Small RNAs in flower development

European Journal of Cell Biology

Volumn 89, Issue 2-3, 2010, Pages 250-257

  Wollmann, Heike ^a   Weigel, Detlef ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

Flower development; Mechanisms; Plant; SRNAs

Indexed keywords

MICRORNA; SMALL INTERFERING RNA; TRANSCRIPTION FACTOR;

EPIGENETICS; FLOWER DEVELOPMENT; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE REGULATORY NETWORK; GENE TARGETING; NONHUMAN; PRIORITY JOURNAL; PROTEIN MODIFICATION; PROTEIN STABILITY; REGULATORY RNA SEQUENCE; RNA ANALYSIS; SHORT SURVEY; SUBSPECIES; TRANSCRIPTION REGULATION;

ANIMALS; FLOWERS; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; GENE SILENCING; MICRORNAS; RIBONUCLEASE III; TRANSCRIPTION FACTORS;

ANIMALIA;

EID: 77149143214     PISSN: 01719335     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ejcb.2009.11.004     Document Type: Short Survey

References (152)

1. Allen E., Xie Z., Gustafson A.M., Carrington J.C. MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005, 121:207-221.
2. Allen R.S., Li J., Stahle M.I., Dubroue A., Gubler F., Millar A.A. Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. Proc. Natl. Acad. Sci. USA 2007, 104:16371-16376.
3. Alvarez-Venegas R., Pien S., Sadder M., Witmer X., Grossniklaus U., Avramova Z. ATX-1, an Arabidopsis homolog of trithorax, activates flower homeotic genes. Curr. Biol. 2003, 13:627-637.
4. Aukerman M.J., Sakai H. Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 2003, 15:2730-2741.
5. Axtell M.J., Bartel D.P. Antiquity of microRNAs and their targets in land plants. Plant Cell 2005, 17:1658-1673.
6. Bagga S., Bracht J., Hunter S., Massirer K., Holtz J., Eachus R., Pasquinelli A.E. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 2005, 122:553-563.
7. Baker C.C., Sieber P., Wellmer F., Meyerowitz E.M. The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Curr. Biol. 2005, 15:303-315.
8. Baskerville S., Bartel D.P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 2005, 11:241-247.
9. Baulcombe D. RNA silencing in plants. Nature 2004, 431:356-363.
10. Behm-Ansmant I., Rehwinkel J., Doerks T., Stark A., Bork P., Izaurralde E. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev. 2006, 20:1885-1898.
11. Bernstein E., Caudy A.A., Hammond S.M., Hannon G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001, 409:363-366.
12. Bohnsack M.T., Czaplinski K., Görlich D. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 2004, 10:185-191.
13. Bomblies K., Dagenais N., Weigel D. Redundant enhancers mediate transcriptional repression of AGAMOUS by APETALA2. Dev. Biol. 1999, 216:260-264.
14. Borchert G.M., Lanier W., Davidson B.L. RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol. 2006, 13:1097-1101.
15. Bowman J.L., Smyth D.R., Meyerowitz E.M. Genes directing flower development in Arabidopsis. Plant Cell 1989, 1:37-52.
16. Brennecke J., Stark A., Russell R.B., Cohen S.M. Principles of microRNA-target recognition. PLoS Biol. 2005, 3:e85.
17. Brennecke J., Aravin A.A., Stark A., Dus M., Kellis M., Sachidanandam R., Hannon G.J. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 2007, 128:1089-1103.
18. Brodersen P., Sakvarelidze-Achard L., Bruun-Rasmussen M., Dunoyer P., Yamamoto Y.Y., Sieburth L., Voinnet O. Widespread translational inhibition by plant miRNAs and siRNAs. Science 2008, 320:1185-1190.
19. Carrington J.C., Ambros V. Role of microRNAs in plant and animal development. Science 2003, 301:336-338.
20. Cerutti H., Casas-Mollano J.A. On the origin and functions of RNA-mediated silencing: from protists to man. Curr. Genet. 2006, 50:81-99.
21. Chapman E.J., Carrington J.C. Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet. 2007, 8:884-896.
22. Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 2004, 303:2022-2025.
