RNA silencing

Current Opinion in Biotechnology

Volumn 11, Issue 2, 2000, Pages 152-156

  Wei Ding, Shou ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ANTIVIRAL ACTIVITY; GENE INACTIVATION; GENE SILENCING; GENETIC ANALYSIS; HOST RESISTANCE; NONHUMAN; PLANT; PRIORITY JOURNAL; REVIEW; RNA DEGRADATION; TRANSPOSON; VIRUS INFECTION;

EID: 0342635467     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(00)00074-4     Document Type: Review

References (50)

1. Napoli C., Lemieux C., Jorgensen R. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous gene in trans. Plant Cell. 2:1990;279-289.
2. Van der Krol A.R., Mur L.A., Beld M., Mol J.N.M., Stuitje A.R. Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell. 2:1990;291-299.
3. Fire A. RNA-triggered gene silencing. Trends Genet. 15:1999;358-363.
4. Vaucheret H., Beclin 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. 16:1998;651-659.
5. Wolffe A.P., Matzke M.A. Epigenetics: regulation through repression. Science. 286:1999;481-486.
6. Cogoni C., Macino G. Homology-dependent gene silencing in plants and fungi: a number of variations on the same theme. Curr Opin Microbiol. 2:1999;657-662.
7. Jensen S., Gassama M.P., Heidmann T. Taming of transposable elements by homology-dependent gene silencing. Nat Genet. 21:1999;209-212.
8. Ruiz F., Vayssie L., Klotz C., Sperling L., Madeddu L. Homology-dependent gene silencing in Paramecium. Mol Biol Cell. 9:1998;931-943.
9. Bahramian M.B., Zarbl H. Transcriptional and posttranscriptional silencing of rodent alpha1(I) collagen by a homologous transcriptionally self-silenced transgene. Mol Cell Biol. 19:1999;274-283.
10. Waterhouse P.M., Smith N.A., Wang M.B. Virus resistance and gene silencing: killing the messenger. Trends Plant Sci. 4:1999;452-457.
11. Tuschl T., Zamore P.D., Lehmann R., Bartel D.P., Sharp P.A. Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev. 13:1999;3191-3197. This study establishes the first cell-free system from syncytial blastoderm Drosophila embryos that recapitulates many key features of RNAi.
12. Baulcombe D.C. Gene silencing: RNA makes RNA makes no protein. Curr Biol. 9:1999;R599-R601.
13. Lindbo J.A., Silva-Rosales L., Proebsting W.M., Dougherty W.G. Induction of a highly specific antiviral state in transgenic plants: implications for regulation of gene expression and virus resistance. Plant Cell. 5:1993;1749-1759.
14. Ingelbrecht I.L., Irvine J.E., Mirkov T.E. Posttranscriptional gene silencing in transgenic sugarcane: dissection of homology-dependent virus resistance in a monocot that has a complex polyploid genome. Plant Physiol. 119:1999;1187-1188.
15. Pinto Y.M., Kok R.A., Baulcombe D.C. Resistance to rice yellow mottle virus (RYMV) in cultivated African rice varieties containing RYMV transgenes. Nat Biotechnol. 17:1999;702-707.
16. Heut H., Mahendra S., Wang J., Sivamani E., Ong C.A., Chen L., de Kochko A., Beachy R.N., Fauquet C. Near immunity to rice tungro spherical virus achieved in rice by a replicase-mediated resistance strategy. Phytopathology. 89:1999;1022-1027.
17. Ratcliff F., Harrison B.D., Baulcombe D.C. A similarity between viral defense and gene silencing in plants. Science. 276:1997;1558-1560.
18. Covey S.N., Al-Kaff N.S., Langara A., Turner D.S. Plants combat infection by gene silencing. Nature. 385:1997;781-782.
19. Ratcliff F.G., MacFarlane S.A., Baulcombe D.C. Gene silencing without DNA: RNA-mediated cross-protection between viruses. Plant Cell. 11:1999;1207-1216. Together with [17,18], this paper demonstrates that virus infection of non-transgenic plants triggers RNA silencing directed against the invading viral RNAs and confirms earlier findings that induction of RNA silencing does not require homologous nuclear DNA sequences. This study also shows for the first time that host recovery is not essential for silencing induction.
20. Vance V.B., Berger P.H., Carrington J.C., Hunt A.G., Shi X.M. 5′ proximal potyviral sequences mediate potato virus X/potyviral synergistic disease in transgenic tobacco. Virology. 206:1995;583-590.
