Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers

Molecular Genetics and Genomics

Volumn 268, Issue 4, 2002, Pages 543-552

  Cervera, M T ^a,b   Ruiz Garcia L ^a,b   Martinez Zapater J M ^a,b  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b INIA   (Spain)

Author keywords

Amplified Fragment Length Polymorphisms (AFLPs); Arabidopsis thaliana; Cytosine methylation; DNA analysis; Methylation pattern

Indexed keywords

CYTOSINE; PLANT DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARABIDOPSIS; ARTICLE; CORRELATION ANALYSIS; DNA FINGERPRINTING; DNA METHYLATION; DNA SEQUENCE; ECOTYPE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

ARABIDOPSIS; DEOXYRIBONUCLEASE ECORI; DEOXYRIBONUCLEASE HPAII; DNA METHYLATION; DNA, PLANT; GENES, PLANT; PHYLOGENY; POLYMORPHISM, GENETIC; RESTRICTION MAPPING; SITE-SPECIFIC DNA METHYLTRANSFERASE (CYTOSINE-SPECIFIC); VARIATION (GENETICS);

ARABIDOPSIS; ARABIDOPSIS THALIANA; EMBRYOPHYTA;

EID: 0036456019     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-002-0772-4     Document Type: Article

References (51)

1. Adams RLP, Burdon RH (1985) Molecular Biology of DNA Methylation. Springer Verlag, New York
2. Bender J, Fink GR (1995) Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell 83:725-734
3. Burn JE, Bagnall DJ, Metzger JD, Dennis ES, Peacock WJ (1993) DNA methylation, vernalization, and the initiation of flowering. Proc Natl Acad Sci USA 90:287-291
4. Cao X, Springer NM, Muszynski MG, Phillips RL, Kaeppler S, Jacobsen SE (2000) Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc Natl Acad Sci USA 97:4979-4984
5. Cervera MT, Remington D, Frigerio JM, Storme V, Ivens B, Boerjan W, Plomion C (2000) Improved AFLP analysis of tree species. Can J For Res 30:1608-1616
6. Cubas P, Vincent C, Coen E (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401:157-161
7. Finnegan EJ, Dennis ES (1993) Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. Nucleic Acids Res 21:2383-2388
8. Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43:189-201
9. Finnegan EJ, Peacock WJ, Dennis ES (1996) Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Acad Sci USA 93:8449-8454
10. Finnegan EJ, Genger RK, Kovac K, Peacock WJ, Dennis ES (1998) DNA methylation and the promotion of flowering by vernalization. Proc Natl Acad Sci 95:5824-5829
11. Finnegan EJ, Peacock WJ, Dennis ES (2000) DNA methylation, a key regulator of plant development and other processes. Curr Opin Genet Dev 10:217-223
12. Fremont M, Siegmann M, Gaulis S, Matthies R, Hess D, Jost JP (1997) Demethylation of DNA by purified chick embryo 5-methylcytosine-DNA glycosylase requires both protein and RNA. Nucleic Acids Res 25:2375-2380
13. 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
14. Gruenbaum Y, Naveh-Many T, Cedar H, Razin A (1981) Sequence specificity of methylation in higher plant DNA. Nature 292:860-862
15. Hafiz IA, Anjum MA, Grewal AG, Chaudhary GA (2001) DNA methylation - An essential mechanism in plant molecular biology. Acta Physiol Plant 23:491-499
16. Holliday R (1987) The inheritance of epigenetic defects. Science 238:163-170
17. Holliday R (1990) DNA methylation and epigenetic inheritance. Philos Trans R Soc Lond B Biol Sci 326:329-338
18. Houlston CE, Lindsay H, Pradham S, Adams RLP (1993) DNA substrate specificity of pea DNA methylase. Biochem J 293:617-624
19. Hsieh CL (1999) In vivo activity of murine de novo methyltransferases, Dnmt3a and Dnmt3b. Mol Cell Biol 19:8211-8218
20. Jacobsen SE, Sakai H, Finnegan EJ, Cao X, Meyerowitz EM (2000) Ectopic hypermethylation of flower-specific genes in Arabidopsis. Curr Biol 10:179-186
21. Jost JP (1993) Nuclear extracts of chicken embryos promote an active demethylation of DNA by excision repair of 5-methyldeoxycytidine. Proc Natl Acad Sci USA 90:4684-4688
