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Messages on small RNA duplexes in plants

  • JPR Symposium
  • Expanding plant non-coding RNA world
  • Published:
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Abstract

Small RNA-mediated gene silencing encompasses diverse developmental events, stress responses, defense against pathogens, and maintenance of genome integrity. Extensive studies in model organisms have unveiled the molecular mechanisms underpinning the RNA silencing phenomena, and the accumulating knowledge have characterized the intricate pathways and the repertoire of proteins responsible for the actions of small RNAs characterized as microRNAs (miRNAs) or small interfering RNAs (siRNAs). Although the single-stranded, matured guide small RNAs direct the effector ribonucleoprotein complexes to induce gene silencing in sequence-specific manner, the double-stranded intermediate, the small RNA duplexes, which are processed as nascent products of the RNase III enzyme activities, act as key to determine the downstream molecular pathways and the fate of small RNAs. Based at the small RNA duplex-centered view, this review describes the recent advances in understanding the small RNA pathways in plants.

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References

  • Adenot X, Elmayan T, Lauressergues D, Boutet S, Bouche N, Gasciolli V, Vaucheret H (2006) DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr Biol 16:927–932

    Article  PubMed  CAS  Google Scholar 

  • Arribas-Hernandez L, Kielpinski LJ, Brodersen P (2016a) mRNA Decay of Most Arabidopsis miRNA Targets Requires Slicer Activity of AGO1. Plant Physiol 171:2620–2632

    PubMed  PubMed Central  CAS  Google Scholar 

  • Arribas-Hernandez L, Marchais A, Poulsen C, Haase B, Hauptmann J, Benes V, Meister G, Brodersen P (2016b) The Slicer Activity of ARGONAUTE1 Is Required Specifically for the Phasing, Not Production, of Trans-Acting Short Interfering RNAs in Arabidopsis. Plant Cell 28:1563–1580

    PubMed  PubMed Central  CAS  Google Scholar 

  • Baumberger N, Baulcombe DC (2005) Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci USA 102:11928–11933

    Article  PubMed  CAS  Google Scholar 

  • Berardini TZ, Bollman K, Sun H, Poethig RS (2001) Regulation of vegetative phase change in Arabidopsis thaliana by cyclophilin 40. Science 291:2405–2407

    Article  PubMed  CAS  Google Scholar 

  • Bohmert K, Camus I, Bellini C, Bouchez D, Caboche M, Benning C (1998) AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J 17:170–180

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bologna NG, Voinnet O (2014) The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annu Rev Plant Biol 65:473–503

    Article  PubMed  CAS  Google Scholar 

  • Bologna NG, Mateos JL, Bresso EG, Palatnik JF (2009) A loop-to-base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159. EMBO J 28:3646–3656

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bologna NG, Schapire AL, Zhai J, Chorostecki U, Boisbouvier J, Meyers BC, Palatnik JF (2013) Multiple RNA recognition patterns during microRNA biogenesis in plants. Genome Res 23:1675–1689

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Carbonell A, Carrington JC (2015) Antiviral roles of plant ARGONAUTES. Curr Opin Plant Biol 27:111–117

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Carbonell A, Fahlgren N, Garcia-Ruiz H, Gilbert KB, Montgomery TA, Nguyen T, Cuperus JT, Carrington JC (2012) Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants. Plant Cell 24:3613–3629

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen HM, Chen LT, Patel K, Li YH, Baulcombe DC, Wu SH (2010) 22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci USA 107:15269–15274

    Article  PubMed  Google Scholar 

  • Creasey KM, Zhai J, Borges F, Van Ex F, Regulski M, Meyers BC, Martienssen RA (2014) miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature 508:411–415

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Csorba T, Kontra L, Burgyan J (2015) viral silencing suppressors: tools forged to fine-tune host-pathogen coexistence. Virology 479–480:85–103

    Article  PubMed  CAS  Google Scholar 

  • Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, Takeda A, Sullivan CM, Gilbert SD, Montgomery TA, Carrington JC (2010) Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nat Struct Mol Biol 17:997–1003

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Deleris A, Gallego-Bartolome J, Bao J, Kasschau KD, Carrington JC, Voinnet O (2006) Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313:68–71

