Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats

Plant Journal

Volumn 49, Issue 1, 2007, Pages 38-45

  Kinoshita, Yuki ^a   Saze, Hidetoshi ^a   Kinoshita, Tetsu ^a   Miura, Asuka ^a   Soppe, Wim J J ^b   Koornneef, Maarten ^b   Kakutani, Tetsuji ^a  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH   (Germany)

Author keywords

DNA methylation; Epigenetic; Imprinting; RNA directed DNA methylation; Transposon

Indexed keywords

CYTOSINE METHYLATION; EPIGENETIC; EPIGENETIC CONTROL; TRANSGENES;

DNA; MUTAGENESIS; PLANTS (BOTANY); RNA;

GENES;

ARABIDOPSIS PROTEIN; FWA PROTEIN, ARABIDOPSIS; HOMEODOMAIN PROTEIN; TRANSCRIPTION FACTOR;

ARABIDOPSIS; ARTICLE; GENE EXPRESSION REGULATION; GENE SILENCING; GENETICS; NUCLEOTIDE REPEAT; SHORT INTERSPERSED REPEAT; TRANSGENIC PLANT;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; GENE EXPRESSION REGULATION, PLANT; GENE SILENCING; HOMEODOMAIN PROTEINS; PLANTS, GENETICALLY MODIFIED; REPETITIVE SEQUENCES, NUCLEIC ACID; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS; TRANSCRIPTION FACTORS;

GENES; METHYLATION; MUTATION; NUCLEIC ACIDS; PLANTS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 33845621109     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2006.02936.x     Document Type: Article

References (53)