23. Chendrimada T.P., Gregory R.I., Kumaraswamy E., Norman J., Cooch N., Nishikura K., Shiekhattar R. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 2005, 436:740-744.
24. Chory J., Ecker J.R., Briggs S., Caboche M., Coruzzi G.M., Cook D., Dangl J., Grant S., Guerinot M.L., Henikoff S., Martienssen R., Okada K., Raikhel N.V., Somerville C.R., Weigel D. National Science Foundation-Sponsored Workshop Report: "The 2010 Project" functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them. Plant Physiol. 2000, 123:423-426.
25. Chuck G., Meeley R., Irish E., Sakai H., Hake S. The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/indeterminate spikelet1. Nat. Genet. 2007, 39:1517-1521.
26. Coen E.S., Meyerowitz E.M. The war of the whorls: genetic interactions controlling flower development. Nature 1991, 353:31-37.
27. Denli A.M., Tops B.B., Plasterk R.H., Ketting R.F., Hannon G.J. Processing of primary microRNAs by the Microprocessor complex. Nature 2004, 432:231-235.
28. Deyholos M.K., Sieburth L.E. Separable whorl-specific expression and negative regulation by enhancer elements within the AGAMOUS second intron. Plant Cell 2000, 12:1799-1810.
29. Didiano D., Hobert O. Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat. Struct. Mol. Biol. 2006, 13:849-851.
30. Doench J.G., Sharp P.A. Specificity of microRNA target selection in translational repression. Genes Dev. 2004, 18:504-511.
31. Dong Z., Han M.H., Fedoroff N. The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc. Natl. Acad. Sci. USA 2008, 105:9970-9975.
32. Drews G.N., Bowman J.L., Meyerowitz E.M. Negative regulation of the Arabidopsis homeotic gene AGAMOUS by the APETALA2 product. Cell 1991, 65:991-1002.
33. Dugas D.V., Bartel B. Sucrose induction of Arabidopsis miR398 represses two Cu/Zn superoxide dismutases. Plant Mol. Biol. 2008, 67:403-417.
34. Eulalio A., Huntzinger E., Izaurralde E. Getting to the root of miRNA-mediated gene silencing. Cell 2008, 132:9-14.
35. Fang Y., Spector D.L. Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Curr. Biol. 2007, 17:818-823.
36. Feinbaum R., Ambros V. The timing of lin-4 RNA accumulation controls the timing of postembryonic developmental events in Caenorhabditis elegans. Dev. Biol. 1999, 210:87-95.
37. Floyd S.K., Bowman J.L. Gene regulation: ancient microRNA target sequences in plants. Nature 2004, 428:485-486.
38. Förstemann K., Tomari Y., Du T., Vagin V.V., Denli A.M., Bratu D.P., Klattenhoff C., Theurkauf W.E., Zamore P.D. Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol. 2005, 3:e236.
39. Förstemann K., Horwich M.D., Wee L., Tomari Y., Zamore P.D. Drosophila microRNAs are sorted into functionally distinct Argonaute complexes after production by Dicer-1. Cell 2007, 130:287-297.
40. Franco-Zorrilla J.M., Valli A., Todesco M., Mateos I., Puga M.I., Rubio-Somoza I., Leyva A., Weigel D., Garcia J.A., Paz-Ares J. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet. 2007, 39:1033-1037.
41. Gandikota M., Birkenbihl R.P., Hohmann S., Cardon G.H., Saedler H., Huijser P. 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 2007, 49:683-693.
42. Gasciolli V., Mallory A.C., Bartel D.P., Vaucheret H. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr. Biol. 2005, 15:1494-1500.
43. Giraldez A.J., Mishima Y., Rihel J., Grocock R.J., Van Dongen S., Inoue K., Enright A.J., Schier A.F. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 2006, 312:75-79.
44. Gregory B.D., O'Malley R.C., Lister R., Urich M.A., Tonti-Filippini J., Chen H., Millar A.H., Ecker J.R. A link between RNA metabolism and silencing affecting Arabidopsis development. Dev. Cell 2008, 14:854-866.
45. Gregory R.I., Yan K.P., Amuthan G., Chendrimada T., Doratotaj B., Cooch N., Shiekhattar R. The microprocessor complex mediates the genesis of microRNAs. Nature 2004, 432:235-240.
46. Gregory R.I., Chendrimada T.P., Cooch N., Shiekhattar R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 2005, 123:631-640.