    Article  PubMed  CAS  Google Scholar 

  • Dong Z, Han MH, Fedoroff N (2008) The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc Natl Acad Sci USA 105:9970–9975

    Article  PubMed  Google Scholar 

  • Eamens AL, Smith NA, Curtin SJ, Wang MB, Waterhouse PM (2009) The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. RNA 15:2219–2235

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Earley KW, Poethig RS (2011) Binding of the cyclophilin 40 ortholog SQUINT to Hsp90 protein is required for SQUINT function in Arabidopsis. J Biol Chem 286:38184–38189

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Elkayam E, Kuhn CD, Tocilj A, Haase AD, Greene EM, Hannon GJ, Joshua-Tor L (2012) The structure of human argonaute-2 in complex with miR-20a. Cell 150:100–110

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Endo Y, Iwakawa HO, Tomari Y (2013) Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly. EMBO Rep 14:652–658

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, Alexander AL, Carrington JC (2006) Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr Biol 16:939–944

    Article  PubMed  CAS  Google Scholar 

  • Fang X, Qi Y (2016) RNAi in Plants: an Argonaute-Centered View. Plant Cell 28:272–285

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Frank F, Sonenberg N, Nagar B (2010) Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2. Nature 465:818–822

    Article  PubMed  CAS  Google Scholar 

  • Frank F, Hauver J, Sonenberg N, Nagar B (2012) Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs. EMBO J 31:3588–3595

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Garcia D, Collier SA, Byrne ME, Martienssen RA (2006) Specification of leaf polarity in Arabidopsis via the trans-acting siRNA pathway. Curr Biol 16:933–938

    Article  PubMed  CAS  Google Scholar 

  • Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD (2010) Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16:43–56

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Guy NC, Garcia YA, Sivils JC, Galigniana MD, Cox MB (2015) Functions of the Hsp90-binding FKBP immunophilins. Subcell Biochem 78:35–68

    Article  PubMed  CAS  Google Scholar 

  • Ha M, Kim VN (2014) Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15:509–524

    Article  PubMed  CAS  Google Scholar 

  • Huang Y, Ji L, Huang Q, Vassylyev DG, Chen X, Ma JB (2009) Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature 461:823–827

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hunter C, Willmann MR, Wu G, Yoshikawa M, de la Luz Gutierrez-Nava M, Poethig SR (2006) Trans-acting siRNA-mediated repression of ETTIN and ARF4 regulates heteroblasty in Arabidopsis. Development 133:2973–2981

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Iki T, Yoshikawa M, Nishikiori M, Jaudal MC, Matsumoto-Yokoyama E, Mitsuhara I, Meshi T, Ishikawa M (2010) In vitro assembly of plant RNA-induced silencing complexes facilitated by molecular chaperone HSP90. Mol Cell 39:282–291

    Article  PubMed  CAS  Google Scholar 

  • Iki T, Yoshikawa M, Meshi T, Ishikawa M (2012) Cyclophilin 40 facilitates HSP90-mediated RISC assembly in plants. EMBO J 31:267–278

    Article  PubMed  CAS  Google Scholar 

  • Iwasaki S, Kobayashi M, Yoda M, Sakaguchi Y, Katsuma S, Suzuki T, Tomari Y (2010) Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes. Mol Cell 39:292–299

    Article  PubMed  CAS  Google Scholar 

  • Iwasaki S, Sasaki HM, Sakaguchi Y, Suzuki T, Tadakuma H, Tomari Y (2015) Defining fundamental steps in the assembly of the Drosophila RNAi enzyme complex. Nature 521:533–536

    Article  PubMed  CAS  Google Scholar 

  • Iwata Y, Takahashi M, Fedoroff NV, Hamdan SM (2013) Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing. Nucleic Acids Res 41:9129–9140

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209–216

    Article  PubMed  CAS  Google Scholar 

  • Kidner CA, Martienssen RA (2004) Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 428:81–84

    Article  PubMed  CAS  Google Scholar 

  • Kobayashi H, Tomari Y (2016) RISC assembly: coordination between small RNAs and Argonaute proteins. Biochim Biophys Acta 1859:71–81

