MicroRNA biogenesis and function in higher plants

Plant Biotechnology Reports

Volumn 3, Issue 2, 2009, Pages 111-126

  Jung, Jae Hoon ^a   Seo, Pil Joon ^a   Park, Chung Mo ^b  

^a Seoul National University   (South Korea)

^b Seoul National University   (South Korea)

Author keywords

Arabidopsis mutants; Plant development; Plant molecular biology

Indexed keywords

ANIMALIA; ARABIDOPSIS; BRYOPHYTA; EMBRYOPHYTA; MAGNOLIOPHYTA;

EID: 64749095020     PISSN: 18635466     EISSN: 18635474     Source Type: Journal    
DOI: 10.1007/s11816-009-0085-8     Document Type: Review

References (161)

1. P Achard A Herr DC Baulcombe NP Harberd 2004 Modulation of floral development by a gibberellin-regulated microRNA Development 131 3357 3365
2. A Adai C Johnson S Mlotshwa S Archer-Evans V Manocha V Vance V Sundaresan 2005 Computational prediction of miRNAs in Arabidopsis thaliana Genome Res 15 78 91
3. E Allen Z Xie AM Gustafson GH Sung JW Spatafora JC Carrington 2004 Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana Nat Genet 36 1282 1290
4. V Ambros B Bartel DP Bartel CB Burge JC Carrington X Chen G Dreyfuss SR Eddy S Griffiths-Jones M Marshall M Matzke G Ruvkun T Tuschl 2003 A uniform system for microRNA annotation RNA 9 277 279
5. T Arazi M Talmor-Neiman R Stav M Riese P Huijser DC Baulcombe 2005 Cloning and characterization of micro-RNAs from moss Plant J 43 837 848
6. M Arteaga-Vazquez J Caballero-Perez JP Vielle-Calzada 2006 A family of microRNAs present in plants and animals Plant Cell 18 3355 3369
7. MJ Aukerman H Sakai 2003 Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes Plant Cell 15 2730 2741
8. K Aung SI Lin CC Wu YT Huang CL Su TJ Chiou 2006 pho2, a phosphate overaccumulator, is caused by a nonsense mutation in a microRNA399 target gene Plant Physiol 141 1000 1011
9. MJ Axtell DP Bartel 2005 Antiquity of microRNAs and their targets in land plants Plant Cell 17 1658 1673
10. R Bari B Datt Pant M Stitt WR Scheible 2006 PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants Plant Physiol 141 988 999
11. DP Bartel 2004 MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 281 297
12. M Baucher M El Jaziri O Vandeputte 2007 From primary to secondary growth: origin and development of the vascular system J Exp Bot 58 3485 3501
13. D Baulcombe 2004 RNA silencing in plants Nature 431 356 363
14. I Bäurle C Dean 2006 The timing of developmental transitions in plants Cell 125 655 664
15. TZ Berardini K Bollman H Sun RS Poethig 2001 Regulation of vegetative phase change in Arabidopsis thaliana by cyclophilin 40 Science 291 2405 2407
16. B Billoud R De Paepe D Baulcombe M Boccara 2005 Identification of new small non-coding RNAs from tobacco and Arabidopsis Biochimie 87 905 910
17. Bollman KM, Aukerman MJ, Park MY, Hunter C, Berardini TZ, Poethig RS (2003) HASTY, the Arabidopsis ortholog of exportin 5/MSN5, regulates phase change and morphogenesis. Development 130:1493-1504
18. E Bonnet Y Van de Peer P Rouzé 2006 The small RNA world of plants New Phytol 171 451 468
19. S Boutet F Vazquez J Liu C Béclin M Fagard A Gratias JB Morel P Crété X Chen H Vaucheret 2003 Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance Curr Biol 13 843 848
20. JL Bowman DR Smyth EM Meyerowitz 1991 Genetic interactions among floral homeotic genes of Arabidopsis Development 112 1 20
21. JL Bowman Y Eshed SF Baum 2002 Establishment of polarity in angiosperm lateral organs Trends Genet 18 134 141
22. RJ Britten EH Davidson 1969 Gene regulation for higher cells: a theory Science 165 349 357
23. P Brodersen L Sakvarelidze-Achard M Bruun-Rasmussen P Dunoyer YY Yamamoto L Sieburth O Voinnet 2008 Widespread translational inhibition by plant miRNAs and siRNAs Science 320 1185 1190
