Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation

Plant Cell

Volumn 12, Issue 3, 2000, Pages 357-368

  Hirochika, Hirohiko ^a   Okamoto, Hiroyuki ^a   Kakutani, Tetsuji ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME NUMBER; DNA METHYLATION; GENE FUNCTION; GENE INSERTION; GENE MUTATION; GENE REPRESSION; GENE SILENCING; GENETIC TRANSCRIPTION; GENETIC TRANSFECTION; MUTANT; PLANT GENOME; REPETITIVE DNA; RETROPOSON; TOBACCO;

ARABIDOPSIS; EMBRYOPHYTA; EUKARYOTA; NICOTIANA TABACUM;

EID: 0034103860     PISSN: 10404651     EISSN: None     Source Type: Journal    
DOI: 10.1105/tpc.12.3.357     Document Type: Article

References (71)

1. Akama, K., Shiraishi, H., Ohta, S., Nakamura, K., Okada, K., and Shimura, Y. (1992). Efficient transformation of Arabidopsis thaliana: Comparison of the efficiencies with various organs, plant ecotypes and Agrobacterium strains. Plant Cell Rep. 12, 7-11.
2. Al-Kaff, N.S., Covey, S.N., Kreike, M.M., Page, A.M., Pinder, R., and Dale, P.J. (1998). Transcriptional and posttranscriptional plant gene silencing in response to a pathogen. Science 279, 2113-2115.
3. Assaad, F.F., Tucker, K.L., and Signer, E.R. (1993). Epigenetic repeat-induced gene silencing (RIGS) in Arabidopsis. Plant Mol. Biol. 22, 1067-1085.
4. Barkan, A., and Martienssen, R.A. (1991). Inactivation of maize transposon Mu suppresses a mutant phenotype by activating an outward-reading promoter near the end of Mu1. Proc. Natl. Acad. Sci. USA 88, 3502-3506.
5. Bender, J., and Fink, G.R. (1995). Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell 83, 725-734.
6. Bennetzen, J.L., (1987). Covalent DNA modification and the regulation of Mutator element in maize. Mol. Gen. Genet. 208, 45-51.
7. Bennetzen, J.L., Springer, P.S., Cresse, A.D., and Hendricks, M. (1993). Specificity and regulation of the Mutator transposable element system in maize. Crit. Rev. Plant Sci. 12, 57-95.
8. Bennetzen, J.L., Schrick, K., Springer, P.S., Brown, W.E., and SanMiguel, P. (1994). Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 37, 565-576.
9. Boeke, J.D., Garfinkel, D.J., Styles, C.A., and Fink, G.R. (1985). Ty elements transpose through an RNA intermediate. Cell 40, 491-500.
10. Casacuberta, J.M., Vernhettes, S., and Grandbastien, M.A. (1995). Sequence variability within the tobacco retrotransposon Tnt1 population. EMBO J. 14, 2670-2678.
11. Chaboissier, M.C., Bucheton, A., and Finnegan, D.J. (1998). Copy number control of a transposable element, the / factor, a LINE-like element in Drosophila. Proc. Natl. Acad. Sci. USA 95, 11781-11785.
12. Covey, S.N., Al-Kaff, N.S., Langara, A., and Turner, D.S. (1997). Plants combat infection by gene silencing. Nature 387, 781-782.
13. Dehio, C., and Schell, J. (1994). Identification of plant genetic loci involved in post-transcriptional mechanisms for meiotically reversible transgene silencing. Proc. Natl. Acad. Sci. USA 91, 5538-5542.
14. Eichinger, D., and Boeke, J.D. (1988). The DNA intermediate in yeast Ty1 element transposition copurifies with virus-like particles: Cell-free Ty1 transposition. Cell 54, 955-966.
15. Elmayan, T., Balzergue, S., Beon, F., Bourdon, V., Daubremet, J., Guenet, Y., Mourrain, P., Palauqui, J.C., Vernhettes, S., Vialle, T., Wostrikoff, K., and Vaucheret, H. (1998). Arabidopsis mutants impaired in cosuppression. Plant Cell 10, 1747-1758.
16. Feuerbach, F., Drouaud, J., and Lucas, H. (1997). Retrovirus-like end processing of the tobacco Tnt1 retrotransposon linear intermediates of replication. J. Virol. 71, 4005-4015.
17. Finnegan, E.J., and Dennis, E.S. (1993). Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. Nucleic Acids Res. 21, 2383-2388.
18. Finnegan, E.J., Peacock, W.J., and Dennis, E.S. (1996). Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc. Natl. Acad. Sci. USA 98, 8449-8454.
19. Flavell, A.J., Dunbar, E., Anderson, R., Pearce, S.R., Hartley, R., and Kumar, A. (1992). Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Res. 20, 3639-3644.
20. Flavell, R.B. (1994). Inactivation of gene expression in plants as a consequence of novel sequence duplications. Proc. Natl. Acad. Sci. USA 91, 3490-3496.
