Post-transcriptional gene-silencing: RNAs on the attack or on the defense?

BioEssays

Volumn 22, Issue 6, 2000, Pages 520-531

  Sijen, Titia ^a   Kooter, Jan M ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; GENE ACTIVATION; GENE SILENCING; PLANT DEFENSE; RNA DEGRADATION; RNA POLYMERASE; SIGNAL TRANSDUCTION; TRANSCRIPTION TERMINATION; TRANSGENE;

ANIMALS; DNA; DNA METHYLATION; GENE SILENCING; MODELS, GENETIC; PLANT VIRUSES; PLANTS, GENETICALLY MODIFIED; RNA; RNA, DOUBLE-STRANDED; RNA, PLANT; TRANSCRIPTION, GENETIC;

INVERTEBRATA; PROTOZOA; RNA VIRUSES; VERTEBRATA;

EID: 0034082199     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1521-1878(200006)22:6<520::AID-BIES5>3.0.CO;2-W     Document Type: Review

References (99)

1. Van der Krol AR, Mur LA, Beld M, Mo JNM, Stuitje AR. Flavonoid genes in petunia: Addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell 1990;2:291-299.
2. Napoli C, Lemieux C, Jorgensen R. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 1990;2:279-289.
3. Vaucheret H, Béclin C, Elmayan T, Feuerbach F, Godon C, Morel J-B, Mourrain P, Palauqui J-C, Vernhettes S. Transgene-induced gene silencing in plants. Plant J 1998;16:651-659.
4. Lindbo JA, Dougherty WG. Untranslatable transcripts of the tobacco etch virus coat protein gene sequence can interfere with tobacco etch virus replication in transgenic plants and protoplasts. Virology 1992;189: 725-733.
5. Fire A, Xu SQ, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998; 391: 806-811.
6. Kennerdell JR, Carthew RW. Use of dsRNA-mediated genetic interference to demonstrate that frizzled and frizzled 2 act in the wingless pathway. Cell 1998; 95: 1017-1026.
7. Ngo H, Tschudi C, Gull K, Ullu E. Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Proc Natl Acad Sci USA 1998;95: 14687-14692.
8. Sanchez Alvarado A, Newmark PA. Double-stranded RNA specifically disrupts gene expression during planarian regeneration. Proc Natl Acad Sci USA 1999;96:5049-5054.
9. Lohmann JU, Endl I, Bosch TCG. Silencing of developmental genes in Hydra. Develop Biol 1999;214:211-214.
10. Wargelius A, Ellingsen S, Fjose A. Double-stranded RNA induces specific developmental defects in zebrafish embryos. Biochem Biophys Res Commun 1999;263:156-161.
11. Li YX, Farrell MJ, Liu R, Mohanty N, Kirby ML. Double-stranded RNA injection produces null phenotypes in zebrafish. Dev Biol 2000;217: 394-405.
12. Wianny F, Zernicka-Goetz M. Specific interference with gene function by double-stranded RNA in early mouse development. Nat Cell Biol 2000; 2:70-75.
13. Tavernarakis N, Wang SL, Dorovkov M, Ryazanov A, Driscoll M. Heritable and inducible genetic intereference by double-starnded RNA encoded by transgenes. Nat Genet 2000;24:180-183
14. Kooter JM, Matzke MA, Meyer P. Listening to the silent genes: Transgene silencing research identifies new mechanisms of gene regulation and pathogen control. Trends Plant Sci 1999; 4: 340-347.
15. Que QD, Wang HY, English JJ, Jorgensen RA. The frequency and degree of cosuppression by sense chalcone synthase transgenes are dependent on transgene promoter strength and are reduced by premature nonsense codons in the transgene coding sequence. Plant Cell 1997;9:1357-1368.
16. Pang SZ, Jan FJ, Gonsalves D. Nontarget DNA sequences reduce the transgene length necessary for RNA-mediated tospovirus resistance in transgenic plants. Proc Natl Acad Sci USA 1997;94: 8261-8266.
