microRNA biogenesis and function in plants

FEBS Letters

Volumn 579, Issue 26, 2005, Pages 5923-5931

  Chen, Xuemei ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Auxin; DCL1; Developmental transitions; Flower development; HEN1; Leaf development; microRNA; Small interfering RNA

Indexed keywords

METHYLTRANSFERASE; MICRORNA; RIBONUCLEASE III;

ARABIDOPSIS; BIOGENESIS; BIOINFORMATICS; COMPLEX FORMATION; GENE FUNCTION; GENETIC CODE; METHYLATION; PLANT DEVELOPMENT; PRIORITY JOURNAL; PROTEIN ANALYSIS; RNA METABOLISM; RNA SEQUENCE; SHORT SURVEY;

ANIMALS; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CELL CYCLE PROTEINS; DNA METHYLATION; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENES, REPORTER; GENOME, PLANT; INDOLEACETIC ACIDS; MICRORNAS; MODELS, BIOLOGICAL; PLANT LEAVES; PLANT PHYSIOLOGY; RIBONUCLEASE III; RNA, PLANT; RNA, SMALL INTERFERING; SIGNAL TRANSDUCTION;

ANIMALIA; ARABIDOPSIS;

EID: 26944437949     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2005.07.071     Document Type: Short Survey

References (110)