    Article  PubMed  CAS  Google Scholar 

  • Kurihara Y, Takashi Y, Watanabe Y (2006) The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 12:206–212

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lakatos L, Csorba T, Pantaleo V, Chapman EJ, Carrington JC, Liu YP, Dolja VV, Calvino LF, Lopez-Moya JJ, Burgyan J (2006) Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressors. EMBO J 25:2768–2780

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lee WC, Lu SH, Lu MH, Yang CJ, Wu SH, Chen HM (2015) Asymmetric bulges and mismatches determine 20-nt microRNA formation in plants. RNA Biol 12:1054–1066

    Article  PubMed  PubMed Central  Google Scholar 

  • Leuschner PJ, Ameres SL, Kueng S, Martinez J (2006) Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep 7:314–320

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li J, Yang Z, Yu B, Liu J, Chen X (2005) Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr Biol 15:1501–1507

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Liu Q, Yao X, Pi L, Wang H, Cui X, Huang H (2009) The ARGONAUTE10 gene modulates shoot apical meristem maintenance and establishment of leaf polarity by repressing miR165/166 in Arabidopsis. Plant J 58:27–40

    Article  PubMed  CAS  Google Scholar 

  • MacRae IJ, Zhou K, Doudna JA (2007) Structural determinants of RNA recognition and cleavage by Dicer. Nat Struct Mol Biol 14:934–940

    Article  PubMed  CAS  Google Scholar 

  • Manavella PA, Hagmann J, Ott F, Laubinger S, Franz M, Macek B, Weigel D (2012a) Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1. Cell 151:859–870

    Article  PubMed  CAS  Google Scholar 

  • Manavella PA, Koenig D, Weigel D (2012b) Plant secondary siRNA production determined by microRNA-duplex structure. Proc Natl Acad Sci USA 109:2461–2466

    Article  PubMed  Google Scholar 

  • Martinez NJ, Chang HM, Borrajo Jde R, Gregory RI (2013) The co-chaperones Fkbp4/5 control Argonaute2 expression and facilitate RISC assembly. RNA 19:1583–1593

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Matranga C, Tomari Y, Shin C, Bartel DP, Zamore PD (2005) Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123:607–620

    Article  PubMed  CAS  Google Scholar 

  • Maunoury N, Vaucheret H (2011) AGO1 and AGO2 act redundantly in miR408-mediated Plantacyanin regulation. PLoS One 6:e28729

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C et al (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133:116–127

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Miyoshi K, Tsukumo H, Nagami T, Siomi H, Siomi MC (2005) Slicer function of Drosophila Argonautes and its involvement in RISC formation. Genes Dev 19:2837–2848

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Miyoshi T, Takeuchi A, Siomi H, Siomi MC (2010) A direct role for Hsp90 in pre-RISC formation in Drosophila. Nat Struct Mol Biol 17:1024–1026

    Article  PubMed  CAS  Google Scholar 

  • Mlotshwa S, Pruss GJ, Peragine A, Endres MW, Li J, Chen X, Poethig RS, Bowman LH, Vance V (2008) DICER-LIKE2 plays a primary role in transitive silencing of transgenes in Arabidopsis. PLoS One 3:e1755

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC (2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133:128–141

    Article  PubMed  CAS  Google Scholar 

  • Morel JB, Godon C, Mourrain P, Beclin C, Boutet S, Feuerbach F, Proux F, Vaucheret H (2002) Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell 14:629–639

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nagano H, Fukudome A, Hiraguri A, Moriyama H, Fukuhara T (2014) Distinct substrate specificities of Arabidopsis DCL3 and DCL4. Nucleic Acids Res 42:1845–1856

    Article  PubMed  CAS  Google Scholar 

  • Nguyen TA, Jo MH, Choi YG, Park J, Kwon SC, Hohng S, Kim VN, Woo JS (2015) Functional Anatomy of the Human Microprocessor. Cell 161:1374–1387

    Article  PubMed  CAS  Google Scholar 

  • Okamura K, Liu N, Lai EC (2009) Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Mol Cell 36:431–444

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Parent JS, Bouteiller N, Elmayan T, Vaucheret H (2015) Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing. Plant J 81:223–232

