MicroRNA networks and developmental plasticity in plants

Trends in Plant Science

Volumn 16, Issue 5, 2011, Pages 258-264

  Rubio Somoza, Ignacio ^a   Weigel, Detlef ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PLANT; PLANT PHYSIOLOGY; REPRODUCTION; REVIEW; TIME;

GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; MICRORNAS; MODELS, GENETIC; PLANT PHYSIOLOGICAL PHENOMENA; PLANTS; REPRODUCTION; TIME FACTORS;

EID: 79955705363     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2011.03.001     Document Type: Review

References (89)

1. Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009, 136:669-687.
2. Chellappan P., et al. siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic. Acids Res. 2010, 38:6883-6894.
3. Wu L., et al. DNA methylation mediated by a microRNA pathway. Mol. Cell 2010, 38:465-475.
4. Rhoades M.W., et al. Prediction of plant microRNA targets. Cell 2002, 110:513-520.
5. Jones-Rhoades M.W., Bartel D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 2004, 14:787-799.
6. Chen M., et al. Functional characterization of plant small RNAs based on next-generation sequencing data. Comput. Biol. Chem. 2010, 34:308-312.
7. Axtell M.J., Bowman J.L. Evolution of plant microRNAs and their targets. Trends Plant Sci. 2008, 13:343-349.
8. Todesco M., et al. A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana. PLoS Genet. 2010, 6:e1001031.
9. Moss E.G. Heterochronic genes and the nature of developmental time. Curr. Biol. 2007, 17:R425-434.
10. Pasquinelli A.E., Ruvkun G. Control of developmental timing by microRNAs and their targets. Annu. Rev. Cell Dev. Biol. 2002, 18:495-513.
11. Rougvie A.E. Intrinsic and extrinsic regulators of developmental timing: from miRNAs to nutritional cues. Development 2005, 132:3787-3798.
12. Chuck G., et al. The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA. Nat. Genet. 2007, 39:544-549.
13. Chuck G., et al. The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/indeterminate spikelet1. Nat. Genet. 2007, 39:1517-1521.
14. Chuck G., et al. Floral meristem initiation and meristem cell fate are regulated by the maize AP2 genes ids1 and sid1. Development 2008, 135:3013-3019.
15. Chuck G., et al. The maize SBP-box transcription factor encoded by tasselsheath4 regulates bract development and the establishment of meristem boundaries. Development 2010, 137:1243-1250.
16. Wang J.W., et al. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell 2009, 138:738-749.
17. Wu G., et al. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 2009, 138:750-759.
18. Poethig R.S. Small RNAs and developmental timing in plants. Curr. Opin. Genet. Dev. 2009, 19:374-378.
19. Telfer A., et al. Phase change and the regulation of trichome distribution in Arabidopsis thaliana. Development 1997, 124:645-654.
20. Tsukaya H., et al. Heteroblasty in Arabidopsis thaliana (L.) Heynh. Planta 2000, 210:536-542.
21. Usami T., et al. The more and smaller cells mutants of Arabidopsis thaliana identify novel roles for SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes in the control of heteroblasty. Development 2009, 136:955-964.
22. 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.
23. Jung J.H., et al. The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell 2007, 19:2736-2748.
24. Wu G., Poethig R.S. Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 2006, 133:3539-3547.
25. Lauter N., et al. microRNA172 down-regulates glossy15 to promote vegetative phase change in maize. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:9412-9417.
26. Yu N., et al. Temporal control of trichome distribution by microRNA156-targeted SPL genes in Arabidopsis thaliana. Plant Cell 2010, 22:2322-2335.
27. Yamaguchi A., et al. The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1. Dev. Cell 2009, 17:268-278.
28. Mathieu J., et al. Repression of flowering by the miR172 target SMZ. PLoS Biol. 2009, 7:e1000148.
29. Yant L., et al. Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2. Plant Cell 2010, 22:2156-2170.
30. Adenot X., et al. DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr. Biol. 2006, 16:927-932.
31. Fahlgren N., et al. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr. Biol. 2006, 16:939-944.
32. Garcia D., et al. Specification of leaf polarity in Arabidopsis via the trans-acting siRNA pathway. Curr. Biol. 2006, 16:933-938.
33. Hunter C., et al. Trans-acting siRNA-mediated repression of ETTIN and ARF4 regulates heteroblasty in Arabidopsis. Development 2006, 133:2973-2981.
34. Yan J., et al. The REDUCED LEAFLET genes encode key components of the trans-acting small interfering RNA pathway and regulate compound leaf and flower development in Lotus japonicus. Plant Physiol. 2010, 152:797-807.
35. Peragine A., et al. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev. 2004, 18:2368-2379.
36. Arazi T., et al. Cloning and characterization of micro-RNAs from moss. Plant J. 2005, 43:837-848.
37. Talmor-Neiman M., et al. Identification of trans-acting siRNAs in moss and an RNA-dependent RNA polymerase required for their biogenesis. Plant J. 2006, 48:511-521.
38. Axtell M.J., et al. Common functions for diverse small RNAs of land plants. Plant Cell 2007, 19:1750-1769.
39. Cho S.H., et al. Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development. PLoS Genet. 2008, 4:e1000314.
40. Schwab R., et al. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 2005, 8:517-527.
41. Wang J.W., et al. Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell 2005, 17:2204-2216.
42. Jiao Y., et al. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat. Genet. 2010, 42:541-544.
43. Lim P.O., et al. Leaf senescence. Annu. Rev. Plant Biol. 2007, 58:115-136.
44. Kim J.H., et al. Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis. Science 2009, 323:1053-1057.
45. Schommer C., et al. Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol. 2008, 6:e230.