24. ME Byrne 2006 Shoot meristem function and leaf polarity: the role of class III HD-ZIP genes PLOS Genet 2 e89
25. JC Carrington V Ambros 2003 Role of microRNAs in plant and animal development Science 301 336 338
26. L Cerutti N Mian A Bateman 2000 Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the PIWI domain Trends Biochem Sci 25 481 482
27. EJ Chapman JC Carrington 2007 Specialization and evolution of endogenous small RNA pathways Nat Rev Genet 8 884 896
28. X Chen 2004 A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development Science 303 2022 2025
29. X Chen 2008 MicroRNA metabolism in plants Curr Top Microbiol Immunol 320 117 136
30. X Chen J Liu Y Cheng D Jia 2002 HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower Development 129 1085 1094
31. TJ Chiou 2007 The role of microRNAs in sensing nutrient stress Plant Cell Environ 30 323 332
32. TJ Chiou K Aung SI Lin CC Wu SF Chiang CL Su 2006 Regulation of phosphate homeostasis by MicroRNA in Arabidopsis Plant Cell 18 412 421
33. DH Chitwood M Guo FT Nogueira MC Timmermans 2007 Establishing leaf polarity: the role of small RNAs and positional signals in the shoot apex Development 134 813 823
34. G Chuck AM Cigan K Saeteurn S Hake 2007 The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA Nat Genet 39 544 549
35. G Chuck H Candela S Hake 2009 Big impacts by small RNAs in plant development Curr Opin Plant Biol 12 81 86
36. JH Clarke D Tack K Findlay M Van Montagu M Van Lijsebettens 1999 The SERRATE locus controls the formation of the early juvenile leaves and phase length in Arabidopsis Plant J 20 493 501
37. J Couzin 2002 Breakthrough of the year: small RNAs make big splash Science 298 2296 2297
38. I De Smet S Vanneste D Inzé T Beeckman 2006 Lateral root initiation or the birth of a new meristem Plant Mol Biol 60 871 887
39. KI Deak J Malamy 2005 Osmotic regulation of root system architecture Plant J 43 17 28
40. Z Dong M Han N Fedoroff 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
41. DV Dugas B Bartel 2008 Sucrose induction of Arabidopsis miR398 represses two Cu/Zn superoxide dismutases Plant Mol Biol 67 403 417
42. A Eamens MB Wang NA Smith PM Waterhouse 2008 RNA silencing in plants: yesterday, today, and tomorrow Plant Physiol 147 456 468
43. SR Eddy 2001 Non-coding RNA genes and the modern RNA world Nat Rev Genet 2 919 929
44. JF Emery SK Floyd J Alvarez Y Eshed NP Hawker A Izhaki SF Baum JL Bowman 2003 Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes Curr Biol 13 1768 1774
45. N Fahlgren MD Howell KD Kasschau EJ Chapman CM Sullivan JS Cumbie SA Givan TF Law SR Grant JL Dangl JC Carrington 2007 High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes PLoS ONE 2 e219
46. Y Fang DL Spector 2007 Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants Curr Biol 17 818 823
47. SK Floyd JL Bowman 2004 Gene regulation: ancient microRNA target sequences in plants Nature 428 485 486
48. EM Friis KR Pedersen PR Crane 2004 Araceae from the early Cretaceous of Portugal: evidence on the emergence of monocotyledons Proc Natl Acad Sci USA 101 16565 16570
49. H Fujii TJ Chiou SI Lin K Aung JK Zhu 2005 A miRNA involved in phosphate-starvation response in Arabidopsis Curr Biol 15 2038 2043
50. Y Fujioka M Utsumi Y Ohba Y Watanabe 2007 Location of a possible miRNA processing site in SmD3/SmB nuclear bodies in Arabidopsis Plant Cell Physiol 48 1243 1253
51. M Gandikota RP Birkenbihl S Hohmann GH Cardon H Saedler P Huijser 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 49 683 693
52. D Garcia 2008 A miRacle in plant development: role of microRNAs in cell differentiation and patterning Semin Cell Dev Biol 19 586 595
53. TA Golden SE Schauer JD Land S Pien AR Mushegian U Grossniklaus DW Meinke A Ray 2002 SHORT INTEGUMENTS1/SUSPENSOR1/CARPEL FACTORY, a Dicer homolog, is a maternal effect gene required for embryo development in Arabidopsis Physiol 130 810 822
