Classification and comparison of small RNAs from plants

Annual Review of Plant Biology

Volumn 64, Issue , 2013, Pages 137-159

  Axtell, Michael J ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Arabidopsis; MicroRNA; SiRNA

Indexed keywords

PLANT RNA; SMALL UNTRANSLATED RNA;

CLASSIFICATION; COMPARATIVE STUDY; GENETICS; PLANT; REVIEW;

PLANTS; RNA, PLANT; RNA, SMALL UNTRANSLATED;

EID: 84877677064     PISSN: 15435008     EISSN: 15452123     Source Type: Book Series    
DOI: 10.1146/annurev-arplant-050312-120043     Document Type: Review

References (124)

1. Allen E, Xie Z, Gustafson AM, Carrington JC. 2005. MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207-21
2. Alves L Jr, Niemeier S, Hauenschild A, Rehmsmeier M, Merkle T. 2009. Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana. Nucleic Acids Res. 37:4010-21
3. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, et al. 2003. A uniform system for microRNA annotation. RNA 9:277-79
4. Aukerman MJ, Sakai H. 2003. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 15:2730-41
5. Axtell MJ. 2008. Evolution of microRNAs and their targets: Are all microRNAs biologically relevant? Biochim. Biophys. Acta 1779:725-34
6. Axtell MJ, Jan C, Rajagopalan R, Bartel DP. 2006. A two-hit trigger for siRNA biogenesis in plants. Cell 127:565-77
7. Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, et al. 2011. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332:960-63
8. Bao N, Lye K-W, Barton MK. 2004. MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Dev. Cell 7:653-62
9. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-97
10. Bartel DP. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136:215-33
11. Bazzini AA, Lee MT, Giraldez AJ. 2012. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336:233-37
12. Beauclair L, Yu A, Bouche N. 2010. MicroRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis. Plant J. 62:454-62
13. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu J-K. 2005. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123:1279-91
14. BreakfieldNW, Corcoran DL, Petricka JJ, Shen J, Sae-Seaw J, et al. 2012. High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. Genome Res. 22:163-76
15. Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, et al. 2008. Widespread translational inhibition by plant miRNAs and siRNAs. Science 320:1185-90
16. Buxdorf K, Hendelman A, Stav R, Lapidot M, Ori N, Arazi T. 2010. Identification and characterization of a novel miR159 target not related to MYB in tomato. Planta 232:1009-22
17. Calarco JP, Borges F, Donoghue MTA, Ex FV, Jullien PE, et al. 2012. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151:194-205
18. Carbonell A, FahlgrenN, Garcia-Ruiz H, Gilbert KB, Montgomery TA, et al. 2012. Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants. Plant Cell 24:3613-29
19. Chellappan P, Xia J, Zhou X, Gao S, Zhang X, et al. 2010. siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res. 38:6883-94
20. Chen H-M, Chen L-T, Patel K, Li Y-H, Baulcombe DC, Wu S-H. 2010. 22-nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc. Natl. Acad. Sci. USA 107:15269-74
21. Chen H-M, Li Y-H, Wu S-H. 2007. Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. Proc. Natl. Acad. Sci. USA 104:3318-23
22. Chen X. 2004. AmicroRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303:2022-25
23. Chen X. 2009. Small RNAs and their roles in plant development. Annu. Rev. Cell Dev. Biol. 25:21-44
24. Chitwood DH, Guo M, Nogueira FTS, Timmermans MCP. 2007. Establishing leaf polarity: the role of small RNAs and positional signals in the shoot apex. Development 134:813-23
25. Cho SH, Addo-Quaye C, Coruh C, Arif MA, Ma Z, et al. 2008. Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development. PLoS Genet. 4:e1000314
26. Chorostecki U, Crosa VA, Lodeyro AF, Bologna NG, Martin AP, et al. 2012. Identification of new microRNA-regulated genes by conserved targeting in plant species. Nucleic Acids Res. 40:8893-904
27. Chu C-C, Lee W-C, Guo W-Y, Pan S-M, Chen L-J, et al. 2005. A copper chaperone for superoxide dismutase that confers three types of copper/zinc superoxide dismutase activity in Arabidopsis. Plant Physiol. 139:425-36
28. Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, et al. 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
29. Cuperus JT, Fahlgren N, Carrington JC. 2011. Evolution and functional diversification of MIRNAgenes. Plant Cell 23:431-42