    Article  PubMed  CAS  Google Scholar 

  • Park JH, Shin C (2015) Slicer-independent mechanism drives small-RNA strand separation during human RISC assembly. Nucleic Acids Res 43:9418–9433

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Park JE, Heo I, Tian Y, Simanshu DK, Chang H, Jee D, Patel DJ, Kim VN (2011) Dicer recognizes the 5′ end of RNA for efficient and accurate processing. Nature 475:201–205

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pumplin N, Voinnet O (2013) RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence. Nat Rev Microbiol 11:745–760

    Article  PubMed  CAS  Google Scholar 

  • Qi Y, Denli AM, Hannon GJ (2005) Biochemical specialization within Arabidopsis RNA silencing pathways. Mol Cell 19:421–428

    Article  PubMed  CAS  Google Scholar 

  • Rand TA, Petersen S, Du F, Wang X (2005) Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 123:621–629

    Article  PubMed  CAS  Google Scholar 

  • Ren G, Chen X, Yu B (2012a) Uridylation of miRNAs by hen1 suppressor1 in Arabidopsis. Curr Biol 22:695–700

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ren G, Xie M, Dou Y, Zhang S, Zhang C, Yu B (2012b) Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis. Proc Natl Acad Sci USA 109:12817–12821

    Article  PubMed  Google Scholar 

  • Schirle NT, MacRae IJ (2012) The crystal structure of human Argonaute2. Science 336:1037–1040

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schott G, Mari-Ordonez A, Himber C, Alioua A, Voinnet O, Dunoyer P (2012) Differential effects of viral silencing suppressors on siRNA and miRNA loading support the existence of two distinct cellular pools of ARGONAUTE1. EMBO J 31:2553–2565

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schuck J, Gursinsky T, Pantaleo V, Burgyan J, Behrens SE (2013) AGO/RISC-mediated antiviral RNA silencing in a plant in vitro system. Nucleic Acids Res 41:5090–5103

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115:199–208

    Article  PubMed  CAS  Google Scholar 

  • Smith MR, Willmann MR, Wu G, Berardini TZ, Moller B, Weijers D, Poethig RS (2009) Cyclophilin 40 is required for microRNA activity in Arabidopsis. Proc Natl Acad Sci USA 106:5424–5429

    Article  PubMed  Google Scholar 

  • Sorin C, Bussell JD, Camus I, Ljung K, Kowalczyk M, Geiss G, McKhann H, Garcion C, Vaucheret H, Sandberg G et al (2005) Auxin and light control of adventitious rooting in Arabidopsis require ARGONAUTE1. Plant Cell 17:1343–1359

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Starega-Roslan J, Krol J, Koscianska E, Kozlowski P, Szlachcic WJ, Sobczak K, Krzyzosiak WJ (2011) Structural basis of microRNA length variety. Nucleic Acids Res 39:257–268

    Article  PubMed  CAS  Google Scholar 

  • Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD (2004) A protein sensor for siRNA asymmetry. Science 306:1377–1380

    Article  PubMed  CAS  Google Scholar 

  • Tomari Y, Du T, Zamore PD (2007) Sorting of Drosophila small silencing RNAs. Cell 130:299–308

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tu B, Liu L, Xu C, Zhai J, Li S, Lopez MA, Zhao Y, Yu Y, Ramachandran V, Ren G et al (2015) Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis. PLoS Genet 11:e1005119

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vargason JM, Szittya G, Burgyan J, Hall TM (2003) Size selective recognition of siRNA by an RNA silencing suppressor. Cell 115:799–811

    Article  PubMed  CAS  Google Scholar 

  • Vazquez F, Blevins T, Ailhas J, Boller T, Meins F Jr (2008) Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res 36:6429–6438

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wang X, Zhang S, Dou Y, Zhang C, Chen X, Yu B, Ren G (2015) Synergistic and independent actions of multiple terminal nucleotidyl transferases in the 3′ tailing of small RNAs in Arabidopsis. PLoS Genet 11:e1005091

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wilson RC, Tambe A, Kidwell MA, Noland CL, Schneider CP, Doudna JA (2015) Dicer-TRBP complex formation ensures accurate mammalian microRNA biogenesis. Mol Cell 57:397–407

