A DNA target of 30 bp is sufficient for RNA-directed DNA methylation

RNA

Volumn 6, Issue 1, 2000, Pages 55-65

  Pélissier, Thierry ^a,c   Wassenegger, Michael ^a,b  

^a IUCT   (Germany)

^b Fraunhofer Abt fur Molec Biotech   (Germany)

^c UNIVERSITÉ CLERMONT AUVERGNE   (France)

Author keywords

Co suppression; Epigenetic change; Gene regulation; Posttranscriptional gene silencing; Transcriptional silencing; Transgenic plants; Viroid host interaction

Indexed keywords

COMPLEMENTARY DNA; VIRUS DNA;

ARTICLE; DNA METHYLATION; GENE EXPRESSION REGULATION; GENE SILENCING; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA VIRUS; TRANSCRIPTION REGULATION; TRANSGENIC PLANT; VIROID;

BASE SEQUENCE; DNA METHYLATION; DNA, PLANT; MOLECULAR SEQUENCE DATA; PLANTS, TOXIC; RNA, VIRAL; SULFITES; TOBACCO; TRANSGENES; VIROIDS;

EMBRYOPHYTA; NICOTIANA OBTUSIFOLIA; NICOTIANA TABACUM; POTATO SPINDLE TUBER VIROID; RNA VIRUSES; SOLANUM TUBEROSUM; VIROIDS;

EID: 0142039054     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S135583820099201X     Document Type: Article

References (57)

