Arabidopsis endogenous small RNAs: highways and byways

Trends in Plant Science

Volumn 11, Issue 9, 2006, Pages 460-468

  Vazquez, Franck ^a  

^a FRIEDRICH MIESCHER INSTITUTE FOR BIOMEDICAL RESEARCH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PLANT RNA; SMALL INTERFERING RNA; TRANSACTIVATOR PROTEIN; VEGETABLE PROTEIN;

ARABIDOPSIS; METABOLISM; NUCLEOTIDE SEQUENCE; REVIEW;

ARABIDOPSIS; CONSERVED SEQUENCE; MICRORNAS; PLANT PROTEINS; RNA, PLANT; RNA, SMALL INTERFERING; TRANS-ACTIVATORS;

ANIMALIA; ARABIDOPSIS;

EID: 33747772001     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2006.07.006     Document Type: Review

References (82)

1. Wassenegger M. The role of the RNAi machinery in heterochromatin formation. Cell 122 (2005) 13-16
2. Jones-Rhoades M.W., et al. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 57 (2006) 19-53
3. Zhang B., et al. Plant microRNA: a small regulatory molecule with big impact. Dev. Biol. 289 (2006) 3-16
4. Meins Jr. F., et al. RNA silencing systems and their relevance to plant development. Annu. Rev. Cell Dev. Biol. 21 (2005) 297-318
5. Vaucheret H. Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev. 20 (2006) 759-771
6. Papp I., et al. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol. 132 (2003) 1382-1390
7. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281-297
8. Park W., et al. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12 (2002) 1484-1495
9. Kurihara Y., and Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl Acad. Sci. U. S. A. 101 (2004) 12753-12758
10. Vazquez F., et al. 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
11. Han M.H., et al. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 1093-1098
12. Kurihara Y., et al. The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 12 (2006) 206-212
13. Yu B., et al. Methylation as a crucial step in plant microRNA biogenesis. Science 307 (2005) 932-935
14. Li J., et al. Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr. Biol. 15 (2005) 1501-1507
15. Yang Z., et al. 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 (2006) 667-675
16. Park M.Y., et al. Nuclear processing and export of microRNAs in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 3691-3696
17. Llave C., et al. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297 (2002) 2053-2056
18. Kasschau K.D., et al. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev. Cell 4 (2003) 205-217
19. Vaucheret H., et al. 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
20. Baumberger N., and Baulcombe D.C. Arabidopsis ARGONAUTE1 is an RNA slicer that selectively recruits microRNAs and short interfering RNAs. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 11928-11933
21. Qi Y., et al. Biochemical specialization within Arabidopsis RNA silencing pathways. Mol. Cell 19 (2005) 421-428
22. Pillai R.S., et al. Inhibition of translational initiation by Let-7 microRNA in human cells. Science 309 (2005) 1573-1576
23. Souret F.F., et al. AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol. Cell 15 (2004) 173-183
24. Zhang B., et al. Conservation and divergence of plant microRNA genes. Plant J. 46 (2006) 243-259
25. Vazquez F., et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell 16 (2004) 69-79
26. 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. 18 (2004) 2368-2379
27. Xie Z., et al. Expression of Arabidopsis miRNA genes. Plant Physiol. 138 (2005) 2145-2154
28. Allen E., et al. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121 (2005) 207-221
29. Xie Z., et al. DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 12984-12989
30. Yoshikawa M., et al. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev. 19 (2005) 2164-2175
31. Williams L., et al. A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 9703-9708
32. Garcia D., et al. Specification of Leaf Polarity in Arabidopsis via the trans-Acting siRNA Pathway. Curr. Biol. 16 (2006) 933-938
33. Adenot X., et al. DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr. Biol. 16 (2006) 927-932
34. Fahlgren N., et al. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr. Biol. 16 (2006) 939-944
35. Gasciolli V., et al. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr. Biol. 15 (2005) 1494-1500
36. Hiraguri A., et al. Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana. Plant Mol. Biol. 57 (2005) 173-188
37. Borsani O., et al. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123 (2005) 1279-1291
38. Herr A.J., et al. RNA polymerase IV directs silencing of endogenous DNA. Science 308 (2005) 118-120
39. Onodera Y., et al. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120 (2005) 613-622