17. English JJ, Davenport GF, Elmayan T, Vaucheret H, Baulcombe DC. Requirenent of sense transcription for homology-dependent virus resistance and trans-inactivation. Plant J 1997;12:597-603.
18. Vaucheret H, Nussaume L, Palauqui JC, Quillere I, Elmayan T. A transcriptionally active state is requred for post-transcriptional silencing (cosuppression) of nitrate reductase host genes and transgenes. Plant Cell 1997;9:1495-1504.
19. Lindbo JA, Silva-Rosales L, Proebsting WM, Dougherty WG. Induction of a highly specific antiviral state in transgenic plants: Implications for regulation of gene expressior and virus resistance. Plant Cell 1993;5: 1749-1759.
20. Dougherty WG, Parks TD. Transgenes and gene suppression: Telling us something new? Curr Opin Cell Biol 1995;7:399-405.
21. Meins F, Kunz C. Silencing of chitinase expression in transgenic plants: An autoregulatory model. In Homologous recombination and gene silencing in plants. Paszkowski, J. (ed.), Kluwer, Dordrecht, The Netherlands: pp. 335-348, 1994.
22. Palauqui JC, Vaucheret H. Transgenes are dispensable for the RNA degradation step of cosuppression. Proc Natl Acad Sci USA 1998;95: 9675-9680.
23. Goodwin J, Chapman K, Swaney S, Parks TD, Wernsman EA, Dougherty WG. Genetic and biochemical dissection of transgenic RNA-mediated virus resistance. Plant Cell 1996;8:95-105.
24. Kunz C, Schüb H, Stam M, Kooter JM, Meins F. Developmentally regulated silencing and reactivation of tobacco chitinase genes. Plant J1996;10:437-450.
25. Stam M, De Bruin R, Kenter S, Van der Hoorn RAL, Van Blokland R, Mol JNM, Kooter JM. Post-transcriptional silencing of chalcone synthase in Petunia by inverted transgene repeats. Plant J 1997;12:63-82.
26. Sijen T, Wellink J, Hiriart JB, Van Kammen A. RNA-mediated virus resistance: Role of repeated transgenes and delineation of targeted regions. Plant Cell 1996;8:2277-2294.
27. English JJ, Mueller E, Baulcombe DC. Suppression of virus accumulation in transgenic plants exhibiting silencing of nuclear genes. Plant Cell 1996;8:179-188.
28. Grant SR. Dissecting the mechanisms of posttranscriptional gene silencing: Divide and conquer. Cell 1999; 96: 303-306.
29. Baulcombe DC, English JJ. Ectopic pairing of homologous DNA and post-transcriptional silencing in transgenic plants. Curr Op Biotechn 1996;7:173-180.
30. Angell SM, Baulcombe DC. Consistent gene silencing in transgenic plants expressing a replicating potato virus X RNA. EMBO J 1997;16: 3675-3684.
31. Jones AL, Thomas CL, Maule AJ. De novo methylation and co-suppression induced by a cytoplasmically replicating plant RNA virus. EMBO J 1998; 17: 6385-6393.
32. Kumagai MH, Donson J, Dellacioppa G, Harvey D, Hanley K, Grill LK. Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proc Natl Acad Sci. USA 1995; 92: 1679-1683.
33. Ruiz MT, Voinnel O, Baulcombe DC. Initiation and maintenance of virus-induced gene silencing. Plant Cell 1998;10:937-946.
34. Kjemtrup S, Sampson KS, Peele CG, Nguyen LV, Conkling MA, Thompson WF, Robertson D. Gene silencing from plant DNA carried by a Geminivirus. Plant J 1998;14:91-100.
35. Baulcombe DC. Fast forward genetics based in virus-induced gene silencing. Curr Opin Plant Biol 1999;2:109-113.
36. Voinnet O, Baulcombe DC, Systemic signaling in gene silencing. Nature 1997;389-553.
37. Voinnet O, Vain P, Angell S, Baulcombe DC. Systemic spread of sequence-specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promoterless DNA. Cell 1998;95: 177-187.