47. Grimson A., Farh K.K., Johnston W.K., Garrett-Engele P., Lim L.P., Bartel D.P. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 2007, 27:91-105.
48. Grimson A., Srivastava M., Fahey B., Woodcroft B.J., Chiang H.R., King N., Degnan B.M., Rokhsar D.S., Bartel D.P. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 2008, 455:1193-1197.
49. Grishok A., Pasquinelli A.E., Conte D., Li N., Parrish S., Ha I., Baillie D.L., Fire A., Ruvkun G., Mello C.C. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 2001, 106:23-34.
50. Grosshans H., Slack F.J. Micro-RNAs: small is plentiful. J. Cell Biol. 2002, 156:17-21.
51. Gunawardane L.S., Saito K., Nishida K.M., Miyoshi K., Kawamura Y., Nagami T., Siomi H., Siomi M.C. A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila. Science 2007, 315:1587-1590.
52. Hammond S.M., Bernstein E., Beach D., Hannon G.J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 2000, 404:293-296.
53. Han J., Lee Y., Yeom K.H., Kim Y.K., Jin H., Kim V.N. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev. 2004, 18:3016-3027.
54. Han M.H., Goud S., Song L., Fedoroff N. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl. Acad. Sci. USA 2004, 101:1093-1098.
55. Han J., Lee Y., Yeom K.H., Nam J.W., Heo I., Rhee J.K., Sohn S.Y., Cho Y., Zhang B.T., Kim V.N. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 2006, 125:887-901.
56. Hutvagner G., Zamore P.D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 2002, 297:2056-2060.
57. Hutvagner G., McLachlan J., Pasquinelli A.E., Balint E., Tuschl T., Zamore P.D. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 2001, 293:834-838.
58. Jiang F., Ye X., Liu X., Fincher L., McKearin D., Liu Q. Dicer-1 and R3D1-L catalyze microRNA maturation in Drosophila. Genes Dev. 2005, 19:1674-1679.
59. Jing Q., Huang S., Guth S., Zarubin T., Motoyama A., Chen J., Di Padova F., Lin S.C., Gram H., Han J. Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell 2005, 120:623-634.
60. Jofuku K.D., den Boer B.G., Van Montagu M., Okamuro J.K. Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 1994, 6:1211-1225.
61. Jones-Rhoades M.W., Bartel D.P., Bartel B. MicroRNAS and their regulatory roles in plants. Annu. Rev. Plant Biol. 2006, 57:19-53.
62. Jung J.H., Seo Y.H., Seo P.J., Reyes J.L., Yun J., Chua N.H., Park C.M. The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell 2007, 19:2736-2748.
63. Ketting R.F., Fischer S.E., Bernstein E., Sijen T., Hannon G.J., Plasterk R.H. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 2001, 15:2654-2659.
64. Khvorova A., Reynolds A., Jayasena S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell 2003, 115:209-216.
65. Kim Y.K., Kim V.N. Processing of intronic microRNAs. EMBO J. 2007, 26:775-783.
66. Kinch, L.N., Grishin, N.V., 2009. The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif. Biol. Direct 4, 2.
67. m7G cap binding-like motif within human Ago2 represses translation. Cell 2007, 129:1141-1151.
68. Kobayashi Y., Weigel D. Move on up, it's time for change - mobile signals controlling photoperiod-dependent flowering. Genes Dev 2007, 21:2371-2384.
69. Kozak M. Faulty old ideas about translational regulation paved the way for current confusion about how microRNAs function. Gene 2008, 423:108-115.
70. Kurihara Y., Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. USA 2004, 101:12753-12758.
71. Kurihara Y., Takashi Y., Watanabe Y. The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 2006, 12:206-212.
72. Lagos-Quintana M., Rauhut R., Lendeckel W., Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 2001, 294:853-858.
73. Lagos-Quintana M., Rauhut R., Yalcin A., Meyer J., Lendeckel W., Tuschl T. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 2002, 12:735-739.
74. Lai E.C., Tomancak P., Williams R.W., Rubin G.M. Computational identification of Drosophila microRNA genes. Genome Biol. 2003, 4:R42.