46. Ellis C.M., et al. AUXIN RESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulate senescence and floral organ abscission in Arabidopsis thaliana. Development 2005, 132:4563-4574.
47. Lim P.O., et al. Auxin response factor 2 (ARF2) plays a major role in regulating auxin-mediated leaf longevity. J. Exp. Bot. 2010, 61:1419-1430.
48. Okushima Y., et al. AUXIN RESPONSE FACTOR 2 (ARF2): a pleiotropic developmental regulator. Plant J. 2005, 43:29-46.
49. Aida M., et al. Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell 1997, 9:841-857.
50. Palatnik J.F., et al. Control of leaf morphogenesis by microRNAs. Nature 2003, 425:257-263.
51. Nath U., et al. Genetic control of surface curvature. Science 2003, 299:1404-1407.
52. Koyama T., et al. TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis. Plant Cell 2007, 19:473-484.
53. Koyama T., et al. TCP transcription factors regulate the activities of ASYMMETRIC LEAVES1 and miR164, as well as the auxin response, during differentiation of leaves in Arabidopsis. Plant Cell 2010, 22:3574-3588.
54. Laufs P., et al. MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development 2004, 131:4311-4322.
55. Nikovics K., et al. The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis. Plant Cell 2006, 18:2929-2945.
56. Ori N., et al. Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato. Nat. Genet. 2007, 39:787-791.
57. Rodriguez R.E., et al. Control of cell proliferation in Arabidopsis thaliana by microRNA miR396. Development 2010, 137:103-112.
58. Juarez M.T., et al. microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature 2004, 428:84-88.
59. Kidner C.A., Martienssen R.A. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 2004, 428:81-84.
60. Li H., et al. The Putative RNA-dependent RNA polymerase RDR6 acts synergistically with ASYMMETRIC LEAVES1 and 2 to repress BREVIPEDICELLUS and MicroRNA165/166 in Arabidopsis leaf development. Plant Cell 2005, 17:2157-2171.
61. McConnell J.R., et al. Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. Nature 2001, 411:709-713.
62. Emery J.F., et al. Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr. Biol. 2003, 13:1768-1774.
63. Mallory A.C., et al. MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region. EMBO J. 2004, 23:3356-3364.
64. Chitwood D.H., et al. Pattern formation via small RNA mobility. Genes Dev. 2009, 23:549-554.
65. Nogueira F.T., et al. Two small regulatory RNAs establish opposing fates of a developmental axis. Genes Dev. 2007, 21:750-755.
66. Nogueira F.T., et al. Regulation of small RNA accumulation in the maize shoot apex. PLoS Genet. 2009, 5:e1000320.
67. Schwab R., et al. Endogenous TasiRNAs mediate non-cell autonomous effects on gene regulation in Arabidopsis thaliana. PLoS ONE 2009, 4:e5980.
68. Scarpella E., et al. Control of leaf and vein development by auxin. Cold Spring Harb. Perspect. Biol. 2010, 2:a001511.
69. Donner T.J., et al. Regulation of preprocambial cell state acquisition by auxin signaling in Arabidopsis leaves. Development 2009, 136:3235-3246.
70. Yu L., et al. HYL1 gene maintains venation and polarity of leaves. Planta 2005, 221:231-242.
71. Allen R.S., et al. Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:16371-16376.
72. Alonso-Peral M.M., et al. The microRNA159-regulated GAMYB-like genes inhibit growth and promote programmed cell death in Arabidopsis. Plant Physiol. 2010, 154:757-771.
73. Millar A.A., Gubler F. The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell 2005, 17:705-721.
74. Allen R.S., et al. MicroR159 regulation of most conserved targets in Arabidopsis has negligible phenotypic effects. Silence 2010, 1:18.
75. Yang J.Y., et al. betaC1, the pathogenicity factor of TYLCCNV, interacts with AS1 to alter leaf development and suppress selective jasmonic acid responses. Genes Dev. 2008, 22:2564-2577.
76. Zhao L., et al. 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.
77. Wollmann H., et al. On reconciling the interactions between APETALA2, miR172 and AGAMOUS with the ABC model of flower development. Development 2010, 137:3633-3642.
78. Liu B., et al. Oryza sativa dicer-like4 reveals a key role for small interfering RNA silencing in plant development. Plant Cell 2007, 19:2705-2718.
79. Moreno-Risueno M.A., et al. Oscillating gene expression determines competence for periodic Arabidopsis root branching. Science 2010, 329:1306-1311.
80. Rubio-Somoza I., et al. Regulation and functional specialization of small RNA-target nodes during plant development. Curr. Opin. Plant Biol. 2009, 12:622-627.
81. Guo H.S., et al. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 2005, 17:1376-1386.
82. Mallory A.C., et al. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr. Biol. 2004, 14:1035-1046.
83. Gifford M.L., et al. Cell-specific nitrogen responses mediate developmental plasticity. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:803-808.
84. Marin E., et al. miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell 2010, 22:1104-1117.
85. Vidal E.A., et al. Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:4477-4482.
86. Yoon E.K., et al. Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development. Nucleic Acids Res. 2010, 38:1382-1391.
87. Krouk G., et al. Nitrate-regulated auxin transport by NRT1.1 defines a mechanism for nutrient sensing in plants. Dev. Cell 2010, 18:927-937.
88. Gutierrez L., et al. Phenotypic plasticity of adventitious rooting in Arabidopsis is controlled by complex regulation of AUXIN RESPONSE FACTOR transcripts and microRNA abundance. Plant Cell 2009, 21:3119-3132.
89. Tian C.E., et al. Disruption and overexpression of auxin response factor 8 gene of Arabidopsis affect hypocotyl elongation and root growth habit, indicating its possible involvement in auxin homeostasis in light condition. Plant J. 2004, 40:333-343.