MicroRNAs and their regulatory roles in plants

Annual Review of Plant Biology

Volumn 57, Issue , 2006, Pages 19-53

  Jones Rhoades, Matthew W ^a   Bartel, David P ^a   Bartel, Bonnie ^b  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b RICE UNIVERSITY   (United States)

Author keywords

Noncoding RNAs; Plant development; Post transcriptional gene regulation; RNA silencing

Indexed keywords

MICRORNA;

GENE SILENCING; GENETICS; GENOME; PHYSIOLOGY; PLANT; PLANT GENOME; REVIEW; RNA PROCESSING;

GENE SILENCING; GENOME, PLANT; MICRORNAS; PLANTS; RNA PROCESSING, POST-TRANSCRIPTIONAL;

ANIMALIA;

EID: 33645525893     PISSN: 15435008     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.arplant.57.032905.105218     Document Type: Review

References (165)

1. Achard P, Herr A, Baulcombe DC, Harberd NP. 2004. Modulation of floral development by a gibberellin-regulated microRNA. Development 131:3357-65
2. Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, et al. 2005. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res. 15:78-91
3. Allen E, Xie Z, Gustafson AM, Carrington JC. 2005. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207-21
4. Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Carrington JC. 2004. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat. Genet. 36:1282-90
5. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, et al. 2003. A uniform system for microRNA annotation. RNA 9:277-79
6. 5a. Arazi T, Talmor-Neiman M, Stav R, Riese M, Huijser P, Baulcombe DC. 2005. Cloning and characterization of micro-RNAs from moss. Plant J. 43:837-48
7. 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
8. Axtell MJ, Bartel DP. 2005. Antiquity of microRNAs and their targets in land plants. Plant Cell 17:1658-73
9. Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, et al. 2005. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122:553-63
10. Baker CC, Sieber P, Wellmer F, Meyerowitz EM. 2005. The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Curr. Biol. 15:303-15
11. Bao N, Lye KW, 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
12. Bao W, O'Malley DM, Whetten R, Sederoff RR. 1993. A laccase associated with lignification in Loblolly Pine xylem. Science 260:672-74
13. Bartel B. 2005. MicroRNAs directing siRNA biogenesis. Nat. Struct. Mol. Biol. 12:569-71
14. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-97
15. Baskerville S, Bartel DP. 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11:241-47
16. Baulcombe D. 2004. RNA silencing in plants. Nature 431:356-63
17. Baumberger N, Baulcombe DC. 2005. Arabidopsis ARGONAUTE1 is an RNA slicer that selectively recruits microRNAs and short interfering RNAs. Proc. Natl. Acad. Sci. USA 102:11928-33
18. Beclin C, Boutet S, Waterhouse P, Vaucheret H. 2002. A branched pathway for transgene-induced RNA silencing in plants. Curr. Biol. 12:684-88
19. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S et al. 2005. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet 37:766-70
20. Bernstein E, Caudy AA, Hammond SM, Hannon GJ. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363-66
21. 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. 17:170-80
22. 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 130:1493-504
23. Bonnet E, Wuyts J, Rouze P, Van de Peer Y. 2004. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc. Natl. Acad. Sci. USA 101:11511-16
24. Boutet S, Vazquez F, Liu J, Beclin C, Fagard M, et al. 2003. Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Curr. Biol. 13:843-48
25. Brennecke J, Stark A, Russell RB, Cohen SM. 2005. Principles of microRNA-target recognition. PLoS Biol. 3:e85
26. Carmell MA, Xuan Z, Zhang MQ, Hannon GJ. 2002. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev. 16:2733-42
27. Chapman EJ, Prokhnevsky AI, Gopinath K, Dolja VV, Carrington JC. 2004. Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes Dev. 18:1179-86
28. Chaw SM, Chang CC, Chen HL, Li WH. 2004. Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J. Mol. Evol. 58:424-41
29. Chen J, Li WX, Xie D, Peng JR, Ding SW. 2004. Viral virulence protein suppresses RNA silencing-mediated defense but upregulates the role of microRNA in host gene expression. Plant Cell 16:1302-13
30. Chen X. 2004. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303:2022-25
31. Chen X, Liu J, Cheng Y, Jia D. 2002. HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower. Development 129:1085-94
32. Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC. 2000. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101:543-53
33. Dharmasiri N, Dharmasiri S, Estelle M. 2005. The F-box protein TIR1 is an auxin receptor. Nature 435:441-45
34. Dharmasiri N, Dharmasiri S, Weijers D, Lechner E, Yamada M, et al. 2005. Plant development is regulated by a family of auxin receptor F box proteins. Dev. Cell 9:109-19
35. Doench JG, Petersen CP, Sharp PA. 2003. siRNAs can function as miRNAs. Genes Dev. 17:438-42
36. Doench JG, Sharp PA. 2004. Specificity of microRNA target selection in translational repression. Genes Dev. 18:504-11
37. Dunoyer P, Lecellier CH, Parizotto EA, Himber C, Voinnet O. 2004. Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing. Plant Cell 16:1235-50
38. 36a. Ebhardt HA, Thi EP, Wang MB, Unrau PJ. 2005. Extensive 3′ modification of plant small RNAs is modulated by helper component-proteinase expression. Proc. Natl. Acad. Sci. USA 102:13398-403