54. BD Gregory RC O'Malley R Lister MA Urich J Tonti-Filippini H Chen AH Millar JR Ecker 2008 A link between RNA metabolism and silencing affecting Arabidopsis development Dev Cell 14 854 866
55. HS Guo Q Xie JF Fei NH Chua 2005 MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development Plant Cell 17 1376 1386
56. SM Hammond E Bernstein D Beach GJ Hannon 2000 An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells Nature 404 293 296
57. J Han Y Lee KH Yeom YK Kim H Jin VN Kim 2004 The Drosha-DGCR8 complex in primary microRNA processing Genes Dev 18 3016 3027
58. A Hiraguri R Itoh N Kondo Y Nomura D Aizawa Y Murai H Koiwa M Seki K Shinozaki T Fukuhara 2005 Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana Plant Mol Biol 57 173 188
59. C Hunter H Sun RS Poethig 2003 The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member Curr Biol 13 1734 1739
60. G Hutvagner PD Zamore 2002 A microRNA in a multiturnover RNAi enzyme complex Science 297 2056 2060
61. SE Jacobsen MP Running EM Meyerowitz 1999 Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems Development 126 5231 5243
62. G Jagadeeswaran A Saini R Sunkar 2009 Biotic and abiotic stress down-regulate miR398 expression in Arabidopsis Planta 229 1009 1014
63. MW Jones-Rhoades DP Bartel 2004 Computational identification of plant micro-RNAs and their targets, including a stress-induced miRNA Mol Cell 14 787 799
64. MW Jones-Rhoades DP Bartel B Barte 2006 MicroRNAs and their regulatory roles in plants Annu Rev Plant Biol 57 19 53
65. JH Jung CM Park 2007 MIR166/165 genes exhibit dynamic expression patterns in regulating shoot apical meristem and floral development in Arabidopsis Planta 225 1327 1338
66. JH Jung YH Seo PJ Seo JL Reyes J Yun NH Chua CM Park 2007 The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis Plant Cell 19 2736 2748
67. JH Jung SG Kim PJ Seo CM Park 2008 Molecular mechanisms underlying vascular development Adv Bot Res 48 1 68
68. KD Kasschau N Fahlgren EJ Chapman CM Sullivan JS Cumbie SA Givan JC Carrington 2007 Genome-wide profiling and analysis of Arabidopsis siRNAs PLoS Biol 5 e57
69. CG Kawashima N Yoshimoto A Maruyama-Nakashita YN Tsuchiya K Saito H Takahashi T Dalmay 2009 Sulphur starvation induces the expression of microRNA-395 and one of its target genes but in different cell types Plant J 57 313 321
70. CA Kidner RA Martienssen 2004 Spatially restricted microRNA directs leaf polarity through ARGONAUTE1 Nature 428 81 84
71. CA Kidner RA Martienssen 2005 The role of ARGONAUTE1 (AGO1) in meristem formation and identity Dev Biol 280 504 517
72. CA Kidner MC Timmermans 2007 Mixing and matching pathways in leaf polarity Curr Opin Plant Biol 10 13 20
73. VN Kim 2005 MicroRNA biogenesis: coordinated cropping and dicing Nat Rev Mol Cell Biol 6 376 385
74. J Kim JH Jung JL Reyes YS Kim SY Kim KS Chung JA Kim M Lee Y Lee V Narry Kim NH Chua CM Park 2005 microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems Plant J 42 84 94
75. BA Krizek JC Fletcher 2005 Molecular mechanisms of flower development: an armchair guide Nat Rev Genet 6 688 698
76. Y Kurihara Y Watanabe 2004 Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions Proc Natl Acad Sci USA 101 12753 12758
77. Y Kurihara Y Takashi Y Watanabe 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
78. C Kutter H Schöb M Stadler F Meins Jr A Si-Ammour 2007 MicroRNA-mediated regulation of stomatal development in Arabidopsis Plant Cell 19 2417 2429
79. S Laubinger T Sachsenberg G Zeller W Busch JU Lohmann G Ratsch D Weigel 2008 Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana Proc Natl Acad Sci USA 105 8795 8800
