _trans_-acting siRNAs in Arabidopsis. Genes Dev. 18, 2368–2379 (2004).
  Article CAS Google Scholar
• Vazquez, F. et al. Endogenous _trans_-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell 16, 69–79 (2004).
  Article CAS Google Scholar
• Rajagopalan, R., Vaucheret, H., Trejo, J. & Bartel, D.P. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 20, 3407–3425 (2006).
  Article CAS Google Scholar
• Axtell, M.J., Jan, C., Rajagopalan, R. & Bartel, D.P.A. Two-hit trigger for siRNA biogenesis in plants. Cell 127, 565–577 (2006).
  Article CAS Google Scholar
• Ronemus, M., Vaughn, M.W. & Martienssen, R.A. MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis. Plant Cell 18, 1559–1574 (2006).
  Article CAS Google Scholar
• Chiba, Y. & Green, P.J. mRNA degredation machinery in plants. J. Plant Biol. 52, 114–124 (2009).
  Article CAS Google Scholar
• Gregory, B.D. et al. A link between RNA metabolism and silencing affecting Arabidopsis development. Dev. Cell 14, 854–866 (2008).
  Article CAS Google Scholar
• Allen, E., Xie, Z., Gustafson, A.M. & Carrington, J.C. microRNA-directed phasing during _trans_-acting siRNA biogenesis in plants. Cell 121, 207–221 (2005).
  Article CAS Google Scholar
• Baumberger, N. & Baulcombe, D.C. Arabidopsis ARGONAUTE1 is an RNA slicer that selectively recruits microRNAs and short interfering RNAs. Proc. Natl. Acad. Sci. USA 102, 11928–11933 (2005).
  Article CAS Google Scholar
• Montgomery, T.A. et al. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 _trans_-acting siRNA formation. Cell 133, 128–141 (2008).
  Article CAS Google Scholar
• Yoshikawa, M., Peragine, A., Park, M.Y. & Poethig, R.S. A pathway for the biogenesis of _trans_-acting siRNAs in Arabidopsis. Genes Dev. 19, 2164–2175 (2005).
  Article CAS Google Scholar
• Xie, Z., Allen, E., Wilken, A. & Carrington, J.C. DICER-LIKE 4 functions in _trans_-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 102, 12984–12989 (2005).
  Article CAS Google Scholar
• Dunoyer, P., Himber, C. & Voinnet, O. DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat. Genet. 37, 1356–1360 (2005).
  Article CAS Google Scholar
• Gasciolli, V., Mallory, A.C., Bartel, D.P. & Vaucheret, H. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing _trans_-acting siRNAs. Curr. Biol. 15, 1494–1500 (2005).
  Article CAS Google Scholar
• Montgomery, T.A. et al. AGO1-miR173 complex initiates phased siRNA formation in plants. Proc. Natl. Acad. Sci. USA 105, 20055–20062 (2008).
  Article CAS Google Scholar
• Park, W., Li, J., Song, R., Messing, J. & Chen, X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12, 1484–1495 (2002).
  Article CAS Google Scholar
• Bouche, N., Lauressergues, D., Gasciolli, V. & Vaucheret, H. An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J. 25, 3347–3356 (2006).
  Article CAS Google Scholar
• Mi, S. et al. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133, 116–127 (2008).
  Article CAS Google Scholar
• Vaucheret, H. AGO1 homeostasis involves differential production of 21-nt and 22-nt miR168 species by MIR168a and MIR168b. PLoS One 4, e6442 (2009).
  Article Google Scholar
• Mallory, A.C. & Vaucheret, H. ARGONAUTE 1 homeostasis invokes the coordinate action of the microRNA and siRNA pathways. EMBO Rep. 10, 521–526 (2009).
  Article CAS Google Scholar
• Johnson, C. et al. Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res. 19, 1429–1440 (2009).
  Article CAS Google Scholar
• Chen, H.M., Li, Y.H. & Wu, S.H. Bioinformatic prediction and experimental validation of a microRNA-directed tandem _trans_-acting siRNA cascade in Arabidopsis. Proc. Natl. Acad. Sci. USA 104, 3318–3323 (2007).