39. Elbashir SM, Lendeckel W, Tuschl T. 2001. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15:188-200
40. Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T. 2001. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20:6877-88
41. Emery JF, Floyd SK, Alvarez J, Eshed Y, Hawker NP, et al. 2003. Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr. Biol. 13:1768-74
42. Floyd SK, Bowman JL. 2004. Gene regulation: ancient microRNA target sequences in plants. Nature 428:485-86
43. 40a. Fujii H, Chiou TJ, Lin SI, Aung K, Zhu JK. 2005. A miRNA involved in phosphate-starvation response in Arabidopsis. Curr. Biol. 15:2038-43
44. Gasciolli V, Mallory AC, Bartel DP, Vaucheret H. 2005. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr. Biol. 15:1494-500
45. Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, et al. 2005. MicroRNAs regulate brain morphogenesis in zebrafish. Science 308:833-38
46. Griffiths-Jones S. 2004. The microRNA registry. Nucleic Acids Res. 32: D109-11
47. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, et al. 2001. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106:23-34
48. 44a. Guddeti S, Zhang de C, Li AL, Leseberg CH, Kang H, et al. 2005. Molecular evolution of the rice miR395 gene family. Cell Res. 15:631-38
49. Guo HS, Xie Q, Fei JF, Chua NH. 2005. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 17:1376-86
50. Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, Kasschau KD. 2005. ASRP: the Arabidopsis Small RNA Project Database. Nucleic Acids Res. 33:D637-40
51. Hamilton AJ, Baulcombe, DC. 1999. A novel species of small antisense RNA in post-transcriptional gene silencing. Science 286:950-52
52. Hammond SM, Bernstein E, Beach D, Hannon GJ. 2000. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404:293-96
53. Han MH, Goud S, Song L, Fedoroff N. 2004. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl. Acad. Sci. USA 101:1093-98
54. 49a. Herr AJ, Jensen MB, Dalmay T, Baulcombe DC. 2005. RNA polymerase IV directs silencing of endogenous DNA. Science 308:118-20
55. Hiraguri A, Itoh R, Kondo N, Nomura Y, Aizawa D, et al. 2005. Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana. Plant Mol. Biol. 57:173-88
56. Hunter C, Sun H, Poethig RS. 2003. The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member. Curr. Biol. 13:1734-39
57. Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD. 2001. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293:834-38
58. Jones-Rhoades MW, Bartel DP. 2004. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14:787-99
59. Juarez MT, Kui JS, Thomas J, Heller BA, Timmermans MC. 2004. microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature 428:84-88
60. 54a. Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, et al. 2005. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat. Genet. 37:761-65
61. Kasschau KD, Xie Z, Allen E, Llave C, Chapman EJ, et al. 2003. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev. Cell 4:205-17
62. Kepinski S, Leyser O. 2005. The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature 435:446-51
63. Khvorova A, Reynolds A, Jayasena SD. 2003. Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209-16
64. Kidner CA, Martienssen RA. 2004. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 428:81-84
65. Kim J, Jung JH, Reyes JL, Kim YS, Kim SY, et al. 2005. microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant J. 42:84-94
66. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, et al. 2005. Combinatorial microRNA target predictions. Nat. Genet. 37:495-500
67. Kurihara Y, Watanabe Y. 2004. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. USA 101:12753-58
68. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. 2001. Identification of novel genes coding for small expressed RNAs. Science 294:853-58
69. Lai EC, Tomancak P, Williams RW, Rubin GM. 2003. Computational identification of Drosophila microRNA genes. Genome Biol. 4:R42
70. Lau NC, Lim LP, Weinstein EG, Bartel DP. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858-62
71. Laufs P, Peaucelle A, Morin H, Traas J. 2004. MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development 131:4311-22
72. Lee RC, Ambros V. 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science 294:862-64
73. Lee RC, Feinbaum RL, Ambros V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843-54
74. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, et al. 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature 425:415-19
75. Lee Y, Kim M, Han J, Yeom KH, Lee S, et al. 2004. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23:4051-60
76. Lewis BP, Burge CB, Bartel DP. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15-20
77. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. 2003. Prediction of mammalian microRNA targets. Cell 115:787-98
78. 71a. 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. 15:1501-7
79. Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP. 2003. Vertebrate microRNA genes. Science 299:1540
80. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769-73
81. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, et al. 2003. The microRNAs of Caenorhabditis elegans. Genes Dev. 17:991-1008