1. Amasino RM. 1986. Acceleration of nucleic acid hybridization rate by polyethylene glycol. Anal Biochem 152:304-307.
2. Baulcombe DC. 1996. RNA as a target and an initiator of post-transcriptional gene silencing in transgenic plants. Plant Mol Biol 32:79-88.
3. Bedbrook J. 1981. A plant nuclear DNA preparation procedure. Plant Mol Biol News 2:24.
4. Bender J. 1998. Cytosine methylation of repeated sequences in eukaryotes: The role of DNA pairing. Trends Biochem Sci 23:252-256.
5. Bestor HB, Tycko B. 1996. Creation of genomic methylation patterns. Nat Genet 12:363-366.
6. Cogoni C, Irelan JT, Schumacher M, Schmidhauser TJ, Selker EU, Macino G. 1996. 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 15:3153-3163.
7. Depicker A, Van Montagu M. 1997. Post-transcriptional gene silencing in plants. Curr Opin Cell Biol 9:373-382.
8. Deragon J-M, Landry BS, Pélissier T, Tutois S, Tourmente S, Picard G. 1994. An analysis of retroposition in plants based on a family of SINEs from Brassica napus. J Mol Evol 39:378-386.
9. Dougherty WG, Parks TD. 1995. Transgenes and gene suppression -Telling us something new. Curr Opin Cell Biol 7:399-405.
10. English JJ, Mueller E, Baulcombe DC. 1996. Suppression of virus accumulation in transgenic plants exhibiting silencing of nuclear genes. Plant Cell 8: 179-188.
11. Fire A. 1999. RNA-triggered gene silencing. Trends Genet 15:358-363.
12. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL. 1992. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89:1827-1831.
13. Goodwin J, Chapman K, Swaney S, Parks TD, Wernsman EA, Dougherty WG. 1996. Genetic and biochemical dissection of transgenic RNA-mediated virus resistance. Plant Cell 8:95-105.
14. Goyon C, Barry C, Gregoire A, Faugeron G, Rossignol JL. 1996. Methylation of DNA repeats of decreasing sizes in Ascobolus immersus. Mol Cell Biol 16:3054-3065.
15. Goyon C, Nogueira TIV, Faugeron G. 1994. Perpetuation of cytosine methylation in Ascobolus immersus implies a novel type of maintenance methylase. J Mol Biol 240:42-51.
16. Harders J, Lukács N, Robert-Nicoud M, Jovin TM, Riesner D. 1989. Imaging of viroids in nuclei from tomato leaf tissue by in situ hybridization and confocal laser scanning microscopy. EMBO J 8:3941-3949.
17. Ingelbrecht I, Van Houdt H, Van Montagu M, Depicker A. 1994. Post-transcriptional silencing of reporter transgenes in tobacco correlates with DNA methylation. Proc Natl Acad Sci USA 91:10502-10506.
18. Jensen S, Gassama MP, Heidmann T. 1999. Taming of transposable elements by homology-dependent gene silencing. Nature Genet 21:209-212.
19. Jones AL, Thomas CL, Maule AJ. 1998. De novo methylation and co-suppression induced by a cytoplasmically replicating plant RNA virus. EMBO J 17:6385-6393.
20. Jorgensen RA, Atkinson RG, Forster RLS, Lucas WJ. 1998. An RNA-based information superhighway in plants. Science 279:1486-1487.
21. Kooter JM, Matzke MA, Meyer P. 1999. Listening to the silent genes: Transgene silencing, gene regulation and pathogen control. Trends Plant Sci 4:340-347.
22. Lee JT, Davidow LS, Warshawsky D. 1999. Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet 21:400-404.
23. Lindbo JA, Silva-Rosales L, Proebsting WM, Dougherty WG. 1993. Induction of a highly specific antiviral state in transgenic plants: Implications for regulation of gene expression and virus resistance. Plant Cell 5:1749-1759.
24. Loss P, Schmitz M, Steger G, Riesner D. 1991. Formation of a thermodynamically metastable structure containing hairpin II is critical for infectivity of potato spindle tuber viroid RNA. EMBO J 10:719-727.
25. Matzke MA, Matzke AJM. 1995. How and why do plants inactivate homologous (trans)genes. Plant Physiol 107:679-685.
26. Matzke MA, Matzke AJM, Eggleston WB. 1996. Paramutation and transgene silencing: A common response to invasive DNA? Trends Plant Sci 1:382-388.
27. Mette MF, van der Winden J, Matzke MA, Matzke AJM. 1999. Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans. EMBO J 18:241-248.
28. Metzlaff M, O'Dell M, Cluster PD, Flavell RB. 1997. RNA-mediated RNA degradation and chalcone synthase A silencing in petunia. Cell 88:845-854.
29. Meyer P. 1995. Understanding and controlling transgene expression. Trends Biotechnol 13:332-337.
30. Montgomery MK, Fire A. 1998. Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends Genet 14:255-258.
31. Palauqui J-C, Balzergue S. 1999. Activation of systemic acquired silencing by localised introduction of DNA. Curr Biol 9:59-66.