  Article CAS Google Scholar
• Addo-Quaye, C., Eshoo, T.W., Bartel, D.P. & Axtell, M.J. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr. Biol. 18, 758–762 (2008).
  Article CAS Google Scholar
• Wang, Y. et al. Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456, 921–926 (2008).
  Article CAS Google Scholar
• Wang, Y. et al. Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461, 754–761 (2009).
  Article CAS Google Scholar
• Eulalio, A., Tritschler, F. & Izaurralde, E. The GW182 protein family in animal cells: new insights into domains required for miRNA-mediated gene silencing. RNA 15, 1433–1442 (2009).
  Article CAS Google Scholar
• El-Shami, M. et al. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev. 21, 2539–2544 (2007).
  Article CAS Google Scholar
• Bies-Etheve, N. et al. RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family. EMBO Rep. 10, 649–654 (2009).
  Article CAS Google Scholar
• He, X.J. et al. An effector of RNA-directed DNA methylation in Arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell 137, 498–508 (2009).
  Article CAS Google Scholar
• Blevins, T. et al. Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res. 34, 6233–6246 (2006).
  Article CAS Google Scholar
• Deleris, A. et al. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313, 68–71 (2006).
  Article CAS Google Scholar
• Diaz-Pendon, J.A., Li, F., Li, W.X. & Ding, S.W. Suppression of antiviral silencing by cucumber mosaic virus 2b protein in Arabidopsis is associated with drastically reduced accumulation of three classes of viral small interfering RNAs. Plant Cell 19, 2053–2063 (2007).
  Article CAS Google Scholar
• Garcia-Ruiz, H. et al. Arabidopsis RNA-dependent RNA polymerases and Dicer-like proteins in antiviral defense and small interfering RNA biogenesis during turnip mosaic virus infection. Plant Cell 22, 481–496 (2010).
  Article CAS Google Scholar
• Mlotshwa, S. et al. DICER-LIKE 2 plays a primary role in transitive silencing of transgenes in Arabidopsis. PLoS One 3, e1755 (2008).
  Article Google Scholar
• Mateos, J.L., Bologna, N.G., Chorostecki, U. & Palatnik, J.F. Identification of MicroRNA processing determinants by random mutagenesis of Arabidopsis MIR172a precursor. Curr. Biol. 20, 49–54 (2010).
  Article CAS Google Scholar
• Song, L., Axtell, M.J. & Fedoroff, N.V. RNA secondary structural determinants of miRNA precursor processing in Arabidopsis. Curr. Biol. 20, 37–41 (2010).
  Article CAS Google Scholar
• Werner, S., Wollmann, H., Schneeberger, K. & Weigel, D. Structure determinants for accurate processing of miR172a in Arabidopsis thaliana. Curr. Biol. 20, 42–48 (2010).
  Article CAS Google Scholar
• Macrae, I.J. et al. Structural basis for double-stranded RNA processing by Dicer. Science 311, 195–198 (2006).
  Article CAS Google Scholar
• MacRae, I.J., Zhou, K. & Doudna, J.A. Structural determinants of RNA recognition and cleavage by Dicer. Nat. Struct. Mol. Biol. 14, 934–940 (2007).
  Article CAS Google Scholar
• Qin, H. et al. Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction. RNA 16, 474–481 (2010).
  Article CAS Google Scholar
• Parisien, M. & Major, F. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452, 51–55 (2008).
  Article CAS Google Scholar
• Meyers, B.C. et al. Criteria for annotation of plant microRNAs. Plant Cell 20, 3186–3190 (2008).
  Article CAS Google Scholar
• Cuperus, J.T. et al. Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing. Proc. Natl. Acad. Sci. USA 107, 466–471 (2010).
  Article CAS Google Scholar
• Llave, C., Xie, Z., Kasschau, K.D. & Carrington, J.C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297, 2053–2056 (2002).
  Article CAS Google Scholar
• Fahlgren, N. et al. Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 15, 992–1002 (2009).
  Article CAS Google Scholar
• Maindonald, J.H. & Braun, J. Data Analysis and Graphics Using R: An Example-Based Approach. (Cambridge University Press, New York, USA, 2007).
  Google Scholar