82. Lingel A, Simon B, Izaurralde E, Sattler M. 2003. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 426:465-69
83. 75a. Liu B, Li P, Li X, Liu C, Cao S, et al. 2005. Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice. Plant Physiol. 139:296-305
84. Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, et al. 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305:1437-41
85. Liu J, Valencia-Sanchez MA, Hannon GJ, Parker R. 2005. MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat. Cell Biol. 7:719-23
86. Llave C, Kasschau KD, Rector MA, Carrington JC. 2002. Endogenous and silencing-associated small RNAs in plants. Plant Cell 14:1605-19
87. Llave C, Xie Z, Kasschau KD, Carrington JC. 2002. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297:2053-56
88. Lu C, Fedoroff N. 2000. A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin. Plant Cell 12:2351-66
89. 80a. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ. 2005. Elucidation of the small RNA component of the transcriptome. Science 309:1525-26
90. Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL. 2005. Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17:2186-203
91. Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U. 2004. Nuclear export of microRNA precursors. Science 303:95-98
92. Lynn K, Fernandez A, Aida M, Sedbrook J, Tasaka M, et al. 1999. The PIN-HEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene. Development 126:469-81
93. Mallory AC, Bartel DP, Bartel B. 2005. MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 17:1360-75
94. Mallory AC, Dugas DV, Bartel DP, Bartel B. 2004. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr. Biol. 14:1035-46
95. Mallory AC, Reinhart BJ, Bartel D, Vance VB, Bowman LH. 2002. A viral suppressor of RNA silencing differentially regulates the accumulation of short interfering RNAs and micro-RNAs in tobacco. Proc. Natl. Acad. Sci. USA 99:15228-33
96. 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
97. 87a. 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 123:607-20
98. Matzke M, Aufsatz W, Kanno T, Daxinger L, Papp I, et al. 2004. Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim. Biophys. Acta 1677:129-41
99. McConnell JR, Barton MK. 1998. Leaf polarity and meristem formation in Arabidopsis. Development 125:2935-42
100. McConnell JR, Emery J, Eshed Y, Bao N, Bowman J, Barton MK. 2001. Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. Nature 411:709-13
101. Mette MF, Aufsatz W, Kanno T, Daxinger L, Rovina P, et al. 2005. Analysis of double-stranded RNA and small RNAs involved in RNA-mediated transcriptional gene silencing. Methods Mol. Biol. 309:61-82
102. Mette MF, van der Winden J, Matzke M, Matzke AJ. 2002. Short RNAs can identify new candidate transposable element families in Arabidopsis. Plant Physiol. 130:6-9
103. Millar AA, Gubler F. 2005. The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell 17:705-21
104. Morel JB, Godon C, Mourrain P, Beclin C, Boutet S, et al. 2002. Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell 14:629-39
105. Moss EG, Lee RC, Ambros V 1997. The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell 88:637-46
106. Motamedi MR, Verdel A, Colmenares SU, Gerber SA, Gygi SP, Moazed D. 2004. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119:789-802
107. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, et al. 2002. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 16:720-28
108. Mourrain P, Beclin C, Elmayan T, Feuerbach F, Godon C, et al. 2000. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101:533-42
109. Moussian B, Haecker A, Laux T. 2003. ZWILLE buffers meristem stability in Arabidopsis thaliana. Dev. Genes Evol. 213:534-40
110. Moussian B, Schoof H, Haecker A, Jurgens G, Laux T. 1998. Role of the ZWILLE gene in the regulation of central shoot meristem cell fate during Arabidopsis embryogenesis. EMBO J. 17:1799-809
111. Nelson JM, Lane B, Freeling M. 2002. Expression of a mutant maize gene in the ventral leaf epidermis is sufficient to signal a switch of the leafs dorsoventral axis. Development 129:4581-89
112. Noma K, Sugiyama T, Cam H, Verdel A, Zofall M, et al. 2004. RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nat. Genet 36:1174-80
113. 101a. Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, Pikaard CS. 2005. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120:613-22
114. Olsen PH, Ambros V. 1999. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216:671-80
115. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, et al. 2003. Control of leaf morphogenesis by microRNAs. Nature 425:257-63
116. Papp I, Mette MF, Aufsatz W, Daxinger L, Schauer SE, et al. 2003. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol. 132:1382-90
117. 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
118. Park MY, Wu G, Gonzalez-Sulser A, Vaucheret H, Poethig RS. 2005. Nuclear processing and export of microRNAs in Arabidopsis. Proc. Natl. Acad. Sci. USA 102:3691-96
119. 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
120. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, et al. 2000. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408:86-89
121. Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS. 2004. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of transacting siRNAs in Arabidopsis. Genes Dev. 18:2368-79
