The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis

Genes and Development

Volumn 12, Issue 11, 1998, Pages 1714-1725

  Jeddeloh, Jeffrey A ^a   Bender, Judith ^b   Richards, Eric J ^a  

^a WASHINGTON UNIVERSITY   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

ddm1; DNA methylation; Epigenetics; Gene silencing; PAI; Phosphoribosylanthranilate isomerase

Indexed keywords

ARABIDOPSIS; ARTICLE; DNA METHYLATION; FLUORESCENCE; GENE EXPRESSION; GENE LOCUS; GENE MUTATION; HOMOZYGOSITY; NONHUMAN; PHYTOCHEMISTRY; PRIORITY JOURNAL;

ARABIDOPSIS;

EID: 2642622566     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.12.11.1714     Document Type: Article

References (61)

1. Allshire, R.C., J.-P. Javerzat, N.J. Redhead, and G. Cranston. 1994. Position effect variegation at fission yeast centromeres. Cell 76: 157-169.
2. Aparicio, O.M., B.L. Billington, and D.E. Gottschling. 1991. Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell 66: 1279-1287.
3. Ausubel, F.M., R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith, and K. Strahl. 1987. Current protocols in molecular biology. John Wiley & Sons, New York, NY.
4. Banks, J.A., P. Masson, and N. Fedoroff. 1988. Molecular mechanisms in the developmental regulation of the maize Suppressor-mutator transposable elements. Genes & Dev. 2: 1364-1380.
5. Bender, J. and G.R. Fink. 1995. Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell 83: 725-734.
6. Bollmann, J., R. Carpenter, and E.S. Coen. 1991. Allelic interactions at the nivea locus of Antirrhinum. Plant Cell 3: 1327-1336.
7. Church, G.M. and W. Gilbert. 1984. Genomic sequencing. Proc. Natl. Acad. Sci. 81: 1991-1995.
8. Cocciolone, S.M. and K.C. Cone. 1993. Pl-Bh, an anthocyanin regulatory gene of maize that leads to a variegated pigmentation. Genetics 135: 575-588.
9. Colot, V. and J.-L. Rossingnol. 1995. Isolation of the Ascobolus immersus sport color gene b2 and study in single cells of gene silencing by methylation induced premeiotically. Genetics 141: 1299-1314.
10. Das, O.P. and J. Messing. 1994. Variegated phenotype and developmental methylation changes of a maize allele originating from epimutation. Genetics 136: 1121-1141.
11. Davies, G.J., M.A. Sheikh, O.J. Ratcliffe, G. Coupland, and I.J. Furner. 1997. Genetics of homology-dependent gene silencing in Arabidopsis; a role for methylation. Plant J. 12: 781-804.
12. Depicker, A. and M.V. Montagu. 1997. Post-transcriptional gene silencing in plants. Curr. Opin. Cell Biol. 9: 373-382.
13. Dernburg, A.F., K.W. Broman, J.C. Fung, W.F. Marshall, J. Phillips, D.A. Agard, and J.W. Sedat. 1996. Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85: 745-759.
14. Duelling, J.H. and C.S. Pikaard. 1993. Transient expression in Arabidopsis thaliana protoplasts derived from rapidly established cell suspension cultures. Plant Cell Rep. 12: 241-244.
15. Dorer, D.R. and S. Henikoff. 1994. Expression of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell 77: 993-1002.
16. Finnegan, E.J., W.J. Peacock, and E.S. Dennis. 1996. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc. Natl. Acad. Sci. 98: 8449-8454.
17. Frommer, M., L.E. McDonald, D.S. Millar, C.M. Collis, F. Watt, G.W. Grigg, P.L. Molloy, and C.L. Paul. 1992. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. 89: 1827-1831.
18. Grewal, S.I. and A.J.S. Klar. 1996. Chromosomal inheritance of epigenetic states in fission yeast during mitosis and meiosis. Cell 86: 95-101.
19. Hollick, J.B., G.I. Patterson, E.H. Coe, Jr., K.C. Cone, and V.L. Chandler. 1995. Allelic interactions heritably alter the activity of a metastable maize p1 allele. Genetics 141: 709-719.
20. Holliday, R. and J.E. Pugh. 1975. DNA modification mechanism and gene activity during development. Science 187: 226-232.
21. Irelan, J.T. and E.U. Selker. 1997. Cytosine methylation associated with repeat-induced point mutation causes epigenetic gene silencing in Neurospora crassa. Genetics 146: 509-523.
22. Jacobsen, S.E. and E.M. Meyerowitz. 1997. Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 277: 1100-1103.
23. mCCG methylation in angiosperms. Plant J. 9: 579-586.
24. Kakutani, T., J.A. Jeddeloh, and E.J. Richards. 1995. Characterization of an Arabidopsis thaliana DNA hypomethylation mutant. Nucleic Acids Res. 23: 130-137.
25. Kakutani, T., J.A. Jeddeloh, S.K. Flowers, K. Munakata, and E.J. Richards. 1996. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc. Natl. Acad. Sci. 93: 12406-12411.
26. Kass, S.U., D. Pruss, and A.P. Wolffe. 1997. How does DNA methylation repress transcription? Trends Genet. 13: 444-449.
27. Kermicle, J.L., W.B. Eggleston, and M. Alleman. 1995. Organization of paramutagenicity in R-stippled maize. Genetics 141: 361-372.
28. Konieczny, A. and F.M. Ausubel. 1993. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J. 4: 403-410.
