Genome methylation and its role in the functioning of eukaryotic organisms

Genetika

Volumn 36, Issue 11, 2000, Pages 1475-1486

  Prokhorchouk, A V ^a   Rouzov, A S ^a  

^a INSTITUTE OF GENE BIOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN; DNA METHYLTRANSFERASE;

ANIMAL; CHEMISTRY; CHROMATIN; CPG ISLAND; DNA REPLICATION; EUKARYOTIC CELL; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; GENETICS; GENOME; GENOME IMPRINTING; HUMAN; METABOLISM; METHYLATION; NEOPLASM; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; REVIEW;

ANIMALS; CHROMATIN; CPG ISLANDS; DNA; DNA MODIFICATION METHYLASES; DNA REPLICATION; DNA-BINDING PROTEINS; EUKARYOTIC CELLS; GENOME; GENOMIC IMPRINTING; HUMANS; METHYLATION; NEOPLASMS; PROTEIN STRUCTURE, TERTIARY; RECOMBINATION, GENETIC; TRANSCRIPTION, GENETIC;

EID: 0034320662     PISSN: 00166758     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (84)

1. Roger L.P., Adams R.L. DNA methylation //Biochem. J. 1990. V. 265. P. 301-320.
2. Jino Y., Yun K., Nishiwaki K. et al. Mosaic and polymorphic Imprinting of the WT1 gene in humans //Nature Genet. 1994. V. 6. P. 305-309.
3. Adams R.L. Eukaryotic LNA methyltransferases - structure and function//BioEssays. 1995. V. 17. P. 139-145.
4. Bestor T.H., Verdin G.L. DNA methyltransferase //Current Opinion in Cell Biol. 1994. V. 6. P. 380-389.
5. Bestor T.H. Activation of mammalian DNA methyltransferases by cleavageof a Zn binding regulatory domain//EMBOJ. 1992. V. 11. P. 2611-2617.
6. Walsh C.P., Bestor T.H. Cytosine methylation and mammalian development //Genes Dev. 1999. V. 13. X 1. P. 26-34.
7. Ng H.-H., Zhang Y., Hendrich B. et al. MBD2 is a transcriptional represser belonging to the MeCPl histon deacetylase complex //Nat. Genet. 1999. V. 23. KB 1. P. 58-61.
8. Mellon I., Bohr VA., Smith LA., Hanawalt P.C. Preferential DNA repair of an active gene in human cell //Proc. Natl Acad. Sei. USA. 1987. V. 83. P. 8878-8882.
9. Lichtenstein M., Keini G., Cedar H., Bergman Y. B cellspecific demethylation: a novel role for the intronic K chain enhancer sequence //Cell. 1994. V. 76. P. 913-923.
10. Zacharias W. Methylation of cytosine influences the DNA structure //DNA methylation. Molecular and Biological Significance / Eds lost J.P., Saluz H.P. Basel, Switherland: Birkhauther Verlag, 1993. P. 27-38.
11. Tazi J., Bird A. Alternative chromatin structure at CpG island //Cell. 1990. V. 2. P. 909-920.
12. Wolffe S., Schröder M., Wittig B. Lack of correlation between DNA methylation and transcriptional inactivation: The chiken Lysozyme gene //Proc. Natl Acad. Sei. USA. 1991. V. 88. P. 271-275.
13. SarahS., Ariel M.,GoiteinR. etal. Regulation of mouse satellite DNA replication time //EMBO J. 1988. V. 7. JNs 2. P. 419-426.
14. Kitsberg D., Selig S., Brandeus M. et al. Allele-specific replication timing of imprinted gene regions //Nature. 1993. V. 364. P. 459-463.
15. Hsieh C.-L., Lieber M.R. CpG methylated minichromosomes become inaccessible for V(D)J recombination after undergoing replication //EMBO J. 1992. V. 11. P. 315-325.
16. Tasheva E.S., Roufa DJ. Densely methylated DNA islands in mammalian chromosomal replication origins //Mol. and Cell. Biol. 1994. V. 14. P. 5636-5644.
17. Hug M., Silke J., Georgiev O. et al. Transcriptional repression by methylation: cooperativity between a CpG cluster and a remote CpG-regions //FEBS Letters. 1996. V. 379. H. 251-254.
18. Boy es J., Bird A. DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein //Cell. 1991. V. 64. P. 1123-1134.
19. Eden S., Cedar H. Role of DNA methylation in the regulation of transcription //Current Biol. 1994. V. 4. P. 255-259.
20. Fajkus J., Vyscot B., Bezdek M. Cyanges in chromatin structure due to hypomethylation induced with 5-azacytidine or DL-ethionine //FEBS Letters. 1992. V. 314. P. 13-16.
21. Talor S.M. 4-Aza-2'-deoxycytidine: cell differentiation DNA methylation //Leukemia. 1993. V. 7. P. 3-8.
22. Horwitz M. Hypermethylated myoblast specificaly defitient in MyoD autoactivation as a consequence of MyoD II Exptl Cell Res. 1996. V. 226. P. 170-182.
23. Singer-Sam J., Riggs A.D. X Chromosom inactivation and DNA methylation //DNA methylation: Molecular Biology and Biological Significance / Eds Jost J.P., Saluz H.P. Basel, Switherland: Birkhauther Verlag, 1993. P. 358-384.