40. Kanno T., et al. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet. 37 (2005) 761-765
41. Vaucheret H. RNA polymerase IV and transcriptional silencing. Nat. Genet. 37 (2005) 659-660
42. Hamilton A., et al. Two classes of short interfering RNA in RNA silencing. EMBO J. 21 (2002) 4671-4679
43. Xie Z., et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2 (2004) e104
44. Cao X., et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr. Biol. 13 (2003) 2212-2217
45. Zilberman D., et al. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299 (2003) 716-719
46. Zilberman D., et al. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr. Biol. 14 (2004) 1214-1220
47. Lippman Z., et al. Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol. 1 (2003) e67
48. Finnegan E.J., et al. Posttranscriptional gene silencing is not compromised in the Arabidopsis CARPEL FACTORY (DICER-LIKE1) mutant, a homolog of Dicer-1 from Drosophila. Curr. Biol. 13 (2003) 236-240
49. Carmell M.A., et al. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev. 16 (2002) 2733-2742
50. Collins R.E., and Cheng X. Structural domains in RNAi. FEBS Lett. 579 (2005) 5841-5849
51. Catalanotto C., et al. Redundancy of the two dicer genes in transgene-induced posttranscriptional gene silencing in Neurospora crassa. Mol. Cell. Biol. 24 (2004) 2536-2545
52. Henderson I.R., et al. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet. 38 (2006) 721-725
53. Reinhart B.J., et al. MicroRNAs in plants. Genes Dev. 16 (2002) 1616-1626
54. Sunkar R., and Zhu J.K. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16 (2004) 2001-2019
55. Jones-Rhoades M.W., and Bartel D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14 (2004) 787-799
56. Wang X.J., et al. Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol. 5 (2004) R65
57. Kakutani T., et al. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 12406-12411
58. Deleris A., et al. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science (2006). http://www.sciencemag.org/ 10.1126/science.1128214 www.sciencemag.org
59. Landthaler M., et al. The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis. Curr. Biol. 14 (2004) 2162-2167
60. Liu Q., et al. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301 (2003) 1921-1925
61. Saito K., et al. Processing of pre-microRNAs by the Dicer-1-Loquacious complex in Drosophila cells. PLoS Biol. 3 (2005) e235
62. Tabara H., et al. 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
63. Chendrimada T.P., et al. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436 (2005) 740-744
64. Haase A.D., et al. TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep. 6 (2005) 961-967
65. Lee Y., et al. The role of PACT in the RNA silencing pathway. EMBO J. 25 (2006) 522-532
66. Lynn K., et al. The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene. Development 126 (1999) 469-481
67. Kidner C.A., and Martienssen R.A. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 428 (2004) 81-84
68. Hunter C., et al. The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member. Curr. Biol. 13 (2003) 1734-1739
69. Bao N., et al. MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Dev. Cell 7 (2004) 653-662
70. Zhang H., et al. Single processing center models for human Dicer and bacterial RNase III. Cell 118 (2004) 57-68
71. Morel J.B., et al. Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell 14 (2002) 629-639
72. Sigova A., et al. A single Argonaute protein mediates both transcriptional and posttranscriptional silencing in Schizosaccharomyces pombe. Genes Dev. 18 (2004) 2359-2367
73. Hammond S.M., et al. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404 (2000) 293-296
74. Verdel A., et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303 (2004) 672-676
75. Schwarz D.S., et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115 (2003) 199-208
76. Ma J.B., et al. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429 (2004) 318-322
77. Ma J.B., et al. Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434 (2005) 666-670
78. Rand T.A., et al. Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 123 (2005) 621-629
79. Miyoshi K., et al. Slicer function of Drosophila Argonautes and its involvement in RISC formation. Genes Dev. 19 (2005) 2837-2848
80. Song J.J., et al. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305 (2004) 1434-1437
81. Parker J.S., et al. Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J. 23 (2004) 4727-4737
82. Liu J., et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305 (2004) 1437-1441