22. Jost JP, Saluz HP (1993) DNA Methylation: Molecular Biology and Biological Significance. Springer-Verlag, Basel
23. Karp A, Edwards KJ (1998) DNA markers: A global overview. In: Caetano- Anollés G, Gresshoff PM (eds) DNA Markers: Protocols, Applications and Overviews. Wiley, New York, pp 1-13
24. Korch C, Hagblom P (1986) In-vivo-modified gonococcal plasmid pJD1. A model system for analysis of restriction enzyme sensitivity to DNA modifications. Eur J Biochem 161:519-524
25. Leutwiler LS, Hough-Evans BR, Meyerowitz EM (1984) The DNA of Arabidopsis thaliana. Mol Gen Genet 194:15-23
26. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of CHROMO-METHYLASE3 for maintenance of CpXpG methylation. Science 292:2077-2080
27. Liu B, Brubaker CL, Mergeai G, Cronn RC, Wendel JF (2001) Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44:321-330
28. Luff B, Pawlowski L, Bender J (1999) An inverted repeat triggers cytosine methylation of identical sequences in Arabidopsis. Molecular Cell 3:505-511
29. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209-220
30. Martienssen RA, Colot V (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293:1070-1074
31. Martínez-Zapater JM, Estelle MA, Somerville CR (1986) A highly repeated DNA sequence in Arabidopsis thaliana. Mol Gen Genet 204:417-423
32. Matsuo K, Silke J, Georgiev O, Marti P, Giovannini N, Rungger D (1998) An embryonic demethylation mechanism involving binding of transcription factors to replicating DNA. EMBO J 17:1446-1453
33. McClelland M, Nelson M, Raschke E (1994) Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res 22:3640-3659
34. Messeguer R, Ganal MW, Steffens JC, Tanksley SD (1991) Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA. Plant Mol Biol 16:753-770
35. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassay with tobacco tissue cultures. Physiol Plant 15:473-479
36. Paszkowski J, Whitham S (2001) Gene silencing and DNA methylation processes. Curr Opin Plant Biol 4:123-129
37. Pradhan S, Adams RLP (1995) Distinct CG and CNG DNA methyltransferases in Pisum sativum. Plant J 7:471-481
38. Reyna-López GE, Simpson J, Ruiz-Herresa J (1997) Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Mol Gen Genet 253:703-710
39. Riddle NC, Richards EJ (2002) The control of natural variation in cytosine methylation in Arabidopsis. Genetics 162:355-363
40. Rohlf FJ (1998) NTSYS-PC Numerical Taxonomy and Multivariate Analysis System. Version 2.0. Exeter Publications, Setauket, N.Y.
41. Ronemus MJ, Galbiati M, Ticknor C, Chen J, Dellaporta SL (1996) Demethylation-induced developmental pleiotropy in Arabidopsis. Science 273:654-657
42. Sadri R, Hornsby PJ (1996) Rapid analysis of DNA methylation using new restriction enzyme sites created by bisulfite modification. Nucleic Acids Res 24:5058-5059
43. Schmitt F, Oakeley EJ, Jost JP (1997) Antibiotics induce genome-wide hypermethylation in cultured Nicotiana tabacum plants. J Biol Chem 272:1534-1540
44. Sneath PHA, Sokal RR (1973) The Principles and Practice of Numerical Classification. WH Freeman, San Francisco
45. Soppe WJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJ (2000) The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell 6:791-802
46. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
47. Vongs A, Kakutani T, Martienssen RA, Richards EJ (1993) Arabidopsis thaliana DNA methylation mutants. Science 260:1926-1928
48. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414
49. Watson JC, Kaufman LS, Thompson WF (1987) Developmental regulation of cytosine methylation in the nuclear ribosomal RNA genes of Pisum sativum. J Mol Biol 193:15-26
50. Weiss A, Keshet I, Razin A, Cedar H (1996) DNA demethylation in vitro: Involvement of RNA. Cell 86:709-718
51. Xiong LZ, Xu CG, Saghai Maroof MA, Zhang Q (1999) Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Gen Genet 261:439-446