The effects of heat induction and the siRNA biogenesis pathway on the transgenerational transposition of ONSEN, a copia-like retrotransposon in Arabidopsis thaliana

Plant and Cell Physiology

Volumn 53, Issue 5, 2012, Pages 824-833

  Matsunaga, Wataru ^a   Kobayashi, Akie ^b   Kato, Atsushi ^a   Ito, Hidetaka ^a,c  

^a HOKKAIDO UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Arabidopsis; Epigenetic; Heat stress; siRNA; Transposon

Indexed keywords

ARABIDOPSIS PROTEIN; MESSENGER RNA; PLANT DNA; SMALL INTERFERING RNA;

ARABIDOPSIS; ARTICLE; BIOSYNTHESIS; CELL DIFFERENTIATION; CYTOLOGY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HEAT; INHERITANCE; ISOLATION AND PURIFICATION; METABOLISM; PHYSIOLOGICAL STRESS; PHYSIOLOGY; RETROPOSON; SOUTHERN BLOTTING;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BIOSYNTHETIC PATHWAYS; BLOTTING, SOUTHERN; CELL DIFFERENTIATION; DNA, PLANT; GENE EXPRESSION REGULATION, PLANT; HOT TEMPERATURE; INHERITANCE PATTERNS; RETROELEMENTS; RNA, MESSENGER; RNA, SMALL INTERFERING; STRESS, PHYSIOLOGICAL; TRANSCRIPTION, GENETIC;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 84861081491     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcr179     Document Type: Article

References (44)