1. V.N. Kim MicroRNA biogenesis: coordinated cropping and dicing Nat. Rev. Mol. Cell Biol. 6 2005 376 385
2. D.P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 2004 281 297
3. A.J. Hamilton, and D.C. Baulcombe A species of small antisense RNA in posttranscriptional gene silencing in plants Science 286 1999 950 952
4. A. Hamilton, O. Voinnet, L. Chappell, and D. Baulcombe Two classes of short interfering RNA in RNA silencing EMBO J. 21 2002 4671 4679
5. Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman, S.E. Jacobsen, and J.C. Carrington Genetic and functional diversification of small RNA pathways in plants PLoS Biol. 2 2004 E104
6. A. Peragine, M. Yoshikawa, G. Wu, H.L. Albrecht, and R.S. Poethig SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis Genes Dev. 18 2004 2368 2379
7. F. Vazquez Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs Mol Cell. 16 2004 69 79
8. E. Allen, Z. Xie, A.M. Gustafson, and J.C. Carrington microRNA-directed phasing during trans-acting siRNA biogenesis in plants Cell 121 2005 207 221
9. Y. Kurihara, and Y. Watanabe Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions Proc. Natl. Acad. Sci. USA 101 2004 12753 12758
10. Y. Lee The nuclear RNase III Drosha initiates microRNA processing Nature 425 2003 415 419
11. A.M. Denli, B.B. Tops, R.H. Plasterk, R.F. Ketting, and G.J. Hannon Processing of primary microRNAs by the microprocessor complex Nature 432 2004 231 235
12. R.I. Gregory, K.P. Yan, G. Amuthan, T. Chendrimada, B. Doratotaj, N. Cooch, and R. Shiekhattar The microprocessor complex mediates the genesis of microRNAs Nature 432 2004 235 240
13. J. Han, Y. Lee, K.H. Yeom, Y.K. Kim, H. Jin, and V.N. Kim The Drosha-DGCR8 complex in primary microRNA processing Genes Dev. 18 2004 3016 3027
14. M. Landthaler, A. Yalcin, and T. Tuschl The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis Curr. Biol. 14 2004 2162 2167
15. H. Zhang, F.A. Kolb, L. Jaskiewicz, E. Westhof, and W. Filipowicz Single processing center models for human Dicer and bacterial RNase III Cell 118 2004 57 68
16. A. Grishok Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing Cell 106 2001 23 34
17. G. Hutvagner, J. McLachlan, A.E. Pasquinelli, E. Balint, T. Tuschl, and P.D. Zamore A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA Science 293 2001 834 838
18. R.F. Ketting, S.E. Fischer, E. Bernstein, T. Sijen, G.J. Hannon, and R.H. Plasterk Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans Genes Dev. 15 2001 2654 2659
19. S.W. Knight, and B.L. Bass A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans Science 293 2001 2269 2271
20. D.S. Schwarz, G. Hutvagner, T. Du, Z. Xu, N. Aronin, and P.D. Zamore Asymmetry in the assembly of the RNAi enzyme complex Cell 115 2003 199 208
21. Y. Lee, K. Jeon, J.T. Lee, S. Kim, and V.N. Kim MicroRNA maturation: stepwise processing and subcellular localization EMBO J. 21 2002 4663 4670
22. M.T. Bohnsack, K. Czaplinski, and D. Gorlich Exportin 5 is a RanGTPdependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs RNA 10 2004 185 191
23. E. Lund, S. Guttinger, A. Calado, J.E. Dahlberg, and U. Kutay Nuclear export of microRNA precursors Science 303 2004 95 98
24. R. Yi, Y. Qin, I.G. Macara, and B.R. Cullen Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs Genes Dev. 17 2003 3011 3016
25. S.E. Jacobsen, M. Running, and E.M. Meyerowitz Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems Development 126 1999 5231 5243
26. A. Ray, J.D. Lang, T. Golden, and S. Ray SHORT INTEGUMENT (SIN1), a gene required for ovule development in Arabidopsis, also controls flowering time Development 122 1996 2631 2638
27. B.W. Schwartz, E.C. Yeung, and D.W. Meinke Disruption of morphogenesis and transformation of the suspensor in abnormal suspensor mutants of Arabidopsis Development 120 1994 3235 3245
28. K.D. Kasschau, Z. Xie, E. Allen, C. Llave, E.J. Chapman, K.A. Krizan, and J.C. Carrington P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction Dev. Cell 4 2003 205 217
29. W. Park, J. Li, R. Song, J. Messing, and X. Chen CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana Curr. Biol. 12 2002 1484 1495
30. B.J. Reinhart, E.G. Weinstein, M.W. Rhoades, B. Bartel, and D.P. Bartel MicroRNAs in plants Genes Dev. 16 2002 1616 1626
31. R. Sunkar, and J.K. Zhu Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis Plant Cell 16 2004 2001 2019
32. A. Khvorova, A. Reynolds, and S.D. Jayasena Functional siRNAs and miRNAs exhibit strand bias Cell 115 2003 209 216
33. M.Y. Park, G. Wu, A. Gonzalez-Sulser, H. Vaucheret, and R.S. Poethig Nuclear processing and export of microRNAs in Arabidopsis Proc. Natl. Acad. Sci. USA 102 2005 3691 3696
34. X.J. Wang, J.L. Reyes, N.H. Chua, and T. Gaasterland Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets Gen. Biol. 5 2004 R65
35. E.J. Chapman, A.I. Prokhnevsky, K. Gopinath, V.V. Dolja, and J.C. Carrington Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step Genes Dev. 18 2004 1179 1186
36. D. Silhavy, A. Molnar, A. Lucioli, G. Szittya, C. Hornyik, M. Tavazza, and J. Burgyan A viral protein suppresses RNA silencing and binds silencing-generated, 21- to 25-nucleotide double-stranded RNAs EMBO J. 21 2002 3070 3080