80. P Laufs A Peaucelle H Morin J Traas 2004 MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems Development 17 4311 4322
81. RC Lee RL Feinbaum V Ambros 1993 The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 Cell 75 843 854
82. Y Lee M Kim J Han KH Yeom S Lee SH Baek VN Kim 2004 MicroRNA genes are transcribed by RNA polymerase II EMBO J 23 4051 4060
83. J Li Z Yang B Yu J Liu X Chen 2005 Methylation protects miRNAs and siRNAs from a 3-end uridylation activity in Arabidopsis Curr Biol 15 1501 1507
84. S Lin R Henriques H Wu Q Niu S Yeh N Chua 2007 Strategies and mechanisms of plant virus resistance Plant Biotechnol Rep 1 125 134
85. J Liu MA Carmell FV Rivas CG Marsden JM Thomson JJ Song SM Hammond L Joshua-Tor GJ Hannon 2004 Argonaute2 is the catalytic engine of mammalian RNAi Science 305 1437 1441
86. C Llave KD Kasschau MA Rector JC Carrington 2002 Endogenous and silencing-associated small RNAs in plants Plant Cell 14 1605 1619
87. C Llave Z Xie KD Kasschau JC Carrington 2002 Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA Science 297 2053 2056
88. D Lobbes G Rallapalli DD Schmidt C Martin J Clarke 2006 SERRATE: a new player on the plant microRNA scene Rep 7 1052 1058
89. C Lu N Fedoroff 2000 A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin Plant Cell 12 2351 2366
90. XY Lu XL Huang 2008 Plant miRNAs and abiotic stress responses Biochem Biophys Res Commun 368 458 462
91. S Lu YH Sun R Shi C Clark L Li VL Chiang 2005 Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis Plant Cell 17 2186 2203
92. C Maher L Stein D Ware 2006 Evolution of Arabidopsis microRNA families through duplication events Genome Res 16 510 519
93. JE Malamy 2005 Intrinsic and environmental response pathways that regulate root system architecture Plant Cell Environ 28 67 77
94. Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38(Suppl):S31-S36
95. AC Mallory DP Bartel B Bartel 2005 MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes Plant Cell 17 1360 1375
96. JR McConnell J Emery Y Eshed N Bao J Bowman MK Barton 2001 Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots Nature 411 709 713
97. M Megraw V Baev V Rusinov ST Jensen K Kalantidis AG Hatzigeorgiou 2006 MicroRNA promoter element discovery in Arabidopsis RNA 12 1612 1619
98. G Meister M Landthaler A Patkaniowska Y Dorsett G Teng T Tuschl 2004 Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs Mol Cell 15 185 197
99. G Michlewski S Guil CA Semple JF Cáceres 2008 Posttranscriptional regulation of miRNAs harboring conserved terminal loops Mol Cell 32 383 393
100. K Miyoshi H Tsukumo T Nagami H Siomi MC Siomi 2005 Slicer function of Drosophila argonautes and its involvement in RISC formation Genes Dev 19 2837 2848
101. TE Mullen WF Marzluff 2008 Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5- to 3- and 3- to 5- Genes Dev 22 50 65
102. L Navarro P Dunoyer F Jay B Arnold N Dharmasiri M Estelle O Voinnet JD Jones 2006 A plant miRNA contributes to antibacterial resistance by repressing auxin signaling Science 312 436 439
103. FT Nogueira AK Sarkar DH Chitwood MC Timmermans 2006 Organ polarity in plants is specified through the opposing activity of two distinct small regulatory RNAs Cold Spring Harb Symp Quant Biol 71 157 164
104. JF Palatnik E Allen X Wu C Schommer R Schwab JC Carrington D Weigel 2003 Control of leaf morphogenesis by microRNAs Nature 425 257 263
105. W Park J Li R Song J Messing X Chen 2002 CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana Curr Biol 12 1484 1495
106. MY Park G Wu A Gonzalez-Sulser H Vaucheret RS Poethig 2005 Nuclear processing and export of microRNAs in Arabidopsis Proc Natl Acad Sci USA 102 3691 3696
107. JE Park JY Park YS Kim PE Staswick J Jeon J Yun SY Kim J Kim YH Lee CM Park 2007 GH3-mediated auxin homeostasis links growth regulation with stress adaptation response in Arabidopsis J Biol Chem 282 10036 10046