21. Fujiwara, T., and Mizuuchi, K. (1988). Retroviral DNA integration: Structure of an integration intermediate. Cell 54, 497-504.
22. Furner, I.J., Sheikh, M.A., and Collett, C.E. (1998). Gene silencing and homology-dependent gene silencing in Arabidopsis: Genetic modifiers and DNA methylation. Genetics 149, 651-662.
23. Garrick, D., Fiering, S., Martin, D.I., and Whitelaw, E. (1998). Repeat-induced gene silencing in mammals. Nature Genet. 18, 56-59.
24. Grandbastien, M.-A. (1998). Activation of plant retrotransposons under stress conditions. Trends Plant Sci. 3, 181-187.
25. Grant, S.R. (1999). Dissecting the mechanisms of posttranscriptional gene silencing: Divide and conquer. Cell 96, 303-306.
26. Green, M.M. (1988). Mobile elements and spontaneous gene mutation. In Eukaryotic Transposable Elements as Mutagenic Agents, M.E. Lambert, J.F. McDonald, and I.B. Weinstein, eds (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press), pp. 41-50.
27. Hirochika, H. (1993). Activation of tobacco retrotransposons during tissue culture. EMBO J. 12, 2521-2528.
28. Hirochika, H. (1997). Retrotransposons of rice: Their regulation and use for genome analysis. Plant Mol. Biol. 35, 231-240.
29. Hirochika, H., and Hirochika, R. (1993). Ty1-copia group retrotransposons as ubiquitous components of plant genomes. Jpn. J. Genet. 68, 35-46.
30. Hirochika, H., Otsuki, H., Yoshikawa, M., Otsuki, Y., Sugimoto, K., and Takeda, S. (1996a). Autonomous transposition of the tobacco retrotransposon Tto1 in rice. Plant Cell 8, 725-734.
31. Hirochika, H., Sugimoto, K., Otsuki, Y., Tsugawa, H., and Kanda, M. (1996b). Retrotransposons of rice involved in mutations induced by tissue culture. Proc. Natl. Acad. Sci. USA 93, 7783-7788.
32. Hood, E.E., Helmer, G.L., Fraley, R.T., and Chilton, M.-D. (1986). The hypervirulence of Agrobacterium tumefaciens A281 is encoded in a region of pTiBio542 outside of T-DNA. J. Bacteriol. 168, 1291-1301.
33. Jeddeloh, J.A., Bender, J., and Richards, E.J. (1998). The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev. 12, 1714-1725.
34. Jeddeloh, J.A., Stokes, T.L., and Richards, E.J. (1999). Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nature Genet. 22, 94-97.
35. Jefferson, R.A., Kavanagh, T.A., and Bevan, M.W. (1987). GUS fusions: β-Glucuronidase as sensitive and versatile gene fusion marker in higher plants. EMBO J. 6, 3901-3907.
36. Jensen, S., Gassama, M.P., and Heidmann, T. (1999). Taming of transposable elements by homology-dependent gene silencing. Nature Genet. 21, 209-212.
37. Kakutani, T. (1997). Genetic characterization of late-flowering traits induced by DNA hypomethylation mutation in Arabidopsis thaliana. Plant J. 12, 1447-1451.
38. Kakutani, T., Jeddeloh, J., and Richards, E. (1995). Characterization of an Arabidopsis thaliana DNA hypomethylation mutant. Nucleic Acids Res. 23, 130-137.
39. Kakutani, T., Jeddeloh, J.A., Flowers, S.K., Munakata, K., and Richards, E.J. (1996). Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc. Natl. Acad. Sci. USA 93, 12406-12411.
40. Kakutani, T., Munakata, K., Richards, E.J., and Hirochika, H. (1999). Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics 151, 831-838.
41. Kass, S.U., Pruss, D., and Wolffe, A.P. (1997). How does DNA methylation repress transcription? Trends Genet. 13, 444-449.
42. Konieczny, A., Voytas, D., Cummings, M., and Ausubel, F. (1991). A superfamily of retrotransposable elements in Arabidopsis thaliana. Genetics 127, 801-809.
43. Lister, C., and Dean, C. (1993). Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana. Plant J. 4, 745-750.
44. Lucas, H., Feuerbach, F., Kunert, K., Grandbastien, M.-A., and Caboche, M. (1995). The tobacco retrotransposon Tnt1 transposes in Arabidopsis thaliana. EMBO J. 14, 2364-2373.
45. Luff, B., Pawlowski, L., and Bender, J. (1999). An inverted repeat triggers cytosine methylation of identical sequences in Arabidopsis. Mol. Cell 3, 505-511.
46. Martienssen, R. (1996). Epigenetic silencing of Mu transposable elements in maize. In Epigenetic Mechanisms of Gene Regulation, A. Riggs, R. Martienssen, and V. Russo, eds (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press), pp. 593-608.
47. Martienssen, R. (1998). Transposons, DNA methylation and gene control. Trends Genet. 14, 263-264.
