New generation of artificial MicroRNA and synthetic trans-acting small interfering RNA vectors for efficient gene silencing in Arabidopsis

Plant Physiology

Volumn 165, Issue 1, 2014, Pages 15-29

  Carbonell, Alberto ^a   Takeda, Atsushi ^b,e   Fahlgren, Noah ^a   Johnson, Simon C ^c,e   Cuperus, Josh T ^d,e   Carrington, James C ^a  

^a DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

^b RITSUMEIKAN UNIVERSITY   (Japan)

^c ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^e OREGON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PLANT RNA; SMALL INTERFERING RNA;

ARABIDOPSIS; GENE SILENCING; GENE VECTOR; GENETICS; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; TRANSGENIC PLANT;

ARABIDOPSIS; BASE SEQUENCE; CLONING, MOLECULAR; GENE SILENCING; GENETIC VECTORS; MICRORNAS; MOLECULAR SEQUENCE DATA; PLANTS, GENETICALLY MODIFIED; RNA, PLANT; RNA, SMALL INTERFERING;

EID: 84899823774     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.113.234989     Document Type: Article

References (56)

1. Addo-Quaye C, Snyder JA, Park YB, Li YF, Sunkar R, Axtell MJ (2009) Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome. RNA 15: 2112-2121
2. Allen E, Xie Z, Gustafson AM, Carrington JC (2005) MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121: 207-221
3. Alvarez JP, Pekker I, Goldshmidt A, Blum E, Amsellem Z, Eshed Y (2006) Endogenous and synthetic microRNAs stimulate simultaneous, efficient, and localized regulation of multiple targets in diverse species. Plant Cell 18: 1134-1151
4. Axtell MJ, Jan C, Rajagopalan R, Bartel DP (2006) A two-hit trigger for siRNA biogenesis in plants. Cell 127: 565-577
5. Baykal U, Zhang Z (2010) Small RNA-mediated gene silencing for plant biotechnology. In AJ Catalano, ed, Gene Silencing: Theory, Techniques and Applications. Nova Science Publishers, Hauppauge, NY, pp 255-269
6. Bernard P, CouturierM (1992) Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes. J Mol Biol 226: 735-745
7. Bologna NG, Mateos JL, Bresso EG, Palatnik JF (2009) A loop-to-base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159. EMBO J 28: 3646-3656
8. Bologna NG, Schapire AL, Palatnik JF (2013) Processing of plant micro-RNA precursors. Brief Funct Genomics 12: 37-45
9. Carbonell A, Fahlgren N, Garcia-Ruiz H, Gilbert KB, Montgomery TA, Nguyen T, Cuperus JT, Carrington JC (2012) Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants. Plant Cell 24: 3613-3629
10. Chapman EJ, Carrington JC (2007) Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 8: 884-896
11. Chen S, Songkumarn P, Liu J, Wang GL (2009) A versatile zero background T-vector system for gene cloning and functional genomics. Plant Physiol 150: 1111-1121
12. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacteriummediated transformation of Arabidopsis thaliana. Plant J 16: 735-743
13. Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, Takeda A, Sullivan CM, Gilbert SD, Montgomery TA, Carrington JC (2010) Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nat Struct Mol Biol 17: 997-1003
14. Cuperus JT, Fahlgren N, Carrington JC (2011) Evolution and functional diversification of MIRNA genes. Plant Cell 23: 431-442
15. Curtis MD, Grossniklaus U (2003) A Gateway cloning vector set for highthroughput functional analysis of genes in planta. Plant Physiol 133: 462-469
16. de Felippes FF, Weigel D (2010) Transient assays for the analysis of miRNA processing and function. Methods Mol Biol 592: 255-264
17. de la Luz Gutiérrez-Nava M, Aukerman MJ, Sakai H, Tingey SV, Williams RW (2008) Artificial trans-acting siRNAs confer consistent and effective gene silencing. Plant Physiol 147: 543-551
18. Dunoyer P, Himber C, Voinnet O (2005) DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat Genet 37: 1356-1360
19. Eamens AL, Agius C, Smith NA, Waterhouse PM, Wang MB (2011) Efficient silencing of endogenous microRNAs using artificial microRNAs in Arabidopsis thaliana. Mol Plant 4: 157-170
20. Engler C, Kandzia R, Marillonnet S (2008) A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3: e3647
21. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, et al (2007) Highthroughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS ONE 2: e219
22. Felippes FF, Wang JW, Weigel D (2012) MIGS: miRNA-induced gene silencing. Plant J 70: 541-547
23. Felippes FF, Weigel D (2009) Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173. EMBO Rep 10: 264-270
24. 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: 1494-1500