38. Palauqui JC, Balzergue S. Activation of systemic acquired silencing by localised introduction of DNA Curr Biol 1999; 9: 59-66.
39. Palauqui JC, Elmayan T, Pollien JM, Vaucherel H. Systemic acquired silencing: Transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions. EMBO J 1997;16:4738-4745.
40. Ding B, Kwon MO, Hammond R, Owens R. Cell-to-cell movement of potato spindle tuber viroid. Plant J 1997;12:931-936.
41. Carrington JC, Kasschau KD, Mahajan SK, Schaad MC. Cell-to-cell and long-distance transport of viruses in plants. Plant Cell 1996;8: 1669-1681.
42. Lucas WJ, Bouchepillon S, Jackson DP, Nguyen L, Baker L, Ding B, Hake S. Selective trafficking of KNOTTED1 homeodomain protein and its mRNA through plasmodesmata. Science 1995;270:1980-1983.
43. Ruiz-Medrano R, Xoconostle-Cazares B, Lucas WJ. Phloem long-distance transport of CmNACP mRNA: implications for supracellular regulation in plants. Development 1999;126:4405-4419.
44. Xoconostle Cazares B, Yu X, Ruiz Medrano R, Wang HL, Monzer J, Yoo BC, McFarland KC, Franceschi VR, Lucas WJ. Plant paralog to viral movement protein that potentiates transport of mRNA into the phloem. Science 1999;283:94-98.
45. Lee KY, Baden C, Howie WJ, Bedbrook J, Dunsmuir P. Post-transcriptional gene silencing of ACC synthase in lomato results from cytoplasmic RNA degradation. Plant J 1997; 12: 1127-1137.
46. Hamilton AJ, Brown S, Han YH, Ishizuka M, Lowe A, Solis AGA, Grierson D. A transgene with repeated DNA causes high frequency, post-transcriptional suppression of ACC-oxidase gene expression in tomato. Plant J 1998; 15: 737-746.
47. Tanzer MM, Thompson WF, Law MD, Wernsman EA, Uknes S. Characterization of post-transcriptionally suppressed transgene expression that confers resistance to tobacco etch virus infection in tobacco. Plant Cell 1997;9:1411-1423.
48. Holtorf H, Schob H, Kunz C, Waldvogel R, Meins F. Stochastic and nonstochastic post-transcriptional silencing of chitinase and beta-1,3-glucanase genes involves increased RNA turnover - Possible role for ribosome-independent RNA degradation. Plant Cell 1999;11: 471-483.
49. Jacobs JJMR, Litiere K, Van Dijk V, Van Eldik GJ, Van Montagu M, Cornelissen M. Post-transcriptional beta-1,3-glucanase gene silencing involves increased transcript turnover that is translation-independent. Plant J 1997;12:885-893.
50. Montgomery MK, Xu SQ, Fire A. RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Proc. Nat. Acad. Sci USA 1998;95:15502-15507.
51. Tuschl T, Zamore PD, Lehmann R, Bartel DP, Sharp PA. Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev 1999;13: 3191-3197.
52. Tabara H, Sarkissian M, Kelly WG, Fleenor J, Grishok A, Timmons L, Fire A, Mello CC. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 1999; 99: 123-132.
53. Bosher JM, Labouesse M. RNA interference: genetic wand and genetic watchdog. Nat Cell Biol 2000,2: E31-E36.
54. Ketting RF, Haverkamp THA, vanLuenen HGAM, Plasterk RHA. mut-7 of C-elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 1999;99: 133-141.
55. Montgomery MK, Fire A. Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends Genet 1998;14:255-258.
56. Waterhouse PM, Graham HW, Wang MB. Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc Natl. Acad. Sci USA 1998;95:13959-13964.