75. Landthaler M., Yalcin A., Tuschl T. The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr. Biol 2004, 14:2162-2167.
76. Lau N.C., Lim L.P., Weinstein E.G., Bartel D.P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 2001, 294:858-862.
77. Laubinger S., Sachsenberg T., Zeller G., Busch W., Lohmann J.U., Rätsch G., Weigel D. 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 2008, 105:8795-8800.
78. Laufs P., Peaucelle A., Morin H., Traas J. MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development 2004, 131:4311-4322.
79. Lee R.C., Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science 2001, 294:862-864.
80. Lee R.C., Feinbaum R.L., Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75:843-854.
81. Lee Y., Jeon K., Lee J.T., Kim S., Kim V.N. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 2002, 21:4663-4670.
82. Lee Y., Ahn C., Han J., Choi H., Kim J., Yim J., Lee J., Provost P., Radmark O., Kim S., Kim V.N. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003, 425:415-419.
83. Lee Y., Kim M., Han J., Yeom K.H., Lee S., Baek S.H., Kim V.N. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 2004, 23:4051-4060.
84. Lee Y.S., Nakahara K., Pham J.W., Kim K., He Z., Sontheimer E.J., Carthew R.W. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 2004, 117:69-81.
85. Lee Y., Hur I., Park S.Y., Kim Y.K., Suh M.R., Kim V.N. The role of PACT in the RNA silencing pathway. EMBO J. 2006, 25:522-532.
86. Lim L.P., Lau N.C., Weinstein E.G., Abdelhakim A., Yekta S., Rhoades M.W., Burge C.B., Bartel D.P. The microRNAs of Caenorhabditis elegans. Genes Dev. 2003, 17:991-1008.
87. Lim L.P., Lau N.C., Garrett-Engele P., Grimson A., Schelter J.M., Castle J., Bartel D.P., Linsley P.S., Johnson J.M. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 2005, 433:769-773.
88. Lingel A., Sattler M. Novel modes of protein-RNA recognition in the RNAi pathway. Curr. Opin. Struct. Biol. 2005, 15:107-115.
89. Liu J. Control of protein synthesis and mRNA degradation by microRNAs. Curr. Opin. Cell Biol. 2008, 20:214-221.
90. Liu J., Carmell M.A., Rivas F.V., Marsden C.G., Thomson J.M., Song J.J., Hammond S.M., Joshua-Tor L., Hannon G.J. Argonaute2 is the catalytic engine of mammalian RNAi. Science 2004, 305:1437-1441.
91. Lobbes D., Rallapalli G., Schmidt D.D., Martin C., Clarke J. SERRATE: a new player on the plant microRNA scene. EMBO Rep. 2006, 7:1052-1058.
92. Lohmann J.U., Weigel D. Building beauty: the genetic control of floral patterning. Dev. Cell 2002, 2:135-142.
93. Lund E., Guttinger S., Calado A., Dahlberg J.E., Kutay U. Nuclear export of microRNA precursors. Science 2004, 303:95-98.
94. Ma J.B., Yuan Y.R., Meister G., Pei Y., Tuschl T., Patel D.J. Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 2005, 434:666-670.
95. MacRae I.J., Doudna J.A. Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr. Opin. Struct. Biol. 2007, 17:138-145.
96. MacRae I.J., Zhou K., Li F., Repic A., Brooks A.N., Cande W.Z., Adams P.D., Doudna J.A. Structural basis for double-stranded RNA processing by Dicer. Science 2006, 311:195-198.
97. Mandel M.A., Bowman J.L., Kempin S.A., Ma H., Meyerowitz E.M., Yanofsky M.F. Manipulation of flower structure in transgenic tobacco. Cell 1992, 71:133-143.
98. Mathieu J., Yant L.J., Murdter F., Kuttner F., Schmid M. Repression of flowering by the miR172 target SMZ. PLoS Biol. 2009, 7:e1000148.
99. Mathonnet G., Fabian M.R., Svitkin Y.V., Parsyan A., Huck L., Murata T., Biffo S., Merrick W.C., Darzynkiewicz E., Pillai R.S., Filipowicz W., Duchaine T.F., Sonenberg N. MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex eIF4F. Science 2007, 317:1764-1767.
100. Matzke M.A., Birchler J.A. RNAi-mediated pathways in the nucleus. Nat. Rev. Genet. 2005, 6:24-35.
101. Maziere P., Enright A.J. Prediction of microRNA targets. Drug Discov. Today 2007, 12:452-458.