30. Debernardi JM, Rodriguez RE, Mecchia MA, Palatnik JF. 2012. Functional specialization of the plant miR396 regulatory network through distinct microRNA-target interactions. PLoS Genet. 8:e1002419
31. de Felippes FF, Wang J, Weigel D. 2012. MIGS: miRNA-induced gene silencing. Plant J. 70:541-47
32. Djuranovic S, Nahvi A, Green R. 2012. miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336:237-40
33. Dolgosheina EV, Morin RD, AksayG, Sahinalp SC,Magrini V, et al. 2008. Conifers have a unique small RNA silencing signature. RNA 14:1508-15
34. Dugas DV, Bartel B. 2008. Sucrose induction of Arabidopsis miR398 represses two Cu/Zn superoxide dismutases. Plant Mol. Biol. 67:403-17
35. Dunoyer P, Brosnan CA, Schott G, Wang Y, Jay F, et al. 2010. An endogenous, systemic RNAi pathway in plants. EMBO J. 29:1699-712
36. Eamens AL, Waterhouse PM. 2011. Vectors and methods for hairpin RNA and artificial microRNAmediated gene silencing in plants. Methods Mol. Biol. 701:179-97
37. Fahlgren N, Carrington JC. 2010. miRNA target prediction in plants. Methods Mol. Biol. 592:51-57
38. Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, et al. 2010. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell 22:1074-89
39. Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, et al. 2006. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr. Biol. 16:939-44
40. Franco-Zorrilla JM, Valli A, TodescoM,Mateos I, Puga MI, et al. 2007. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet. 39:1033-37
41. Fusaro AF, Matthew L, Smith NA, Curtin SJ, Dedic-Hagan J, et al. 2006. RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway. EMBO Rep. 7:1168-75
42. Gandikota M, Birkenbihl RP, H?ohmann S, Cardon GH, Saedler H, Huijser P. 2007. The miRNA156/157 recognition element in the 3- UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J. 49:683-93
43. Gehring M, Bubb KL, Henikoff S. 2009. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324:1447-51
44. Guo H, Ingolia NT, Weissman JS, Bartel DP. 2010. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466:835-40
45. Havecker ER, Wallbridge LM, Hardcastle TJ, Bush MS, Kelly KA, et al. 2010. The Arabidopsis RNAdirected DNA methylation Argonautes functionally diverge based on their expression and interaction with target loci. Plant Cell 22:321-34
46. Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, et al. 2006. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNAmethylation patterning. Nat. Genet. 38:721-25
47. Henz SR, Cumbie JS, Kasschau KD, Lohmann JU, Carrington JC, et al. 2007. Distinct expression patterns of natural antisense transcripts in Arabidopsis. Plant Physiol. 144:1247-55
48. Herr AJ, Molnár A, Jones A, Baulcombe DC. 2006. Defective RNA processing enhances RNA silencing and influences flowering of Arabidopsis. Proc. Natl. Acad. Sci. USA 103:14994-5001
49. Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, et al. 2007. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA-and tasiRNA-directed targeting. Plant Cell 19:926-42
50. Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, et al. 2009. Genome-wide demethylation of Arabidopsis endosperm. Science 324:1451-54
51. Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, et al. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337:1360-64
52. Jin H, Vacic V, Girke T, Lonardi S, Zhu J-K. 2008. Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol. Biol. 9:6
53. Johnson C, Kasprzewska A, Tennessen K, Fernandes J, Nan G-L, et al. 2009. Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res. 19:1429-40
54. Jones-Rhoades MW. 2012. Conservation and divergence in plant microRNAs. Plant Mol. Biol. 80:3-16
55. Jones-Rhoades MW, Bartel DP. 2004. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14:787-99
56. JouannetV,MorenoAB, ElmayanT, Vaucheret H, CrespiMD,MaizelA. 2012. CytoplasmicArabidopsis AGO7 accumulates in membrane-associated siRNA bodies and is required for ta-siRNA biogenesis. EMBO J. 31:1704-13
57. Juliano C,Wang J, Lin H. 2011. Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms. Annu. Rev. Genet. 45:447-69
58. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, et al. 2007. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 5:e57
59. Katiyar-Agarwal S, Gao S, Vivian-Smith A, Jin H. 2007. A novel class of bacteria-induced small RNAs in Arabidopsis. Genes Dev. 21:3123-34
60. Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas A Jr, et al. 2006. A pathogen-inducible endogenous siRNA in plant immunity. Proc. Natl. Acad. Sci. USA 103:18002-7