21. Pruss G., Ge X., Shi X.M., Carrington J.C., Bowman Vance V. Plant viral synergism: the potyviral genome encodes a broad-range pathogenicity enhancer that transactivates replication of heterologous viruses. Plant Cell. 9:1997;859-868.
22. Anandalakshmi R., Pruss G.J., Ge X., Marathe R., Mallory A.C., Smith T.H., Vance V.B. A viral suppressor of gene silencing in plants. Proc Natl Acad Sci USA. 95:1998;13079-13084.
23. Brigneti G., Voinnet O., Li W.X., Ji L.H., Ding S.W., Baulcombe D.C. Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. EMBO J. 17:1998;6739-6746.
24. Kasschau K.D., Carrington J.C. A counterdefensive strategy of plant viruses: suppression of posttranscriptional gene silencing. Cell. 95:1998;461-470.
25. Ding S.W., Li W.X., Symons R.H. A novel naturally occurring hybrid gene encoded by a plant RNA virus facilitates long distance virus movement. EMBO J. 14:1995;5762-5772.
26. Ding S.W., Anderson B.J., Haase H.R., Symons R.H. New overlapping gene encoded by the cucumber mosaic virus genome. Virology. 198:1994;593-601.
27. Ding S.W., Shi B.J., Li W.X., Symons R.H. An interspecies hybrid RNA virus is significantly more virulent than either parental virus. Proc Natl Acad Sci USA. 93:1996;7470-7474.
28. Li H.W., Lucy A.P., Guo H.S., Li W.X., Ji L.H., Wong S.M., Ding S.W. Strong host resistance targeted against a viral suppressor of the plant gene silencing defence mechanism. EMBO J. 18:1999;2683-2691. This study provides an indication that a host can inactivate the viral suppressor of RNA silencing defense by the hypersensitive virus resistance. By domain swapping with a homologous virulence protein, this work also establishes a two-domain structure for an avirulence protein. The first domain is essential and sufficient for resistance activation, whereas the second is required for cell death induction and is functionally dependent on the first domain.
29. Martin G.B. Functional analysis of plant disease resistance genes and their downstream effectors. Curr Opin Plant Biol. 2:1999;273-279.
30. Voinnet O., Pinto Y.M., Baulcombe D.C. Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci USA. 96:1999;14147-14152. This study shows that diverse virus types encode suppressors of post-transcriptional gene silencing using an efficient procedure developed by the authors and, together with an earlier study [23], defines three types of viral suppressors.
31. Lucy A.P., Guo H.S., Li W.X., Ding S.W. Suppression of post transcriptional gene silencing by a plant viral protein localized in the nucleus. EMBO J. 19:2000;. in press. This study shows that Cmv2b is a nuclear protein and suggests that intracellular signaling of post-transcriptional gene silencing may include an important phase in the nucleus. This paper also describes the first mutants of a viral silencing suppressor defective in silencing suppression and shows a direct correlation between silencing suppression and induction of viral diseases.
32. Beclin C., Berthome R., Palauqui J.C., Tepfer M., Vaucheret H. Infection of tobacco or Arabidopsis plants by CMV counteracts systemic post-transcriptional silencing of nonviral (trans)genes. Virology. 252:1998;313-317.
33. Baulcombe D.C. Fast forward genetics based on virus-induced gene silencing. Curr Opin Plant Biol. 2:1999;109-113.
34. Jones A.L., Hamilton A.J., Voinnet O., Thomas C.L., Maule A.J., Baulcombe D.C. RNA-DNA interactions and DNA methylation in post-transcriptional gene silencing. Plant Cell. 11:1999;2291-2301. This paper addresses the role of DNA methylation in RNA silencing. The authors demonstrate that silencing induction of a GFP transgene by virus-induced gene silencing (VIGS) or local leaf infiltration with Agrobacterium is associated with nuclear DNA methylation. VIGS targeting the 35S promoter of a transgene also leads to methylation of the promoter sequence. However, VIGS of an endogenous gene occurs in the absence of DNA methylation and suppression of the GFP transgene silencing by two different viral suppressors does not decrease DNA methylation.