1. Cao, X. and Jacobsen, S.E. (2002) Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr. Biol. 12, 1138-1144.
2. Chan, S., Zilberman, D., Xie, Z., Johansen, L.K., Carrington, J.C. and Jacobsen, S.E. (2004) RNA silencing genes control de novo DNA methylation. Science, 303, 1336.
3. 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.
4. Choi, Y., Gehring, M., Johnson, L., Hannon, M., Harada, J.J., Goldberg, R.B., Jacobsen, S.E. and Fischer, R.L. (2002) DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis. Cell, 110, 33-42.
5. Clough, S.J. and Bent, A.F. (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735-743.
6. Elmayan, T., Proux, F. and Vaucheret, H. (2005) Arabidopsis RPA2: a genetic link among transcriptional gene silencing, DNA repair, and DNA replication. Curr. Biol. 8, 1919-1925.
7. Gehring, M., Huh, J.H., Hsieh, T.F., Penterman, J., Choi, Y., Harada, J.J., Goldberg, R.B., Fischer, R.L. (2006) DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell, 124, 495-506.
8. Grewal, S.I. and Rice, J.C. (2004) Regulation of heterochromatin by histone methylation and small RNAs. Curr. Opin. Cell Biol. 16, 230-238.
9. Grossniklaus, U., Vielle-Calzada, J.P., Hoeppner, M.A. and Gagliano, W.B. (1998) Maternal control of embryogenesis by MEDEA, a polycomb group gene in Arabidopsis. Science, 280, 446-450.
10. Hirochika, H., Okamoto, H. and Kakutani, T. (2000) Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell, 12, 357-369.
11. 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.
12. Kakutani, T. (1997) Genetic characterization of late-flowering traits induced by DNA hypomethylation mutation in Arabidopsis thaliana. Plant J. 12, 1447-1451.
13. Kakutani, T., Jeddeloh, J., Flowers, S., Munakata, K. and Richards, E. (1996) Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc. Natl Acad. Sci. USA, 93, 12406-12411.
14. Kakutani, T., Munakata, K., Richards, E. and Hirochika, H. (1999) Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics, 163, 1109-1122.
15. Kaneda, M., Okano, M., Hata, K., Sado, T., Tsujimoto, N., Li, E. and Sasaki, H. (2004) Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature, 429, 900-903.
16. Kankel, M.W., Ramsey, D.E., Stokes, T.L., Flowers, S.K., Haag, J.R., Jeddeloh, J.A., Riddle, N.C., Verbsky, M.L. and Richards, E.J. (2003) Arabidopsis MET1 cytosine methyltransferase mutants. Genetics, 163, 1109-1122.
17. Kato, M., Miura, A., Bender, J., Jacobsen, S. and Kakutani, T. (2003) Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr. Biol. 13, 421-426.
18. Kato, M., Takashima, K. and Kakutani, T. (2004) Epigenetic control of CACTA transposon mobility in Arabidopsis thaliana. Genetics, 168, 961-969.
19. Kinoshita, T., Yadegari, R., Harada, J.J., Goldberg, R.B. and Fischer, R.L. (1999) Imprinting of the MEDEA polycomb gene in the Arabidopsis endosperm. Plant Cell, 11, 1945-1952.
20. Kinoshita, T., Miura, A., Choi, Y., Kinoshita, Y., Cao, X., Jacobsen, S.E., Fischer, R.L. and Kakutani, T. (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science, 303, 521-523.
21. Koornneef, M., Hanhart, C. and Veen, J.V.D. (1991) A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol. Gen. Genet. 229, 57-66.
22. Li, E., Beard, C. and Jaenisch, R. (1993) Role for DNA methylation in genomic imprinting. Nature, 366, 362-365.
23. 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.
24. Lippman, Z., Gendrel, A.V., Black, M. et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature, 430, 471-476.
25. Llave, C., Kasschau, K., Rector, M. and Carrington, J. (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell, 14, 1605-1619.
26. Martienssen, R.A. (2003) Maintenance of heterochromatin by RNA interference of tandem repeats. Nat. Genet. 35, 213-214.
27. Matzke, M.A., Mette, M.F., Aufsatz, W., Jakowisch, J. and Matzke, A.J. (1999) Host defenses to parasitic sequences and the evolution of epigenetic control mechanisms. Genetica, 107, 271-287.
28. Melquist, S. and Bender, J. (2003) Transcription from an upstream promoter controls methylation signaling from an inverted repeat of endogenous genes in Arabidopsis. Genes Dev. 17, 2036-2047.
29. Mette, M.F., Aufsatz, W., van der Winden, J., Matzke, M.A. and Matzke, A.J. (2000) Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J. 19, 5194-5201.
30. 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.
31. Miura, A., Kato, M., Watanabe, K., Kawabe, H., Kotani, H. and Kakutani, T. (2004) Genomic localization of endogenous mobile CACTA family transposons in natural variants of Arabidopsis thaliana. Mol. Genet. Genom. 270, 524-532.
32. Myouga, F., Tsuchimoto, S., Noma, K., Ohtsubo, H. and Ohtsubo, E. (2001) Identification and structural analysis of SINE elements in the Arabidopsis thaliana genome. Genes Genet. Syst. 74, 169-179.
33. Neumann, B., Kubicka, P. and Barlow, D.P. (1995) Characteristics of imprinted genes. Nat. Genet. 9, 12-13.
34. Paulin, R., Grigg, G.W., Davey, M.W. and Piper, A.A. (1998) Urea improves efficiency of bisulphite-mediated sequencing of 5′-methylcytosine in genomic DNA. Nucleic Acids Res. 26, 5009-5010.
35. Pikaard, C.S. (2000) The epigenetics of nucleolar dominance. Trends Genet. 16, 495-500.
36. Rangwala, S.H. and Richards, E.J. (2004) The value-added genome: building and maintaining genomic cytosine methylation landscapes. Curr. Opin. Genet. Dev. 14, 686-691.
37. Ronemus, M., Galbiati, M., Ticknor, C., Chen, J. and Dellaporta, S. (1996) Demethylation-induced developmental pleiotropy in Arabidopsis. Science, 273, 654-657.
38. Saze, H., Scheid, O.M. and Paszkowski, J. (2003) Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat. Genet. 34, 65-69.
39. Scott, R.J. and Spielman, M. (2004) Epigenetics: imprinting in plants and mammals - the same but different? Curr. Biol. 14, R201-R203.
40. Selker, E., Tountas, N., Cross, S., Margolin, B., Murphy, J., Bird, A. and Freitag, M. (2003) The methylated component of the Neurospora crassa genome. Nature, 422, 893-897.
41. Shih, M.C., Heinrich, P. and Goodman, H.M. (1991) Cloning and chromosomal mapping of nuclear genes encoding chloroplast and cytosolic glyceraldehyde-3-phosphate-dehydrogenase from Arabidopsis thaliana. Gene, 104, 133-138.
42. Singer, T., Yordan, C. and Martienssen, R. (2001) Robertson's Mutator transposons in A. thaliana are regulated by the chromatin remodeling gene decrease in DNA Methylation (DDM1). Genes Dev. 15, 591-692.
43. Soppe, W.J., Jacobsen, S.E., Alonso-Blanco, C., Jackson, J.P., Kakutani, T., Koornneef, M. and Peeters, A.J.M. (2000) The late flowering phenotype of fwa mutants is caused by gain-offunction epigenetic alleles of a homeodomain gene. Mol. Cell. 6, 791-802.
44. Spillane, C., Baroux, C., Escobar-Restrepo, J.M., Page, D.R., Laoueille, S. and Grossniklaus, U. (2004) Transposons and tandem repeats are not involved in the control of genomic imprinting at the MEDEA locus in Arabidopsis. Cold Spring Harb. Symp. Quant. Biol. 69, 465-475.
45. Stam, M., Belele, C., Dorweiler, J.E. and Chandler, V.L. (2002) Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev. 16, 1906-1918.
46. Stokes, T.L., Kunkel, B.N. and Richards, E.J. (2002) Epigenetic variation in Arabidopsis disease resistance. Genes Dev. 16, 171-182.
47. Takeda, S., Tadele, S., Hofmann, I. et al. (2004) BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis. Genes Dev. 18, 782-793.
48. 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.
49. Vielle-Calzada, J.P., Thomas, J., Spillane, C., Coluccio, A., Hoeppner, M.A. and Grossniklaus, U. (1999) Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM1 activity. Genes Dev. 13, 2971-2982.
50. Vongs, A., Kakutani, T., Martienssen, R.A. and Richards, E.J. (1993) Arabidopsis thaliana DNA methylation mutants. Science, 260, 1926-1928.
51. Wesley, S.V., Helliwell, C.A., Smith, N.A. et al. (2001) Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J. 27, 581-590.
52. Xiao, W., Gehring, M., Choi, Y., Margossian, L., Pu, H., Harada, J.J., Goldberg, R.B., Pennell, R.I. and Fischer, R.L. (2003) Imprinting of the MEA polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev. Cell, 5, 891-901.
53. Yoder, J.A., Walsh, C.P. and Bestor, T.H. (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13, 335-340.