61. Khraiwesh B, Arif MA, Seumel GI, Ossowski S, Weigel D, et al. 2010. Transcriptional control of gene expression by microRNAs. Cell 140:111-22
62. Kumakura N, Takeda A, Fujioka Y,Motose H, Takano R,Watanabe Y. 2009. SGS3 and RDR6 interact and colocalize in cytoplasmic SGS3/RDR6-bodies. FEBS Lett. 583:1261-66
63. Law JA, Ausin I, Johnson LM, Vashisht AA, Zhu J-K, et al. 2010. A protein complex required for polymerase V transcripts and RNA-directed DNA methylation in Arabidopsis. Curr. Biol. 20: 951-56
64. Law JA, Jacobsen SE. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11:204-20
65. Li F, Pignatta D, Bendix C, Brunkard JO, Cohn MM, et al. 2012. MicroRNA regulation of plant innate immune receptors. Proc. Natl. Acad. Sci. USA 109:1790-95
66. Lisch D, Bennetzen JL. 2011. Transposable element origins of epigenetic gene regulation. Curr. Opin. Plant Biol. 14:156-61
67. Llave C, Kasschau KD, Rector MA, Carrington JC. 2002. Endogenous and silencing-associated small RNAs in plants. Plant Cell 14:1605-19
68. Lu C, Kulkarni K, Souret FF, MuthuValliappan R, Tej SS, et al. 2006. MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res. 16:1276-88
69. Luo Q-J, Mittal A, Jia F, Rock CD. 2012. An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis. Plant Mol. Biol. 80:117-29
70. Ma Z, Coruh C, Axtell MJ. 2010. Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell 22:1090-103
71. Mallory AC, Reinhart BJ, Jones-Rhoades MW, Tang G, Zamore PD, et al. 2004. MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5- region. EMBO J. 23:3356-64
72. Manavella PA, Koenig D, Weigel D. 2012. Plant secondary siRNA production determined by microRNA-duplex structure. Proc. Natl. Acad. Sci. USA 109:2461-66
73. Margis R, Fusaro AF, Smith NA, Curtin SJ, Watson JM, et al. 2006. The evolution and diversification of Dicers in plants. FEBS Lett. 580:2442-50
74. MatzkeM,Kanno T, DaxingerL,HuettelB,Matzke AJ. 2009. RNA-mediated chromatin-based silencing in plants. Curr. Opin. Cell Biol. 21:367-76
75. McCue AD, Nuthikattu S, Reeder SH, Slotkin RK. 2012. Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA. PLoS Genet. 8:e1002474
76. Melnyk CW,Molnar A, Bassett A, BaulcombeDC. 2011. Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana. Curr. Biol. 21:1678-83
77. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, et al. 2008. Criteria for annotation of plant microRNAs. Plant Cell 20:3186-90
78. Moissiard G, Parizotto EA, Himber C, Voinnet O. 2007. Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins. RNA 13:1268-78
79. Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, et al. 2008. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133:128-41
80. Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, et al. 2008. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res. 18:571-84
81. Mosher RA, Melnyk CW. 2010. siRNAs and DNA methylation: seedy epigenetics. Trends Plant Sci. 15:204-10
82. Mosher RA, Melnyk CW, Kelly KA, Dunn RM, Studholme DJ, Baulcombe DC. 2009. Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460: 283-86
83. Mosher RA, Schwach F, Studholme D, Baulcombe DC. 2008. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc. Natl. Acad. Sci. USA 105:3145-50
84. Mosher RA, Tan EH, Shin J, Fischer RL, Pikaard CS, Baulcombe DC. 2011. An atypical epigenetic mechanism affects uniparental expression of Pol IV-dependent siRNAs. PLoS ONE 6:e25756
85. NobutaK,LuC, Shrivastava R, PillayM,DePaoliE, et al. 2008. Distinct size distribution of endogeneous siRNAs in maize: evidence from deep sequencing in the mop1-1 mutant. Proc. Natl. Acad. Sci. USA 105:14958-63
86. Olmedo-Monfil V, Duran-Figueroa N, Arteaga-Vazquez M, Demesa-Arevalo E, Autran D, et al. 2010. Control of female gamete formation by a small RNA pathway in Arabidopsis. Nature 464:628-32
87. Ossowski S, Schwab R, Weigel D. 2008. Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J. 53:674-90
88. Pak J, Fire A. 2007. Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315:241-44
89. Parizotto EA, Dunoyer P, Rahm N, Himber C, Voinnet O. 2004. In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA. Genes Dev. 18:2237-42
90. Park W, Li J, Song R, Messing J, Chen X. 2002. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12:1484-95
91. Piriyapongsa J, Jordan IK. 2008. Dual coding of siRNAs and miRNAs by plant transposable elements. RNA 14:814-21
92. Qi Y, He X, Wang X-J, Kohany O, Jurka J, Hannon GJ. 2006. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443:1008-12
93. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 20:3407-25