37. J.M. Vargason, G. Szittya, J. Burgyan, and T.M. Tanaka Hall Size selective recognition of siRNA by an RNA silencing suppressor Cell 115 2003 799 811
38. K. Ye, L. Malinina, and D.J. Patel Recognition of small interfering RNA by a viral suppressor of RNA silencing Nature 426 2003 874 878
39. P. Dunoyer, C.H. Lecellier, E.A. Parizotto, C. Himber, and O. Voinnet Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing Plant Cell 16 2004 1235 1250
40. I. Papp Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors Plant Physiol. 132 2003 1382 1390
41. K.M. Bollman, M.J. Aukerman, M.Y. Park, C. Hunter, T.Z. Berardini, and R.S. Poethig HASTY, the Arabidopsis ortholog of exportin 5/MSN5, regulates phase change and morphogenesis Development 130 2003 1493 1504
42. M.H. Han, S. Goud, L. Song, and N. Fedoroff The Arabidopsis doublestranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation Proc. Natl. Acad. Sci. USA 101 2004 1093 1098
43. F. Vazquez, V. Gasciolli, P. Crete, and H. Vaucheret The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing Curr. Biol. 14 2004 346 351
44. Q. Liu, T.A. Rand, S. Kalidas, F. Du, H.E. Kim, D.P. Smith, and X. Wang R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway Science 301 2003 1921 1925
45. H. Tabara, E. Yigit, H. Siomi, and C.C. Mello The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans Cell 109 2002 861 871
46. S. Boutet Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance Curr. Biol. 13 2003 843 848
47. X. Chen, J. Liu, Y. Cheng, and D. Jia HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower Development 129 2002 1085 1094
48. B. Yu, Z. Yang, J. Li, S. Minakhina, M. Yang, R.W. Padgett, R. Steward, and X. Chen Methylation as a crucial step in plant microRNA biogenesis Science 307 2005 932 935
49. T. Sijen, J. Fleenor, F. Simmer, K.L. Thijssen, S. Parrish, L. Timmons, R.H. Plasterk, and A. Fire On the role of RNA amplification in dsRNA-triggered gene silencing Cell 107 2001 465 476
50. F.E. Vaistij, L. Jones, and D.C. Baulcombe Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase Plant Cell 14 2002 857 867
51. J. Li, Z. Yang, B. Yu, J. Liu, and X. Chen Methylation protects miRNAs and siRNAs from a 3′ end uridylation activity in Arabidopsis Curr. Biol. 15 2005 1501 1507
52. B. Shen, and H.M. Goodman Uridine addition after microRNA-directed cleavage Science 306 2004 997
53. A. Adai, C. Johnson, S. Mlotshwa, S. Archer-Evans, V. Manocha, V. Vance, and V. Sundaresan Computational prediction of miRNAs in Arabidopsis thaliana Gen. Res. 15 2005 78 91
54. E. Bonnet, J. Wuyts, P. Rouze, and Y. Van de Peer Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes Proc. Natl. Acad. Sci. USA 101 2004 11511 11516
55. M.W. Jones-Rhoades, and D.P. Bartel Computational identification of plant microRNAs and their targets, including a stress-induced miRNA Mol. Cell 14 2004 787 799
56. M.W. Rhoades, B.J. Reinhart, L.P. Lim, C.B. Burge, B. Bartel, and D.P. Bartel Prediction of plant microRNA targets Cell 110 2002 513 520
57. R. Sunkar, T. Girke, P.K. Jain, and J.K. Zhu Cloning and characterization of microRNAs from rice Plant Cell 17 2005 1397 1411
58. A.J. Fleming Formation of primordia and phyllotaxy Curr. Opin. Plant Biol. 8 2005 53 58
59. J. Friml Auxin transport - shaping the plant Curr. Opin. Plant Biol. 6 2003 7 12
60. S. Kepinski, and O. Leyser Plant development: auxin in loops Curr. Biol. 15 2005 R208 R210
61. O. Leyser Regulation of shoot branching by auxin Trends Plant Sci. 8 2003 541 545
62. D. Weijers, and G. Jurgens Auxin and embryo axis formation: the ends in sight Curr. Opin. Plant Biol. 8 2005 32 37
63. N. Dharmasiri, S. Dharmasiri, and M. Estelle The F-box protein TIR1 is an auxin receptor Nature 435 2005 441 445
64. S. Kepinski, and O. Leyser The Arabidopsis F-box protein TIR1 is an auxin receptor Nature 435 2005 446 451
65. O. Leyser Molecular genetics of auxin signaling Annu. Rev. Plant Biol. 53 2002 377 398
66. A.W. Woodward, and B. Bartel Auxin: regulation, action, and interaction Ann. Bot. (Lond) 95 2005 707 735
67. B. Bartel, and D.P. Bartel MicroRNAs: at the root of plant development Plant Physiol. 132 2003 709 717
68. A.C. Mallory, D.P. Bartel, and B. Bartel MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes Plant Cell 17 2005 1360 1375
69. H.S. Guo, Q. Xie, J.F. Fei, and N.H. Chua MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development Plant Cell 17 2005 1376 1386
70. M. Aida, T. Ishida, H. Fukaki, H. Fujisawa, and M. Tasaka Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant Plant Cell 9 1997 841 857
71. S. Takada, K. Hibara, T. Ishida, and M. Tasaka The CUP-SHAPED COTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation Development 128 2001 1127 1135
72. C.W. Vroemen, A.P. Mordhorst, C. Albrecht, M.A. Kwaaitaal, and S.C. de Vries The CUP-SHAPED COTYLEDON3 gene is required for boundary and shoot meristem formation in Arabidopsis Plant Cell 15 2003 1563 1577
73. P. Laufs, A. Peaucelle, H. Morin, and J. Traas MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems Development 131 2004 4311 4322
74. A.C. Mallory, D.V. Dugas, D.P. Bartel, and B. Bartel MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs Curr. Biol. 14 2004 1035 1046