102. Meister G., Landthaler M., Patkaniowska A., Dorsett Y., Teng G., Tuschl T. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 2004, 15:185-197.
103. Mi S., Cai T., Hu Y., Chen Y., Hodges E., Ni F., Wu L., Li S., Zhou H., Long C., Chen S., Hannon G.J., Qi Y. Sorting of small RNAs into Arabidopsis Argonaute complexes is directed by the 5′ terminal nucleotide. Cell 2008, 133:116-127.
104. Millar A.A., Waterhouse P.M. Plant and animal microRNAs: similarities and differences. Funct. Integr. Genomics 2005, 5:129-135.
105. Mishima Y., Giraldez A.J., Takeda Y., Fujiwara T., Sakamoto H., Schier A.F., Inoue K. Differential regulation of germline mRNAs in soma and germ cells by zebrafish miR-430. Curr. Biol. 2006, 16:2135-2142.
106. Mizukami Y., Ma H. Ectopic expression of the floral homeotic gene AGAMOUS in transgenic Arabidopsis plants alters floral organ identity. Cell 1992, 71:119-131.
107. Montgomery T.A., Howell M.D., Cuperus J.T., Li D., Hansen J.E., Alexander A.L., Chapman E.J., Fahlgren N., Allen E., Carrington J.C. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 2008, 133:128-141.
108. Morlando M., Ballarino M., Gromak N., Pagano F., Bozzoni I., Proudfoot N.J. Primary microRNA transcripts are processed co-transcriptionally. Nat. Struct. Mol. Biol. 2008, 15:902-909.
109. Mourelatos Z., Dostie J., Paushkin S., Sharma A., Charroux B., Abel L., Rappsilber J., Mann M., Dreyfuss G. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 2002, 16:720-728.
110. Nikovics K., Blein T., Peaucelle A., Ishida T., Morin H., Aida M., Laufs P. The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis. Plant Cell 2006, 18:2929-2945.
111. Okamura K., Ishizuka A., Siomi H., Siomi M.C. Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev. 2004, 18:1655-1666.
112. Okamura K., Hagen J.W., Duan H., Tyler D.M., Lai E.C. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 2007, 130:89-100.
113. Olsen P.H., Ambros V. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol 1999, 216:671-680.
114. Palatnik J.F., Allen E., Wu X., Schommer C., Schwab R., Carrington J.C., Weigel D. Control of leaf morphogenesis by microRNAs. Nature 2003, 425:257-263.
115. Papp I., Mette M.F., Aufsatz W., Daxinger L., Schauer S.E., Ray A., van der Winden J., Matzke M., Matzke A.J. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol. 2003, 132:1382-1390.
116. Park M.Y., Wu G., Gonzalez-Sulser A., Vaucheret H., Poethig R.S. Nuclear processing and export of microRNAs in Arabidopsis. Proc. Natl. Acad. Sci. USA 2005, 102:3691-3696.
117. Park W., Li J., Song R., Messing J., Chen X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 2002, 12:1484-1495.
118. Parker J.S., Roe S.M., Barford D. Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 2005, 434:663-666.
119. Pasquinelli A.E., Reinhart B.J., Slack F., Martindale M.Q., Kuroda M.I., Maller B., Hayward D.C., Ball E.E., Degnan B., Müller P., Spring J., Srinivasan A., Fishman M., Finnerty J., Corbo J., Levine M., Leahy P., Davidson E., Ruvkun G. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000, 408:86-89.
120. Peters L., Meister G. Argonaute proteins: mediators of RNA silencing. Mol. Cell 2007, 26:611-623.
121. Ramachandran V., Chen X. Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 2008, 321:1490-1492.
122. Reinhart B.J., Slack F.J., Basson M., Pasquinelli A.E., Bettinger J.C., Rougvie A.E., Horvitz H.R., Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000, 403:901-906.
123. Reinhart B.J., Weinstein E.G., Rhoades M.W., Bartel B., Bartel D.P. MicroRNAs in plants. Genes Dev. 2002, 16:1616-1626.
124. Rhoades M.W., Reinhart B.J., Lim L.P., Burge C.B., Bartel B., Bartel D.P. Prediction of plant microRNA targets. Cell 2002, 110:513-520.
125. Robins H., Li Y., Padgett R.W. Incorporating structure to predict microRNA targets. Proc. Natl. Acad. Sci. USA 2005, 102:4006-4009.