1. Bennetzen, J.L. (1987) Covalent DNA modification and the regulation of mutator element transposition in maize. Mol. Gen. Genet. 208: 45-51.
2. Brutnell, T.P., May, B.P. and Dellaporta, S.L. (1997) The Ac-st2 element of maize exhibits a positive dosage effect and epigenetic regulation. Genetics 147: 823-834. (Pubitemid 27418590)
3. Brzeski, J. and Jerzmanowski, A. (2003) Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J. Biol. Chem. 278: 823-828. (Pubitemid 36790755)
4. Capy, P., Gasperi, G., Biemont, C. and Bazin, C. (2000) Stress and transposable elements: co-evolution or useful parasites? Heredity 85: 101-106.
5. Chan, S.W., Henderson, I.R. and Jacobsen, S.E. (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet. 6: 351-360. (Pubitemid 40577179)
6. Chandler, V.L. and Walbot, V. (1986) DNA modification of a maize transposable element correlates with loss of activity. Proc. Natl Acad. Sci. USA 83: 1767-1771. (Pubitemid 16018644)
7. Church, G.M. and Gilbert, W. (1984) Genomic sequencing. Proc. Natl Acad. Sci. USA 81: 1991-1995. (Pubitemid 14146592)
8. Feng, S., Jacobsen, S.E. and Reik, W. (2010) Epigenetic reprogramming in plant and animal development. Science 330: 622-627.
9. Feschotte, C., Jiang, N. and Wessler, S.R. (2002) Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 3: 329-341. (Pubitemid 34506715)
10. Gasciolli, V., Mallory, A.C., Bartel, D.P. and 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. (Pubitemid 41187489)
11. Hashida, S.N., Kitamura, K., Mikami, T. and Kishima, Y. (2003) Temperature shift coordinately changes the activity and the methylation state of transposon Tam3 in Antirrhinum majus. Plant Physiol. 132: 1207-1216. (Pubitemid 36872871)
12. Hashida, S.N., Uchiyama, T., Martin, C., Kishima, Y., Sano, Y. and Mikami, T. (2006) The temperature-dependent change in methylation of the Antirrhinum transposon Tam3 is controlled by the activity of its transposase. Plant Cell 18: 104-118. (Pubitemid 43951318)
13. Hirochika, H. (1993) Activation of tobacco retrotransposons during tissue culture. EMBO J. 12: 2521-2528. (Pubitemid 23194203)
14. Hirochika, H., Okamoto, H. and Kakutani, T. (2000) Silencing of retrotransposons in arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12: 357-369.
15. Ito, H., Gaubert, H., Bucher, E., Mirouze, M., Vaillant, I. and Paszkowski, J. (2011) An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 472: 115-119.
16. Jacobsen, S.E. and Henderson, I.R. (2007) Epigenetic inheritance in plants. Nature 447: 418-424. (Pubitemid 46816748)
17. Jeddeloh, J.A., Stokes, T.L. and Richards, E.J. (1999) Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat. Genet. 22: 94-97. (Pubitemid 29214813)
18. Lippman, Z., May, B., Yordan, C., Singer, T. and Martienssen, R. (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol. 1: E67.
19. Lisch, D. (2009) Epigenetic regulation of transposable elements in plants. Annu. Rev. Plant Biol. 60: 43-66.
20. Lister, R., O'Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H. et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
21. Martienssen, R.A. and Colot, V. (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293: 1070-1074. (Pubitemid 32758076)
22. Martienssen, R.A., Singer, T. and Yordan, C. (2001) Robertson's mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1). Genes Dev. 15: 591-602. (Pubitemid 32205147)
23. Martienssen, R. and Slotkin, R.K. (2007) Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8: 272-285. (Pubitemid 46439291)
24. Mirouze, M., Reinders, J., Bucher, E., Nishimura, T., Schneeberger, K., Ossowski, S. et al. (2009) Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461: 427-430.
25. Miura, A., Yonebayashi, S., Watanabe, K., Toyama, T., Shimada, H. and Kakutani, T. (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411: 212-214. (Pubitemid 32455182)
26. Mosher, R.A., Melnyk, C.W., Kelly, K.A., Dunn, R.M., Studholme, D.J. and Baulcombe, D.C. (2009) Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460: 283-286.
27. 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. (Pubitemid 21905660)
28. Rabinowicz, P.D., Palmer, L.E., May, B.P., Hemann, M.T., Lowe, S.W., McCombie, W.R. et al. (2003) Genes and transposons are differentially methylated in plants, but not in mammals. Genome Res. 13: 2658-2664. (Pubitemid 37541154)
29. Reinders, J., Wulff, B.B., Mirouze, M., Mari-Ordonez, A., Dapp, M., Rozhon, W. et al. (2009) Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev. 23: 939-950.
30. Richards, E.J. and Rangwala, S.H. (2007) Differential epigenetic regulation within an Arabidopsis retroposon family. Genetics 176: 151-160. (Pubitemid 350021016)
31. Scortecci, K.C., Dessaux, Y., Petit, A. and Van Sluys, M.A. (1997) Somatic excision of the Ac transposable element in transgenic Arabidopsis thaliana after 5-azacytidine treatment. Plant Cell Physiol. 38: 336-343. (Pubitemid 27210907)
32. Slotkin, R.K. and Martienssen, R. (2007) Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8: 272-285. (Pubitemid 46439291)
33. Slotkin, R.K., Vaughn, M., Borges, F., Tanurdzic, M., Becker, J.D., Feijo, J.A. et al. (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136: 461-472.
34. Steward, N., Kusano, T. and Sano, H. (2000) Expression of ZmMET1, a gene encoding a DNA methyltransferase from maize, is associated not only with DNA replication in actively proliferating cells, but also with altered DNA methylation status in cold-stressed quiescent cells. Nucleic Acids Res. 28: 3250-3259. (Pubitemid 30662289)
35. Takeda, S., Sugimoto, K., Kakutani, T. and Hirochika, H. (2001) Linear DNA intermediates of the Tto1 retrotransposon in Gag particles accumulated in stressed tobacco and Arabidopsis thaliana. Plant J. 28: 307-317. (Pubitemid 33066395)
36. 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. (Pubitemid 28077010)
37. Tompa, R., McCallum, C.M., Delrow, J., Henikoff, J.G., Van Steensel, B. and Henikoff, S. (2002) Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3. Curr. Biol. 12: 65-68. (Pubitemid 34063355)
38. Tran, R.K., Zilberman, D., De Bustos, C., Ditt, R.F., Henikoff, J.G., Lindroth, A.M. et al. (2005) Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol. 6: R90.
39. Tsukahara, S., Kobayashi, A., Kawabe, A., Mathieu, O., Miura, A. and Kakutani, T. (2009) Bursts of retrotransposition reproduced in Arabidopsis. Nature 461: 423-426.
40. Vaucheret, H. (2008) Plant ARGONAUTES. Trends Plant Sc. 13: 350-358.
41. Vitte, C. and Bennetzen, J.L. (2006) Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc. Natl Acad. Sci. USA 103: 17638-17643. (Pubitemid 44852213)
42. Vongs, A., Kakutani, T., Martienssen, R.A. and Richards, E.J. (1993) Arabidopsis thaliana DNA methylation mutants. Science 260: 1926-1928. (Pubitemid 23258270)
43. Wessler, S.R. (1996) Turned on by stress. Plant retrotransposons. Curr. Biol. 6: 959-961.
44. Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S., Chan, S.W., Chen, H. et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126: 1189-1201. (Pubitemid 44380289)