57. English JJ, Baulcombe DC. The influence of small changes in transgene transcription on homology-dependent virus resistance and gene silencing Plant J. 1997; 12: 1311-1318.
58. Cogoni C, Mancino P. Posttransciptional gene silencing in Neurospora by a RecQ DNA helicase. Science 1999;286:2342-2344.
59. Wassenegger M, Pelissier T. A model for RNA-mediated gene silencing in higher plants. Plant Mol. Biol. 1998; 37: 349-362.
60. Branch AD. A good antisense molecule is hard to find. Trends Biochem. Sci 1998;23:45-50.
61. Bourque JE. Antisense strategies for genetic manipulations in plants Plant Sci 1995;105:125-149.
62. Aubourg S, Kreis M, Lecharny A. The DEAD box RNA helicase family in Arabidopsis thaliana. Nucl Acids Res 1999;27:628-636.
63. Metzlaff M, ODell M, Cluster PD, Flavell RB, RNA-mediated RNA degradation and chalcone synthase A silencing in Petunia. Cell 1997; 88:845-854.
64. Schiebel W, Haas B, Marinkovíc S, Klanner A, Sänger HL. RNA-directed RNA polymerase from tomato leaves. II Catalytic in vitro properties. J Biol Chem 1993; 268: 11858-11867.
65. Ikegami M, Fraenkel-Conrat H. Characterization of the RNA-dependent RNA polymerase of tobacco leaves. J Biol Chem 1979; 254: 149-154.
66. Fraenkel-Conrat H. RNA-directed RNA polymerases of plants. Crit Rev Plant Sci 1986; 4: 213-226.
67. Hamilton AJ, Baulcombe DC. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 1999;286: 950-952.
68. Schiebel W, Pelissier T, Riedel L, Thalmeir S, Schiebel R, Kempe D, Lottspeich F, Sanger HL, Wassenegger M. Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato. Plant Cell 1998;10; 2087-2101.
69. Cogoni C, Macino G. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 1999; 399:166-169.
70. Cogoni C, Irelan JT, Schumacher M, Schmidhauser T, Selker U, Macino G. Transgene silencing of the al-1 gene in vegetative cells of Neurospora is mediated by a cytoplasmic effector and does not depend on DNA-DNA interactions or DNA methylation. EMBO J 1996;15:3153-3163.
71. Krinke L, Wulff DL. The cleavage specificity of RNAse III. Nucleic Acids Res 1990;18:4809-4815.
72. Sano T, Nagayama A, Ogawa T, Ishida I, Okada Y. Transgenic potato expressing a double-stranded RNA-specific ribonuclease is resistant to potato spindle tuber viroid. Nat Biotechnol 1997; 15: 1290-1294.
73. Matousek J, Trnena L, Oberhauser R, Lichtenstein CP, Nellen W. dsRNA degrading nucleases are differently expressed in tobacco anthers. Biol Chem Hoppe-Seyler 1994;375:261-269.
74. Siwecka MA. Purification and some properties of a novel dsRNA degrading nuclease bound to rye germ ribosomes. Acta Biochim. Pol 1997;44:61-68.
75. Lima WF, Mohan V, Crooke ST. The influence of antisense oligonucleotide-induced RNA structure on Escherichia coli RNase H1 activity. J Biol Chem 1997;272:18191-18199.
76. Proud CG. PKR: A new name and new roles. Trends Biochem Sci 1995;20241-246.
77. Langland J, Langland L, Roth D. Differential localization and accumulation of the plant double stranded RNA-dependent protein kinase during virus infection. Plant Physiol Biochem 1998;36:395-400.
78. Ogawa T, Hori T, Ishida I. Virus-induced cell death in plants expressing the mammalian 2′,5′ oligoadenylate system. Nat Biotechnol 1996;14: 1538-1539.
79. Mitra A, Higgins DW, Langenberg WG, Nie H, Sengupta DN, Silverman RH. A mammalian 2-5A system functions as an antiviral pathway in transgenic plants. Proc Natl Acad Sci USA 1996;93:6780-6785.