75. C.C. Baker, P. Sieber, F. Wellmer, and E.M. Meyerowitz The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis Curr. Biol. 15 2005 303 315
76. J.F. Emery, S.K. Floyd, J. Alvarez, Y. Eshed, N.P. Hawker, A. Izhaki, S.F. Baum, and J.L. Bowman Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes Curr. Biol. 13 2003 1768 1774
77. Y. Eshed, S.F. Baum, J.V. Perea, and J.L. Bowman Establishment of polarity in lateral organs of plants Curr. Biol. 11 2001 1251 1260
78. R.A. Kerstetter, K. Bollman, R.A. Taylor, K. Bomblies, and R.S. Poethig KANADI regulates organ polarity in Arabidopsis Nature 411 2001 706 709
79. J.R. McConnell, J. Emery, Y. Eshed, N. Bao, J. Bowman, and M.K. Barton Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots Nature 411 2001 709 713
80. D. Otsuga, B. DeGuzman, M.J. Prigge, G.N. Drews, and S.E. Clark REVOLUTA regulates meristem initiation at lateral positions Plant J. 25 2001 223 236
81. A.C. Mallory, B.J. Reinhart, M.W. Jones-Rhoades, G. Tang, P.D. Zamore, M.K. Barton, and D.P. Bartel MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region EMBO J. 23 2004 3356 3364
82. N. Bao, K.W. Lye, and M.K. Barton MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome Dev. Cell 7 2004 653 662
83. S.K. Floyd, and J.L. Bowman Gene regulation: ancient microRNA target sequences in plants Nature 428 2004 485 486
84. M.T. Juarez, J.S. Kui, J. Thomas, B.A. Heller, and M.C. Timmermans microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity Nature 428 2004 84 88
85. N.A. McHale, and R.E. Koning MicroRNA-directed cleavage of Nicotiana sylvestris PHAVOLUTA mRNA regulates the vascular cambium and structure of apical meristems Plant Cell 16 2004 1730 1740
86. T. Jack Molecular and genetic mechanisms of floral control Plant Cell 16 Suppl 2004 S1 S17
87. M.J. Aukerman, and H. Sakai Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes Plant Cell 15 2003 2730 2741
88. X. Chen A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development Science 303 2004 2022 2025
89. R. Schwab, J.F. Palatnik, M. Riester, C. Schommer, M. Schmid, and D. Weigel Specific effects of microRNAs on the plant transcriptome Dev. Cell 8 2005 517 527
90. R.C. Lee, R.L. Feinbaum, and V. Ambros The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 Cell 75 1993 843 854
91. B.J. Reinhart, F.J. Slack, M. Basson, A.E. Pasquinelli, J.C. Bettinger, A.E. Rougvie, H.R. Horvitz, and G. Ruvkun The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans Nature 403 2000 901 906
92. B. Wightman, I. Ha, and G. Ruvkun Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans Cell 75 1993 855 862
93. A.A. Millar, and F. Gubler The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development Plant Cell 17 2005 705 721
94. M. Schmid, N.H. Uhlenhaut, F. Godard, M. Demar, R. Bressan, D. Weigel, and J.U. Lohmann Dissection of floral induction pathways using global expression analysis Development 130 2003 6001 6012
95. J.F. Palatnik, E. Allen, X. Wu, C. Schommer, R. Schwab, J.C. Carrington, and D. Weigel Control of leaf morphogenesis by microRNAs Nature 425 2003 257 263
96. P. Achard, A. Herr, D.C. Baulcombe, and N.P. Harberd Modulation of floral development by a gibberellin-regulated microRNA Development 131 2004 3357 3365
97. R.A. Kerstetter, and R.S. Poethig The specification of leaf identity during shoot development Annu. Rev. Cell. Dev. Biol. 14 1998 373 398
98. N. Lauter, A. Kampani, S. Carlson, M. Goebel, and S.P. Moose microRNA172 down-regulates glossy15 to promote vegetative phase change in maize Proc. Natl. Acad. Sci. USA 2005
99. T. Dalmay, A. Hamilton, S. Rudd, S. Angell, and D.C. Baulcombe 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 2000 543 553
100. C. Hunter, H. Sun, and R.S. Poethig The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member Curr. Biol. 13 2003 1734 1739
101. P. Mourrain Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance Cell 101 2000 533 542
102. U. Nath, B.C. Crawford, R. Carpenter, and E. Coen Genetic control of surface curvature Science 299 2003 1404 1407
103. Z. Xie, K.D. Kasschau, and J.C. Carrington Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation Curr. Biol. 13 2003 784 789
104. H. Vaucheret, F. Vazquez, P. Crete, and D.P. Bartel The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development Genes Dev. 18 2004 1187 1197
105. B.C. Yoo, F. Kragler, E. Varkonyi-Gasic, V. Haywood, S. Archer-Evans, Y.M. Lee, T.J. Lough, and W.J. Lucas A systemic small RNA signaling system in plants Plant Cell 16 2004 1979 2000
106. C.A. Kidner, and R.A. Martienssen Spatially restricted microRNA directs leaf polarity through ARGONAUTE1 Nature 428 2004 81 84
107. E.A. Parizotto, P. Dunoyer, N. Rahm, C. Himber, and O. Voinnet In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA Genes Dev. 18 2004 2237 2242
108. V. Gasciolli, A.C. Mallory, D.P. Bartel, and H. Vaucheret Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs Curr. Biol. 15 2005 1494 1500
109. Xie, Z., Allen, E., Wilken, A. and Carrington, J.C. (2005) DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. PNAS (in press).
110. Yoshikawa, M., Peragine, A., Park, M.Y. and Poethig, R.S. (2005) A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev. (in press).