108. JS Parker SM Roe D Barford 2004 Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity EMBO J 23 4727 4737
109. A Peragine M Yoshikawa G Wu HL Albrecht RS Poethig 2004 SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis Genes Dev 18 2368 2379
110. JR Phillips T Dalmay D Bartels 2007 The role of small RNAs in abiotic stress FEBS Lett 581 3592 3597
111. RS Poethig 2003 Phase change and the regulation of developmental timing in plants Science 301 334 336
112. O Pontes CS Pikaard 2008 siRNA and miRNA processing: new functions for Cajal bodies Curr Opin Genet Dev 18 197 203
113. MJ Prigge D Otsuga JM Alonso JR Ecker GN Drews SE Clark 2005 Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development Plant Cell 17 61 76
114. R Rajagopalan H Vaucheret J Trejo DP Bartel 2006 A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana Genes Dev 20 3407 3425
115. V Ramachandran X Chen 2008 Small RNA metabolism in Arabidopsis Trends Plant Sci 13 368 374
116. J Reeder M Höchsmann M Rehmsmeier B Voss R Giegerich 2006 Beyond Mfold: recent advances in RNA bioinformatics J Biotechnol 124 41 55
117. BJ Reinhart FJ Slack M Basson AE Pasquinelli JC Bettinger AE Rougvie HR Horvitz G Ruvkun 2000 The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans Nature 403 901 906
118. BJ Reinhart EG Weinstein MW Rhoades B Bartel DP Bartel 2002 MicroRNAs in plants Genes Dev 16 1616 1626
119. JL Reyes NH Chua 2007 ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination Plant J 49 592 606
120. MW Rhoades BJ Reinhart LP Lim CB Burge B Bartel DP Bartel 2002 Prediction of plant microRNA targets Cell 110 513 520
121. M Ronemus MW Vaughn RA Martienssen 2006 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
122. P Ru L Xu H Ma H Huang 2006 Plant fertility defects induced by the enhanced expression of microRNA167 Cell Res 16 457 465
123. A Rybak H Fuchs L Smirnova C Brandt EE Pohl R Nitsch FG Wulczyn 2008 A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment Nat Cell Biol 10 987 993
124. SE Schauer SE Jacobsen DW Meinke A Ray 2002 DICER-LIKE1: blind men and elephants in Arabidopsis development Trends Plant Sci 7 487 491
125. R Schwab JF Palatnik M Riester C Schommer M Schmid D Weigel 2005 Specific effects of microRNAs on the plant transcriptome Dev Cell 8 517 527
126. DS Schwarz G Hutvagner T Du Z Xu N Aronin PD Zamore 2003 Asymmetry in the assembly of the RNAi enzyme complex Cell 115 199 208
127. VK Sharma C Carles JC Fletcher 2003 Maintenance of stem cell populations in plants Proc Natl Acad Sci USA 1 11823 11829
128. B Shen HM Goodman 2004 Uridine addition after microRNA-directed cleavage Science 306 997
129. L Song MH Han J Lesicka N Fedoroff 2007 Arabidopsis primary microRNA processing proteins HYL1 and DCL1 define a nuclear body distinct from the Cajal body Proc Natl Acad Sci USA 104 5437 5442
130. C Sorin JD Bussell I Camus K Ljung M Kowalczyk G Geiss H McKhann C Garcion H Vaucheret G Sandberg C Bellini 2005 Auxin and light control of adventitious rooting in Arabidopsis require ARGONAUTE1 Plant Cell 17 1343 1359
131. FF Souret JP Kastenmayer PJ Green 2004 AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets Mol Cell 15 173 183
132. R Sunkar JK Zhu 2004 Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis Plant Cell 16 2001 2019
133. R Sunkar T Girke PK Jain JK Zhu 2005 Cloning and characterization of microRNAs from rice Plant Cell 17 1397 1411
134. R Sunkar V Chinnusamy J Zhu JK Zhu 2007 Small RNAs as big players in plant abiotic stress responses and nutrient deprivation Trends Plant Sci 12 301 309
135. M Talmor-Neiman R Stav L Klipcan K Buxdorf DC Baulcombe T Arazi 2006 Identification of trans-acting siRNAs in moss and an RNA-dependent RNA polymerase required for their biogenesis Plant J 48 511 521