80. Mette MF, Van der Winden J. Matzke MA, Matzke AJM. Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans. EMBO J 1999;18:241-248.
81. Wassenegger M, Heimes S, Riedel L, Sanger HL. RNA-directed de novo methylation of genomic sequences in plants. Cell 1994;76:567-576.
82. Pelissier T, Thalmeir S, Kempe D, Sanger HL, Wassenegger M. Heavy de novo methylation at symmetrical and non-symmetrical sites is a hallmark of RNA-direcled DNA methylation. Nucl Acids Res 1999;27:1625-1634.
83. Stam M, Viterbo A, Mol JNM, Kooter JM. Position-dependent methylation and transcriptional silencing of transgenes in inverted T-DNA repeats: Implications for posttranscriptional silencing of homologous host genes in plants. Mol Cell Biol 1998;18:6165-6177.
84. Luff B, Pawlowski L, Bender J. An inverted repeat triggers cytosine methylation of identical sequences in Arabidopsis. Mol Cell 1999;3: 505-511.
85. Van der Meer IM (1991). Ph.D. Thesis, Vrije Universiteit Amsterdam, The Netherlands.
86. Covey SN, Al-Kaff NS, Langrara, Turner DS. Plants combat infection by gene silencing. Nature 1997;385:781.
87. Ratcliff F, Harrison BD, Baulcombe DC. A similarity between viral defense and gene silencing in plants. Science 1997;276:1558-1560.
88. Ratcliff FG, MacFarlane SA, Baulcombe DC. Gene silencing without DNA: RNA-meciated cross-protection between viruses. Plant Cell 1999;11:1207-1215.
89. Brigneti G, Voinnet O, Li W-X, Ji L-H, Ding S-W. Viral pathogenicity determinants are suppressor of transgene silencing in Nicotiana benthamiana. EMBO J 1998;17:6739-6746.
90. Kasschau KD, Carrington JC. A counterdefensive strategy of plant viruses: suppression of posttranscriptional silencing. Cell 1998;95: 461-470.
91. Voinnet O, Pinto YM, Baulcombe DC Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci USA 1999;96:14147-14152.
92. Carrington JC, Whitham SA. Viral invasion and host defense: strategies and counter-strategies. Curr Opin Plant Biol 1998;1:336-341.
93. Pruss G, Ge X, Shi XM, Carrington JC, Vance VB. Plant viral synergism: The potyviral genome encodes a broad-range pathogenicity enhancer that transactivates replication of heterologous viruses. Plant Cell 1997; 9:859-868.
94. Jorgensen RA, Atkinson RG, Foster RLS, Lucas WJ. An RNA-based information superhighway in plants. Science 1998;279:1486-1487.
95. Guo HS, Garcia JA. Delayed resistance to plum pox potyvirus mediated by a mutated RNA replicase gene: involvement of a gene-silencing mechanism. Mol Plant-Microbe Interact 1997;10:190-10.
96. Hammond-Kosack KE, Jones JDG. Resistance gene-dependent plant defense responses. Plant Cell 1996;8:1773-1791.
97. Laugé R, Joosten MHAJ, Haanstra JPW, Goodwin PH, Lindhout P, De Wit PJGM. Successful search for a resistance gene in tomato targeted against a virulence factor of a fungal pathogen. Proc Natl Acad Sci USA 1998;95:9014-9018.
98. Elmayan T, Balzergue S, Beon F, Bourdon V, Daubremet J, Guenet Y, Mourrain P, Palauqui JC, Vernhettes S, Vialle T, Wostrikoff K, Vaucheret H. Arabidopsis mutants impaired in cosuppression. Plant Cell 1998;10:1747-1757.
99. Cogoni C, Macmo G. Isolation of quelling-defective (qde) mutants impaired in posttranscriptional transgene-induced gene silencing in Neurospora crassa. Proc Natl Acad Sci USA 1997;94: 10233-10238.