29. Last, R.L. and G.R. Fink. 1988. Tryptophan-requiring mutants of the plant Arabidopsis thaliana. Science 240: 305-310.
30. Li, E., T.H. Bestor, and R. Jaenisch. 1992. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: 915-926.
31. Li, J., J. Zhao, A.B. Rose, R. Schmidt, and R.L. Last. 1995. Arabidopsis phosphoribosylanthranilate isomerase: Molecular genetic analysis of triplicate tryptophan pathway genes. Plant Cell 7: 447-461.
32. Martienssen, R.A. 1996. Epigenetic phenomena: Paramutation and gene silencing in plants. Curr. Biol. 6: 810-813.
33. Martienssen, R. and A. Baron. 1994. Coordinate suppression of mutation caused by Robertson's Mutator transposons in maize. Genetics 136: 1157-1170.
34. Martienssen, R.A. and E.J. Richards. 1995. DNA methylation in eukaryotes. Curr. Opin. Genet. Dev. 5: 234-242.
35. Martienssen, R., A. Barkan, W.C. Taylor, and M. Freeling. 1990. Somatically heritable switches in the DNA modification of Mu transposable elements monitored with a suppressible mutant in maize. Genes & Dev. 4: 331-343.
36. Matzke, M.A. and A.J.M. Matzke. 1993. Genomic imprinting in plants: Parental effects and trans-inactivation phenomena. Annu Rev. Plant Physiol. Plant Mol. Biol. 44: 53-76.
37. McClelland, M., M. Nelson, and E. Raschke. 1994. Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res. 22: 3640-3659.
38. Metzlaff, M., M. O'Dell, P.D. Cluster, and R.B. Flavell. 1997. RNA-mediated RNA degradation and chalcone synthase A silencing in petunia. Cell 88: 845-854.
39. Meyer, P. and H. Saedler. 1996. Homology-dependent gene silencing in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47: 23-48.
40. Meyer, P., I. Heidmann, and I. Niedenhof. 1993. Differences in DNA-methylation are associated with a paramutation phenomenon in transgenic petunia. Plant J. 4: 89-100.
41. Meyer, P., I. Niedenhof, and M.t. Lohuis. 1994. Evidence for cytosine methylation of nonsymmetrical sequences in transgenic Petunia hybrida. EMBO J. 13: 2084-2088.
42. iapy) is correlated with methylation state and is influence by parental lineage. Genes & Dev. 8: 1463-1472.
43. Mittlesten Scheid, O., K. Afsar, and J. Paszkowski. 1998. Release of epigenetic gene silencing by trans-acting mutations in Arabidopsis. Proc. Natl. Acad. Sci. 95: 632-637.
44. Pal-Bhadra, M., U. Bhadra, and J.A. Birchler. 1997. Cosuppression in Drosophila: Gene silencing of Alcohol dehydrogenase by white-Adh transgenes in Polycomb dependent. Cell 90: 479-490.
45. Patterson, G., C.J. Thorpe, and V.L. Chandler. 1993. Paramutation, an allelic interaction, is associated with a stable and heritable reduction of transcription of the maize B regulatory gene. Genetics 135: 881-894.
46. Pillus, L. and J. Rine. 1989. Epigenetic inheritance of transcriptional states in S. cerevisiae. Cell 59: 637-647.
47. Pirrotta, V. 1997. Chromatin-silencing mechanisms in Drosophila maintain patterns of gene expression. Trends Genet. 13: 314-318.
48. Ratcliffe, F., B.D. Harrison, and D.C. Baulcombe. 1997. A similarity between viral defense and gene silencing in plants. Science 276: 1558-1560.
49. Richards, E.J. 1997. DNA methylation and plant development. Trends Genet. 13: 319-323.
50. Riggs, A.D. 1975. X inactivation, differentiation, and DNA methylation. Cytogenet. Cell Genet. 14: 9-25.
51. Ronchi, A., K. Petroni, and C. Tonelli. 1995. The reduced expression of endogenous duplications (REED) in the maize R gene family is mediated by DNA methylation. EMBO J. 14: 5318-5328.
52. Ronemus, M.J., M. Galbiati, C. Ticknor, J. Chen, and S.L. Dellaporta. 1996. Demethylation-induced developmental pleiotropy in Arabidopsis. Science 273: 654-657.
53. Sherman, J.M. and L. Pillus. 1997. An uncertain silence. Trends Genet. 13: 308-313.
54. Tanzer, M.M., W.F. Thompson, M.D. Law, E.A. Wernsman, and S. Uknes. 1997. Characterization of post-transcriptionally suppressed transgene expression that confers resistance to tobacco etch virus infection in tobacco. Plant Cell 9: 1411-1423.
55. Todd, J.J. and L.O. Vodkin. 1996. Duplications that suppress and deletions that restore expression from a chalcone synthase multigene family. Plant Cell 8: 687-699.
56. Vongs, A., T. Kakutani, R.A. Martienssen, and E.J. Richards. 1993. Arabidopsis thaliana DNA methylation mutants. Science 260: 1926-1928.
57. Wallrath, L.L. and S.C.R. Elgin. 1995. Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes & Dev. 9: 1263-1277.
58. Weber, H., C. Ziechmann, and A. Graessmann. 1990. In vitro DNA methylation inhibits gene expression in transgenic tobacco. EMBO J. 9: 4409-4415.
59. Wigler, M., D. Levy, and M. Perucho. 1981. The somatic replication of DNA methylation. Cell 24: 33-40.
60. Ye, F. and E.R. Signer. 1996. RIGS (repeat-induced gene silencing) in Arabidopsis is transcriptional and alters chromatin configuration. Proc. Natl. Acad. Sci. 93: 10881-10886.
61. Yoder, J.A., C.P. Walsh, and T.H. Bestor. 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13: 335-340.