126. Rodriguez A., Griffiths-Jones S., Ashurst J.L., Bradley A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 2004, 14:1902-1910.
127. Ruby J.G., Jan C.H., Bartel D.P. Intronic microRNA precursors that bypass Drosha processing. Nature 2007, 448:83-86.
128. Saito K., Ishizuka A., Siomi H., Siomi M.C. Processing of pre-microRNAs by the Dicer-1-Loquacious complex in Drosophila cells. PLoS Biol. 2005, 3:e235.
129. Schauer S.E., Jacobsen S.E., Meinke D.W., Ray A. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci. 2002, 7:487-491.
130. Schmid M., Uhlenhaut N.H., Godard F., Demar M., Bressan R., Weigel D., Lohmann J.U. Dissection of floral induction pathways using global expression analysis. Development 2003, 130:6001-6012.
131. Schwab R., Palatnik J.F., Riester M., Schommer C., Schmid M., Weigel D. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 2005, 8:517-527.
132. Schwab R., Ossowski S., Riester M., Warthmann N., Weigel D. Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 2006, 18:1121-1133.
133. Schwarz D.S., Hutvagner G., Du T., Xu Z., Aronin N., Zamore P.D. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003, 115:199-208.
134. Shabalina S.A., Koonin E.V. Origins and evolution of eukaryotic RNA interference. Trends Ecol. Evol. 2008, 23:578-587.
135. Song L., Han M.H., Lesicka J., Fedoroff N. Arabidopsis primary microRNA processing proteins HYL1 and DCL1 define a nuclear body distinct from the Cajal body. Proc. Natl. Acad. Sci. USA 2007, 104:5437-5442.
136. Tolia N.H., Joshua-Tor L. Slicer and the Argonautes. Nat. Chem. Biol. 2007, 3:36-43.
137. Tomari Y., Du T., Zamore P.D. Sorting of Drosophila small silencing RNAs. Cell 2007, 130:299-308.
138. Vazquez F., Gasciolli V., Crete P., Vaucheret H. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr. Biol. 2004, 14:346-351.
139. Vazquez F., Vaucheret H., Rajagopalan R., Lepers C., Gasciolli V., Mallory A.C., Hilbert J.L., Bartel D.P., Crete P. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell 2004, 16:69-79.
140. Wightman B., Ha I., Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 1993, 75:855-862.
141. Wu L., Fan J., Belasco J.G. MicroRNAs direct rapid deadenylation of mRNA. Proc. Natl. Acad. Sci. USA 2006, 103:4034-4039.
142. Würschum T., Gross-Hardt R., Laux T. APETALA2 regulates the stem cell niche in the Arabidopsis shoot meristem. Plant Cell 2006, 18:295-307.
143. Xie Z., Johansen L.K., Gustafson A.M., Kasschau K.D., Lellis A.D., Zilberman D., Jacobsen S.E., Carrington J.C. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2004, 2:e104.
144. Yang L., Liu Z., Lu F., Dong A., Huang H. SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J. 2006, 47:841-850.
145. Yang Z., Ebright Y.W., Yu B., Chen X. 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. 2006, 34:667-675.
146. Yekta S., Shih I.H., Bartel D.P. MicroRNA-directed cleavage of HOXB8 mRNA. Science 2004, 304:594-596.
147. Yi R., Qin Y., Macara I.G., Cullen B.R. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev. 2003, 17:3011-3016.
148. Yigit E., Batista P.J., Bei Y., Pang K.M., Chen C.C., Tolia N.H., Joshua-Tor L., Mitani S., Simard M.J., Mello C.C. Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell 2006, 127:747-757.
149. Yu B., Yang Z., Li J., Minakhina S., Yang M., Padgett R.W., Steward R., Chen X. Methylation as a crucial step in plant microRNA biogenesis. Science 2005, 307:932-935.
150. Zeng Y., Yi R., Cullen B.R. MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc. Natl. Acad. Sci. USA 2003, 100:9779-9784.
151. Zhang B., Wang Q., Pan X. MicroRNAs and their regulatory roles in animals and plants. J. Cell. Physiol. 2007, 210:279-289.
152. Zhao L., Kim Y., Dinh T.T., Chen X. miR172 regulates stem cell fate and defines the inner boundary of APETALA3 and PISTILLATA expression domain in Arabidopsis floral meristems. Plant J 2007, 51:840-849.