32. Park YD, Papp I, Moscone EA, Iglesias VA, Vaucheret H, Matzke AJM, Matzke MA. 1996. Gene silencing mediated by promoter homology occurs at the level of transcription and results in meiotically heritable alterations in methylation and gene activity. Plant J 9:183-194.
33. Paulin R, Grigg GW, Davey MW, Piper AA. 1998. Urea improves efficiency of bisulphite-mediated sequencing of 5′-methylcytosine in genomic DNA. Nucleic Acids Res 26:5009-5010.
34. Pélissier T, Thalmeir S, Kempe D, Sänger HL, Wassenegger M. 1999. Heavy de novo methylation at symmetrical and non-symmetrical sites is a hallmark of RNA-directed DNA methylation. Nucleic Acids Res 27:1625-1634.
35. Prins M, Goldbach R. 1996. RNA-mediated virus resistance in transgenic plants. Arch Virol 141:2259-2276.
36. Reik W, Constancia M. 1997. Making sense or antisense? Nature 389:669-671.
37. Rossignol J-L, Faugeron G. 1994. Gene inactivation triggered by recognition between DNA repeats. Experientia 50:307-317.
38. Ruiz T, Voinnet O, Baulcombe DC. 1998. Initiation and maintenance of virus-induced gene silencing. Plant Cell 10:937-946.
39. Sänger HL. 1987. Viroid replication. In: Diener TO, ed. The viroids. New York: Plenum Press. pp 117-166.
40. Sänger HL, Schiebel W, Riedel L, Pélissier T, Wassenegger M. 1996. The possible links between RNA-directed DNA methylation (RdDM), sense and antisense RNA, gene silencing, symptom-induction upon microbial infections and RNA-directed RNA polymerase (RDRP). In: Stacey G, Mullin B, Gresshoff PM, eds. Biology of plant-microbe interactions. St. Paul, Minnesota: International Society for Molecular Plant-Microbe Interactions, pp 533-540.
41. Schiebel W, Pélissier T, Riedel L, Thalmeir S, Schiebel R, Kempe D, Lottspeich F, Sänger HL, Wassenegger M. 1998. Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato. Plant Cell 10:2087-2101.
42. Schindler IM, Mühlbach HP. 1992. Involvement of nuclear DNA-dependent RNA polymerases in potato spindle tuber viroid replication: A reevaluation. Plant Sci 84:221-229.
43. Schmitz A, Riesner D. 1998. Correlation between bending of the VM region and pathogenicity of different potato spindle tuber viroid strains. RNA 4:1295-1303.
44. Schnölzer M, Haas B, Ramm K, Hofmann H, Sänger HL. 1985. Correlation between structure and pathogenicity of potato spindle tuber viroid (PSTV). EMBO J 4:2181-2190.
45. Schuurs TA, Schaeffer EAM, Wessels JGH. 1997. Homology-dependent silencing of the SC3 gene in Schizophyllum commune. Genetics 147:589-596.
46. Sijen T, Wellink J, Hiriart JB, van Kammen A. 1996. RNA-mediated virus resistance: Role of repeated transgenes and delineation of targeted regions. Plant Cell 8:2277-2294.
47. Stam M, Mol JNM, Kooter JM. 1997. The silence of genes in transgenic plants. Ann Bot 79:3-12.
48. Tabler M, Tzortzakaki S, Tsagris M. 1992. Processing of linear longer-than-unit-length potato spindle tuber viroid RNAs into infectious monomeric circular molecules by a G-specific endoribonuclease. Virology 190:746-753.
49. Van Blokland R, Van der Geest N, Mol JNM, Kooter JM. 1994. Transgene-mediated suppression of chalcone synthase expression in Petunia hybrida results from an increase in RNA turnover. Plant J 6:861-877.
50. Vaucheret H, Béclin C, Elmayan T, Feuerbach F, Godon C, Morel J-B, Mourrain P, Palauqui J-C, Vernhettes S. 1998. Transgene-induced gene silencing in plants. Plant J 16:651-659.
51. Voinnet O, Vain P, Angell S, Baulcombe DC. 1998. Systemic spread of sequence-specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promoterless DNA. Cell 95:177-187.
52. Wassenegger M, Heimes S, Riedel L, Sänger HL 1994a. RNA-directed de-novo methylation of genomic sequences in plants. Cell 76:567-576.
53. Wassenegger M, Heimes S, Sänger HL 1994b. An infectious viroid RNA replicon evolved from an in vitro-generated noninfectious viroid deletion mutant via a complementary deletion in-vivo. EMBO J 13:6172-6177.
54. Wassenegger M, Pélissier T. 1998. A model for RNA-mediated gene silencing in higher plants. Plant Mol Biol 37:349-362.
55. Wassenegger M, Pélissier T. 1999. Signalling in gene silencing. Trends Plant Sci 4:207-209.
56. Waterhouse PM, Graham MW, Wang MB. 1998. Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc Natl Acad Sci USA 95:13959-13964.
57. Yoshioka Y, Matsumoto S, Kojima S, Ohshima K, Okada N, Machida Y. 1993. Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs. Proc Natl Acad Sci USA 90:6562-6566.