    Article  PubMed  CAS  Google Scholar 

  • Woehrer SL, Aronica L, Suhren JH, Busch CJ, Noto T, Mochizuki K (2015) A Tetrahymena Hsp90 co-chaperone promotes siRNA loading by ATP-dependent and ATP-independent mechanisms. EMBO J 34:559–577

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wu L, Zhang Q, Zhou H, Ni F, Wu X, Qi Y (2009) Rice MicroRNA effector complexes and targets. Plant Cell 21:3421–3435

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y (2010) DNA methylation mediated by a microRNA pathway. Mol Cell 38:465–475

    Article  PubMed  CAS  Google Scholar 

  • Ye K, Malinina L, Patel DJ (2003) Recognition of small interfering RNA by a viral suppressor of RNA silencing. Nature 426:874–878

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ye R, Wang W, Iki T, Liu C, Wu Y, Ishikawa M, Zhou X, Qi Y (2012) Cytoplasmic assembly and selective nuclear import of Arabidopsis Argonaute4/siRNA complexes. Mol Cell 46:859–870

    Article  PubMed  CAS  Google Scholar 

  • Yoshikawa M (2013) Biogenesis of trans-acting siRNAs, endogenous secondary siRNAs in plants. Genes Genet Syst 88:77–84

    Article  PubMed  CAS  Google Scholar 

  • Yoshikawa M, Iki T, Tsutsui Y, Miyashita K, Poethig RS, Habu Y, Ishikawa M (2013) 3′ fragment of miR173-programmed RISC-cleaved RNA is protected from degradation in a complex with RISC and SGS3. Proc Natl Acad Sci USA 110:4117–4122

    Article  PubMed  Google Scholar 

  • Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X (2005) Methylation as a crucial step in plant microRNA biogenesis. Science 307:932–935

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhai J, Zhao Y, Simon SA, Huang S, Petsch K, Arikit S, Pillay M, Ji L, Xie M, Cao X et al (2013) Plant microRNAs display differential 3′ truncation and tailing modifications that are ARGONAUTE1 dependent and conserved across species. Plant Cell 25:2417–2428

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang H, Kolb FA, Jaskiewicz L, Westhof E, Filipowicz W (2004) Single processing center models for human Dicer and bacterial RNase III. Cell 118:57–68

    Article  PubMed  CAS  Google Scholar 

  • Zhang X, Zhao H, Gao S, Wang WC, Katiyar-Agarwal S, Huang HD, Raikhel N, Jin H (2011) Arabidopsis Argonaute 2 regulates innate immunity via miRNA393(*)-mediated silencing of a Golgi-localized SNARE gene, MEMB12. Mol Cell 42:356–366

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang X, Niu D, Carbonell A, Wang A, Lee A, Tun V, Wang Z, Carrington JC, Chang CE, Jin H (2014) ARGONAUTE PIWI domain and microRNA duplex structure regulate small RNA sorting in Arabidopsis. Nat Commun 5:5468

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang Z, Liu X, Guo X, Wang XJ, Zhang X (2016) Arabidopsis AGO3 predominantly recruits 24-nt small RNAs to regulate epigenetic silencing. Nat Plants 2:16049

    Article  PubMed  CAS  Google Scholar 

  • Zhao Y, Yu Y, Zhai J, Ramachandran V, Dinh TT, Meyers BC, Mo B, Chen X (2012) The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Curr Biol 22:689–694

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhu H, Hu F, Wang R, Zhou X, Sze SH, Liou LW, Barefoot A, Dickman M, Zhang X (2011) Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell 145:242–256

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhu H, Zhou Y, Castillo-Gonzalez C, Lu A, Ge C, Zhao YT, Duan L, Li Z, Axtell MJ, Wang XJ et al (2013) Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1. Nat Struct Mol Biol 20:1106–1115

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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Acknowledgements

I thank Dr. Misato Ohtani and Dr. Reina Komiya for giving me the opportunity to publish this review related to the JPR symposium held in 2015.

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  1. Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Suita, Osaka, 565-0871, Japan

    Taichiro Iki

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Iki, T. Messages on small RNA duplexes in plants. J Plant Res 130, 7–16 (2017). https://doi.org/10.1007/s10265-016-0876-2

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