136. G Tang BJ Reinhart DP Bartel PD Zamore 2003 A biochemical framework for RNA silencing in plants Genes Dev 17 49 63
137. H Vaucheret 2006 Post-transcriptional small RNA pathways in plants: mechanisms and regulations Genes Dev 20 759 771
138. H Vaucheret 2008 Plant ARGONAUTES Trends Plant Sci 13 350 358
139. H Vaucheret F Vazquez P Crete DP Bartel 2004 The action of Argonaute1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development Genes Dev 18 1187 1197
140. F Vazquez H Vaucheret R Rajagopalan C Lepers V Gasciolli AC Mallory JL Hilbert DP Bartel P Crété 2004 Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs Mol Cell 16 69 79
141. O Voinnet 2008 Use, tolerance and avoidance of amplified RNA silencing by plants Trends Plant Sci 13 317 328
142. XJ Wang JL Reyes NH Chua T Gaasterland 2004 Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets Genome Biol 5 R65
143. JW Wang R Schwab B Czech E Mica D Weigel 2008 Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana Plant Cell 20 1231 1243
144. L Williams SP Grigg M Xie S Christensen JC Fletcher 2005 Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes Development 132 3657 3668
145. MR Willmann RS Poethig 2005 Time to grow up: the temporal role of smallRNAs in plants Curr Opin Plant Biol 8 548 552
146. MR Willmann RS Poethig 2007 Conservation and evolution of miRNA regulatory programs in plant development Curr Opin Plant Biol 10 503 511
147. G Wu RS Poethig 2006 Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3 Development 133 3539 3547
148. MF Wu Q Tian JW Reed 2006 Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction Development 133 4211 4218
149. Z Xie KD Kasschau JC Carrington 2003 Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation Curr Biol 13 784 789
150. Z Xie LK Johansen AM Gustafson KD Kasschau AD Lellis D Zilberman SE Jacobsen JC Carrington 2004 Genetic and functional diversification of small RNA pathways in plants PloS Biol 2 E104
151. Z Xie E Allen N Fahlgren A Calamar SA Givan JC Carrington 2005 Expression of Arabidopsis MIRNA genes Plant Physiol 138 2145 2154
152. H Yamasaki SE Abdel-Ghany CM Cohu Y Kobayashi T Shikanai M Pilon 2007 Regulation of copper homeostasis by micro-RNA in Arabidopsis J Biol Chem 282 16369 16378
153. Yamasaki H, Hayashi M, Fukazawa M, Kobayashi Y, Shikanai T (2009) SQUAMOSA promoter binding protein-like7 is a central regulator for copper homeostasis in Arabidopsis. Plant Cell (in press)
154. JH Yang SJ Han EK Yoon WS Lee 2006 Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells Nucleic Acids Res 34 1892 1899
155. L Yang Z Liu F Lu A Dong H Huang 2006 SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis Plant J 47 841 850
156. Z Yang YW Ebright B Yu X Chen 2006 HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2- OH of the 3- terminal nucleotide Nucleic Acids Res 34 667 675
157. B Yu Z Yang J Li S Minakhina M Yang RW Padgett R Steward X Chen 2005 Methylation as a crucial step in plant microRNA biogenesis Science 307 932 935
158. B Zhang X Pan CH Cannon GP Cobb TA Anderson 2006 Conservation and divergence of plant microRNA genes Plant J 46 243 259
159. X Zhang IR Henderson C Lu PJ Green SE Jacobsen 2007 Role of RNA polymerase IV in plant small RNA metabolism Proc Natl Acad Sci USA 104 4536 4541
160. L Zhao Y Kim TT Dinh X Chen 2007 miR172 regulates stem cell fate and defines the inner boundary of APETALA3 and PISTILLATA expression domain in Arabidopsis floral meristems Plant J 51 840 849
161. GK Zhou M Kubo R Zhong T Demura ZH Ye 2007 Overexpression of miR165 affects apical meristem formation, organ polarity establishment and vascular development in Arabidopsis Plant Cell Physiol 48 391 404