94. Reinhart BJ,Weinstein EG, Rhoades MW, Bartel B, Bartel DP. 2002. MicroRNAs in plants. Genes Dev. 16:1616-26
95. RhoadesMW,Reinhart BJ,Lim LP, Burge CB, Bartel B, BartelDP. 2002. Prediction of plantmicroRNA targets. Cell 110:513-20
96. Ron M, Alandete Saez M, EshedWilliams L, Fletcher JC, McCormick S. 2010. Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis. Genes Dev. 24:1010-21
97. Ruiz-Ferrer V, Voinnet O. 2009. Roles of plant small RNAs in biotic stress responses. Annu. Rev. Plant Biol. 60:485-510
98. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D. 2005. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 8:517-27
99. Shin C,Nam J-W, Farh KK-H, Chiang HR, Shkumatava A, BartelDP. 2010. Expanding the microRNA targeting code: functional sites with centered pairing. Mol. Cell 38:789-802
100. Shivaprasad PV, Chen H-M, Patel K, Bond DM, Santos BACM, Baulcombe DC. 2012. A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell 24:859-74
101. Slotkin RK, VaughnM, Borges F, TanurdzícM, Becker JD, et al. 2009. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136:461-72
102. Song X, Li P, Zhai J, Zhou M, Ma L, et al. 2012. Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. Plant J. 69:462-74
103. Talmor-Neiman M, Stav R, Klipcan L, Buxdorf K, Baulcombe DC, Arazi T. 2006. Identification of trans-acting siRNAs in moss and an RNA-dependent RNA polymerase required for their biogenesis. Plant J. 48:511-21
104. Tang G, Reinhart BJ, Bartel DP, Zamore PD. 2003. A biochemical framework for RNA silencing in plants. Genes Dev. 17:49-63
105. Tanurdzic M, Vaughn MW, Jiang H, Lee T-J, Slotkin RK, et al. 2008. Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol. 6:2880-95
106. Tay Y, Kats L, Salmena L,Weiss D, Tan SM, et al. 2011. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 147:344-57
107. Todesco M, Balasubramanian S, Cao J, Ott F, Sureshkumar S, et al. 2012. Natural variation in biogenesis efficiency of individual Arabidopsis thaliana microRNAs. Curr. Biol. 22:166-70
108. Todesco M, Rubio-Somoza I, Paz-Ares J, Weigel D. 2010. A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana. PLoS Genet. 6:e1001031
109. Vaucheret H. 2008. Plant ARGONAUTES. Trends Plant Sci. 13:350-58
110. Vazquez F, Blevins T, Ailhas J, Boller T,Meins F Jr. 2008. Evolution of ArabidopsisMIR genes generates novel microRNA classes. Nucleic Acids Res. 36:6429-38
111. Voinnet O. 2009. Origin, biogenesis, and activity of plant microRNAs. Cell 136:669-87
112. Wesley SV, Helliwell CA, Smith NA, Wang M, Rouse DT, et al. 2001. Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J. 27:581-90
113. Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Rowley MJ, et al. 2012. Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev. 26:1825-36
114. Willmann MR, Endres MW, Cook RT, Gregory BD. 2011. The functions of RNA-dependent RNA polymerases in Arabidopsis. Arabidopsis Book 9:e0146
115. WuL, Mao L,Qi Y. 2012. Roles of DICER-LIKE andARGONAUTEproteins in TAS-derived siRNAs triggered DNA methylation. Plant Physiol. 160:990-99
116. Wu L, Zhou H, Zhang Q, Zhang J, Ni F, et al. 2010. DNA methylation mediated by a microRNA pathway. Mol. Cell 38:465-75
117. Yan J, Gu Y, Jia X, Kang W, Pan S, et al. 2012. Effective small RNA destruction by the expression of a short tandem target mimic in Arabidopsis. Plant Cell 24:415-27
118. Yang L, Wu G, Poethig RS. 2012. Mutations in the GW-repeat protein SUO reveal a developmental function for microRNA-mediated translational repression in Arabidopsis. Proc. Natl. Acad. Sci. USA 109:315-20
119. Ye R, Wang W, Iki T, Liu C, Wu Y, et al. 2012. Cytoplasmic assembly and selective nuclear import of Arabidopsis ARGONAUTE4/siRNA complexes. Mol. Cell 46:859-70
120. Yoshikawa M, Peragine A, Park MY, Poethig RS. 2005. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev. 19:2164-75
121. Zhai J, Jeong D-H, De Paoli E, Park S, Rosen BD, et al. 2011. MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev. 25:2540-53
122. Zhang X, Xia J, Lii YE, Barrera-Figueroa BE, Zhou X, et al. 2012. Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function. Genome Biol. 13:R20
123. Zhong X, Hale CJ, Law JA, Johnson LM, Feng S, et al. 2012. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat. Struct. Mol. Biol. 19:870-75
124. Zong J, Yao X, Yin J, Zhang D, Ma H. 2009. Evolution of the RNA-dependent RNA polymerase (RdRP) genes: duplications and possible losses before and after the divergence of major eukaryotic groups. Gene 447:29-39