48. Matzke, M.A., Matzke, A.J.M., and Eggleston, W.B. (1996). Para-mutation and transgene silencing: A common response to invasive DNA? Trends Plant Sci. 1, 382-388.
49. Meyer, P., and Saedler, H. (1996). Homology-dependent gene silencing in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47, 23-48.
50. Mittelsten Scheid, O., Afsar, K., and Paszkowski, J. (1998). Release of epigenetic gene silencing by trans-acting mutations in Arabidopsis. Proc. Natl. Acad. SCi. USA 95, 632-637.
51. Nagata, T., Okada, K., Takebe, I., and Matsui, C. (1981). Delivery of tobacco mosaic virus RNA into plant protoplasts mediated by reverse-phase evaporation vesicles (liposomes). Mol. Gen. Genet. 184, 161-165.
52. Pal-Bhadra, M., Bhadra, U., and Birchler, J.A. (1997). Cosuppression in Drosophila: Gene silencing of Alcohol dehydrogenase by white-Adh transgenes is Polycomb dependent. Cell 90, 479-490.
53. Pearce, S.R., Harrison, G., Li, D., Heslop-Harrison, J.S., Kumar, A., and Flavell, A.J. (1996). The Ty1-copia group retrotransposons in Vicia species: Copy number, sequence heterogeneity and chromosomal localisation. MoL. Gen. Genet. 250, 305-315.
54. Pouteau, S., Huttner, E., Grandbastien, M.-A., and Caboche, M. (1991). Specific expression of the tobacco Tnt1 retrotransposon in protoplasts. EMBO J. 10, 1911-1918.
55. Pruitt, R.E., and Meyerowitz, E.M. (1986). Characterization of the genome of Arabidopsis thaliana. J. MoL. Biol. 187, 169-183.
56. Ratcliff, F., Harrison, B.D., and Baulcombe, D.C. (1997). A similarity between viral defense and gene silencing in plants. Science 276, 1558-1560.
57. Ronchi, A., Petroni, K., and Tonelli, C. (1995). The reduced expression of endogenous duplications (REED) in the maize R gene family is mediated by DNA methylation. EMBO J. 14, 5318-5328.
58. Ronemus, M.J., Galbiati, M., Ticknor, C., Chen, J., and Dellaporta, S.L. (1996). Demethylation-induced developmental pleiotropy in Arabidopsis. Science 273, 654-657.
59. SanMiguel, P., and Bennetzen, J.L. (1998). Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. 81, 37-44.
60. SanMiguel, P. Tikhonov, A., Jin, Y.-K., Melake-Berhan, A., Springer, P.S., Edwards, K.J., Avramova, Z., and Bennetzen, J.L. (1996). Nested retrotransposons in the intergenic regions of the maize genome. Science 274, 765-768.
61. Selker, E.U. (1999). Gene silencing: Repeats that count. Cell 97, 157-160.
62. Surzycki, S.A., and Belknap, W.R. (1999). Characterization of repetitive DNA elements in Arabidopsis. J. Mol. Evol. 48, 684-691.
63. Takeda, S., Sugimoto, K., Otsuki, H., and Hirochika, H. (1998). Transcriptional activation of the tobacco retrotransposon Tto1 by wounding and methyl jasmonate. Plant Mol. Biol. 36, 365-376.
64. Takeda, S., Sugimoto, K., Otsuki, H., and Hirochika, H. (1999). A 13-bp c/s-regulatory element in the LTR promoter of the tobacco retrotransposon Tto1 is involved in responsiveness to tissue culture, wounding, methyl jasmonate and fungal elicitors. Plant J. 18, 383-393.
65. Valvekens, D., Van Montagu, M., and Van Lijsebettens, M. (1988). Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana root expiants by using kanamycin selection. Proc. Natl. Acad. Sci. USA 85, 5536-5540.
66. Vaucheret, H., Beclin, C., Elmayan, T., Feuerbach, F., Godon, C., Morel, J.B., Mourrain, P., Palauqui, J.C., and Vernhettes, S. (1998). Transgene-induced gene silencing in plants. Plant J. 16, 651-659.
67. Vongs, A., Kakutani, T., and Martienssen, R.A., and Richards, E.J. (1993). Arabidopsis thaliana DNA methylation mutants. Science 260, 1926-1928.
68. Voytas, D.F., Cummings, M.P., Konieczny, A., Ausubel, F.M., and Rodermel, S.R. (1992). Copia-like retrotransposons are ubiquitous among plants. Proc. Natl. Acad. Sci. USA 89, 7124-7128.
69. Walsh, C.P., Chaillet, J.R., and Bester, T.H. (1998). Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nature Genet. 20, 116-117.
70. Wessler, S.R., Bureau, T.E., and White, S.E. (1995). LTR-retrotransposons and MITEs: Important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5, 814-821.
71. Yoder, J.A., Walsh, C.P., and Bester, T.H. (1997). Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13, 335-340.