122. Pillai RS, Artus CG, Filipowicz W. 2004. Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis. RNA 10:1518-25
123. Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, et al. 2005. Inhibition of translational initiation by let-7 microRNA in human cells. Science 309:1573-76
124. Qi Y, Denli AM, Hannon GJ. 2005. Biochemical specialization within Arabidopsis RNA silencing pathways. Mol. Cell 19:421-28
125. Reinhart BJ, Bartel DP. 2002. Small RNAs correspond to centromere heterochromatic repeats. Science 297:1831
126. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, et al. 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901-6
127. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. 2002. MicroRNAs in plants. Genes Dev. 16:1616-26
128. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. 2002. Prediction of plant microRNA targets. Cell 110:513-20
129. Schauer SE, Jacobsen SE, Meinke DW, Ray A. 2002. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci. 7:487-91
130. 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
131. 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
132. Sen GL, Blau HM. 2005. Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies. Nat. Cell Biol. 7:633-36
133. Slack FJ, Basson M, Liu Z, Ambros V, Horvitz HR, Ruvkun G. 2000. The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol. Cell 5:659-69
134. Song JJ, Liu J, Tolia NH, Schneiderman J, Smith SK, Martienssen RA, et al. 2003. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat. Struct. Biol. 10:1026-32
135. Song JJ, Smith SK, Hannon GJ, Joshua-Tor L. 2004. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305:1434-37
136. Souret FF, Kastenmayer JP, Green PJ. 2004. AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol. Cell 15:173-83
137. Sunkar R, Girke T, Jain PK, Zhu JK. 2005. Cloning and characterization of microRNAs from rice. Plant Cell 17:1397-411
138. Sunkar R, Girke T, Zhu JK. 2005. Identification and characterization of endogenous small interfering RNAs from rice. Nucleic Acids Res. 33:4443-54
139. Sunkar R, Zhu JK. 2004. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001-19
140. Tang G, Reinhart BJ, Bartel DP, Zamore PD. 2003. A biochemical framework for RNA silencing in plants. Genes Dev. 17:49-63
141. Telfer A, Poethig RS. 1998. HASTY: a gene that regulates the timing of shoot maturation in Arabidopsis thaliana. Development 125:1889-98
142. Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD. 2004. A protein sensor for siRNA asymmetry. Science 306:1377-80
143. Vaucheret H, Vazquez F, Crete P, Bartel DP. 2004. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev. 18:1187-97
144. Vazquez F, Gasciolli V, Crete P, Vaucheret H. 2004. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr. Biol. 14:346-51
145. Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, et al. 2004. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell 16:69-79
146. Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, et al. 2004. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303:672-76
147. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833-37
148. Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY. 2005. Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell 17:2204-16
149. Wang XJ, Reyes JL, Chua NH, Gaasterland T. 2004. Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol. 5:R65
150. Wightman B, Ha I, Ruvkun G. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75:855-62
151. Williams L, Grigg SP, Xie M, Christensen S, Fletcher JC. 2005. Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes. Development 132:3657-68
152. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, et al. 2005. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434:338-45
153. Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC. 2005. Expression of Arabidopsis MIRNA genes. Plant Physiol. 138:2145-54
154. 141a. Xie Z, Allen E, Wilken A, Carrington JC. 2005. DICER-LIKE 4 functions in transacting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 102:12984-89
155. Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, et al. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2:E104
156. Xie Z, Kasschau KD, Carrington JC. 2003. Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr. Biol. 13:784-89
157. Yan KS, Yan S, Farooq A, Han A, Zeng L, Zhou MM. 2003. Structure and conserved RNA binding of the PAZ domain. Nature 426:468-74
158. Yekta S, Shih IH, Bartel DP. 2004. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304:594-96
159. Yi R, Qin Y, Macara IG, Cullen BR. 2003. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev. 17:3011-16
160. 146a. 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
161. Yu B, Yang Z, Li J, Minakhina S, Yang M, et al. 2005. Methylation as a crucial step in plant microRNA biogenesis. Science 307:932-35
162. 147a. Zamore, PD, Tuschl, T, Sharp, PA, Bartel, DP. 2000. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101:25-33
163. Zhong R, Ye ZH. 2004. Amphivasal vascular bundle 1, a gain-of-function mutation of the IFL1/REV gene, is associated with alterations in the polarity of leaves, stems and carpels. Plant Cell Physiol. 45:369-85
164. Zilberman D, Cao X, Jacobsen SE. 2003. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299:716-19
165. Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr. Biol. 14:1214-20