25. Huntzinger E, Izaurralde E (2011) Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet 12: 99-110
26. Koncz C, Mayerhofer R, Koncz-Kalman Z, Nawrath C, Reiss B, Redei GP, Schell J (1990) Isolation of a gene encoding a novel chloroplast protein by T-DNA tagging in Arabidopsis thaliana. EMBO J 9: 1337-1346
27. Koornneef M, Hanhart CJ, van der Veen JH (1991) A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol Gen Genet 229: 57-66
28. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25
29. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079
30. Liang G, He H, Li Y, Yu D (2012) A new strategy for construction of artificial miRNA vectors in Arabidopsis. Planta 235: 1421-1429
31. Martínez de Alba AE, Elvira-Matelot E, Vaucheret H (2013) Gene silencing in plants: a diversity of pathways. Biochim Biophys Acta 1829: 1300-1308
32. Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, et al (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 59 terminal nucleotide. Cell 133: 116-127
33. Molnar A, Bassett A, Thuenemann E, Schwach F, Karkare S, Ossowski S, Weigel D, Baulcombe D (2009) Highly specific gene silencing by artificial microRNAs in the unicellular alga Chlamydomonas reinhardtii. Plant J 58: 165-174
34. Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC (2008a) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133: 128-141
35. Montgomery TA, Yoo SJ, Fahlgren N, Gilbert SD, Howell MD, Sullivan CM, Alexander A, Nguyen G, Allen E, Ahn JH, et al (2008b) AGO1-miR173 complex initiates phased siRNA formation in plants. Proc Natl Acad Sci USA 105: 20055-20062
36. Niu QW, Lin SS, Reyes JL, Chen KC, Wu HW, Yeh SD, Chua NH (2006) Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance. Nat Biotechnol 24: 1420-1428
37. Ossowski S, Schwab R, Weigel D (2008) Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J 53: 674-690
38. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D (2003) Control of leaf morphogenesis by microRNAs. Nature 425: 257-263
39. 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: 2237-2242
40. Qu J, Ye J, Fang R (2007) Artificial microRNA-mediated virus resistance in plants. J Virol 81: 6690-6699
41. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20: 3407-3425
42. Rajeswaran R, AreggerM, Zvereva AS, Borah BK, Gubaeva EG, PoogginMM (2012) Sequencing of RDR6-dependent double-stranded RNAs reveals novel features of plant siRNA biogenesis. Nucleic Acids Res 40: 6241-6254
43. Schellmann S, Schnittger A, Kirik V, Wada T, Okada K, Beermann A, Thumfahrt J, Jürgens G, Hülskamp M (2002) TRIPTYCHON and CAPRICE mediate lateral inhibition during trichome and root hair patterning in Arabidopsis. EMBO J 21: 5036-5046
44. Schultz EA, Haughn GW (1991) LEAFY, a homeotic gene that regulates inflorescence development in Arabidopsis. Plant Cell 3: 771-781
45. Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18: 1121-1133
46. Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16: 2001-2019
47. Takeda A, Iwasaki S, Watanabe T, Utsumi M, Watanabe Y (2008) The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant Cell Physiol 49: 493-500
48. Wang X, Yang Y, Yu C, Zhou J, Cheng Y, Yan C, Chen J (2010) A highly efficient method for construction of rice artificial microRNA vectors. Mol Biotechnol 46: 211-218
49. Wang X, Yang Y, Zhou J, Yu C, Cheng Y, Yan C, Chen J (2012) Two-step method for constructing Arabidopsis artificial microRNA vectors. Biotechnol Lett 34: 1343-1349
50. Warthmann N, Chen H, Ossowski S, Weigel D, Hervé P (2008) Highly specific gene silencing by artificial miRNAs in rice. PLoS ONE 3: e1829
51. Weigel D, Alvarez J, Smyth DR, Yanofsky MF, Meyerowitz EM (1992) LEAFY controls floral meristem identity in Arabidopsis. Cell 69: 843-859
52. Xie Z, Allen E, Wilken A, Carrington JC (2005) DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci USA 102: 12984-12989
53. Yan H, Zhong X, Jiang S, Zhai C, Ma L (2011) Improved method for constructing plant amiRNA vectors with blue-white screening and MAGIC. Biotechnol Lett 33: 1683-1688
54. Yoshikawa M, Peragine A, Park MY, Poethig RS (2005) A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 19: 2164-2175
55. Zhou J, Yu F, Chen B, Wang X, Yang Y, Cheng Y, Yan C, Chen J (2013) Universal vectors for constructing artificial microRNAs in plants. Biotechnol Lett 35: 1127-1133
56. Zhu H, Hu F, Wang R, Zhou X, Sze SH, Liou LW, Barefoot A, DickmanM, Zhang X (2011) Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell 145: 242-256