35. Angell S.M., Baulcombe D.C. Potato virus X amplicon-mediated silencing of nuclear genes. Plant J. 20:1999;357-362. This paper extends the authors' 1997 finding (EMBO J 1997, 16:3675-3684) that transgenic expression of a replicating potato virus X (PVX) construct (termed a PVX amplicon) reproducibly and consistently activates post-transcriptional gene silencing and shows that PVX amplicons can silence stably integrated transgenes and endogenous genes.
36. Hamilton A.J., Brown S., Han Y.H., Ishizuka M., Lowe A., Solis A.G.A., Grierson D. A transgene with repeated DNA causes high frequency, post-transcriptional suppression of ACC-oxidase gene expression in tomato. Plant J. 15:1998;737-746.
37. Waterhouse P.M., Graham M.W., Wang M.B. Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc Natl Acad Sci USA. 95:1998;13959-13964.
38. Winkler R.G., Frank M.R., Galbraith D.W., Feyereisen R., Feldmann K.A. Systematic reverse genetics of transfer-DNA-tagged lines of Arabidopsis. Isolation of mutations in the cytochrome p450 gene superfamily. Plant Physiol. 118:1998;743-750.
39. Parinov S., Sevugan M., De Ye Yang W.C., Kumaran M., Sundaresan V. Analysis of flanking sequences from dissociation insertion lines: a database for reverse genetics in Arabidopsis. Plant Cell. 11:1999;2263-2270.
40. Mette M.F., van der Winden J., Matzke M.A., Matzke A.J. Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans. EMBO J. 18:1999;241-248. This paper provides an indication that an inverted-repeat promoter transcript produced in transgenic plants is able to trigger methylation and silencing of a homologous promoter in trans.
41. Kooter J.M., Matzke M.A., Meyer P. Listening to the silent genes: transgene silencing, gene regulation and pathogen control. Trends Plant Sci. 9:1999;340-347.
42. ••], this paper provides a direct link between RNAi and transposon silencing in nematodes and reports the cloning of the first two cellular components required for RNAi.
43. ••], this paper provides a direct link between RNAi and transposon silencing in nematodes and reports the cloning of the first two cellular components required for RNAi.
44. Cogoni C., Macino G. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature. 399:1999;166-169. This paper describes the isolation of the qde-1 gene required for RNA silencing in Neurospora. As the qde-1 protein shows homology to a plant RNA-dependent RNA polymerase (RdRP), it further adds credibility to previous models invoking the involvement of RdRP in RNA silencing.
45. Schiebel W., Pelissier T., Riedel L., Thalmeir S., Schiebel R., Kempe D., Lottspeich F., Sanger H.L., Wassenegger M. Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato. Plant Cell. 10:1998;2087-2101.
46. Hamilton A.J., Baulcombe D.C. A species of small antisense RNA in post-transcriptional gene silencing in plants. Science. 286:1999;950-952. This paper reports the identification of a small antisense RNA species of a uniform length that is associated with four types of RNA silencing in both transgenic and non-transgenic plants. The properties of such short antisense RNAs led to predictions that they are specificity determinants and components of the mobile systemic signal for post-translational gene silencing (PTGS). The 25-nucleotide antisense RNA discovered will be a useful molecular marker for PTGS.
47. Schmidt A., Palumbo G., Bozzetti M.P., Tritto P., Pimpinelli S., Schafer U. Genetic and molecular characterization of sting, a gene involved in crystal formation and meiotic drive in the male germ line of Drosophila melanogaster. Genetics. 151:1999;749-760.
48. Cogoni C., Macino G. Post-transcriptional gene silencing in Neurospora by a RecQ DNA helicase. Science. 286:1999;2342-2344. This paper reports the isolation of the qde-3 gene and shows the encoded protein is homologous to the RecQ family helicases.
49. Chakraverty R.K., Hickson I.D. Defending genome integrity during DNA replication: a proposed role for RecQ family helicases. BioEssays. 21:1999;286-294.
50. Suzuki N., Shiratori M., Goto M., Furuichi Y. Werner syndrome helicase contains a 5′→3′ exonuclease activity that digests DNA and RNA strands in DNA/DNA and RNA/DNA duplexes dependent on unwinding. Nucleic Acids Res. 27:1999;2361-2368.