24. YisraeliJ., AdelsteinR.S., MelloudD. etal. Muscle-specific activation of a methylated chimeric actin gene //Cell. 1986. V. 46. P. 409-16.
25. Anteguer F., Boyes J., Bird A. High levels of de novo methylation and altered chromation structure at CpG islands in cell lines //Cell. 1990. V. 62. P. 503-514.
26. Vertino P.M., IssaJ.P., Pereira-Smith O.M., Baylin S.B. Stabilization of DNA methyltransferase levels and CpG island hypermethylation precede SV40-induced immortalization of human fibroblasts //Cell Growth Differ. 1994. V. 5. P. 1395-1402.
27. Smith G.M., Whelm J., PresciniR. etal. DNA-methylation of the E-selectin promoter represses NF-KB transactivation //Biochem. and Biophys. Res. Comm. 1993. V. 194. P. 115-122.
28. Watt F., Molloy PL. Cytosin methylation prevents binding to DNA of a HeLa cell transcription factor required for optimal expression of the adenovirus major late promoter //Genes and Develop. 1988. V. 2. P. 1136-1143.
29. Iguchi-Ariga S.M.M., Schaffner W. CpG methylation of the cAMP-responsive enhancer/promoter sequence, TGACGTCA, abolishes specific factor binding as well as transcriptional activation //Genes and Develop. 1989. V. 3. P. 612-619.
30. Prendergast G.C., Lawe D., Ziff E.B. Association of Myn, the Murine homolog of Max, with c-Myc stimulates methylation-sensitive DNA binding and ras cotransformation //Cell. 1991. V. 65. P. 395-407.
31. Comb M., Goodman H.W. CpG methylation inhibits proenkephalin gene expression and binding of the transcription factor AP-2 //Nucl. Acids Res. 1990. V. 18. P. 3975-3982.
32. Kovesdi L, Reichet R., Nevins J.R. Role of an adenovirus E2 promoter binding factor in El A-mediated coordinate gene control //Proc. Natl Acad. Sei. USA. 1987. V. 84. P. 2180-2184.
33. Boyes J., Bird A. Repression of by DNA methylation depends on CpG density and promoter strength: evidence for invilment of a methyl-CpG binding protein //EMBO J. 1992. V. 11. P. 327-333.
34. Pawlak A., Bryans M., Jost J.-P. An avian 40 kD nukleoprotein binds preferentially to a promoter sequence containing one single pair of methylated CpG //Nucl. Acids Res. 1991. V. 19. P. 1029-1034.
35. Siegfried Z., Eden S., Mendelsohn M. et al. DNA methylation repress transcription in vivo //Nat. Genet. 1999. V. 22. JSfo 2. P. 203-206.
36. Jost J.-P., Hofsteenge J. The represser MDBP-2 is a member of the histon HI family that dinds preferentially in vitro and in vivo methylated nonspecific DNA sequences //Proc. Natl Acad. Sei. USA. 1992. V. 89. p.-9503.
37. Bruhat A., Jost J.P. Phosphorilation/dephosphorilation of the represser MDPB-2-H1 selectively affects the level of transcription from a methylated promoter in vitro //Nucl. Acids Res. 1996. V. 24. .Ns 10. P. 1816-1821.
38. MacleordD.,CharltonJ.,MullinsJ.,Bird A.P.Spl sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island //Genes and Develop. 1994. V. 8. P. 2282-2292.
39. Huynh K.D., Bardwell VJ. The BCL-6 POZ domain and other POZ domains interact with the co-repressors N-CoR and SMRT//Oncogene. 1998. V. 17. P. 2473-2484.
40. Samiec P.S., Goodman J.L. Evaluation of methylated DNA binding protein-1 in mouse liver //Toxicol Sei. 1999. V. 49. N 2. P. 255-262.
41. Little M., WainwrightB. Methylation and p!6: Suppressing the suppressor //Nature Med. 1995. V. 1. P. 633634.
42. Joel P., Shao W., Pratt K. A nuclear protein with enhanced binding to methylated Spl sites in the AIDS virus promoter //Nucl. Acids Res. 1993. V. 21. P. 5786-5793.
43. Mancini D.N., Sink S.M., Archer T.K., Rodenhiser D.I. Site specific DNA methylation in the neurofibromatosis (NF1) promoter interfers with binding of CREB and SP1 transcription factors //Oncogene. 1999. V. 18. Ms 28. p. 4108-4119.
44. Tulchinsky E.M., Georgiev G.P., Lukanidin EM. Novel AP-1 site created by DNA methylation //Oncogene. 1996. V. 12. NO 8. P. 1737-1745.
45. Buschhausen G., Witting B., Graessmann M., Graessmann A. Chromatin structure is required to block transcription of the methylated herpes simplex virus thymidine kinase gene //Proc. Natl Acad. Sei. USA. 1987. V. 84. P. 1171-1181.
46. BrandeisM., FrankD., Keshetl. etal. Spl elements protect a CpG island from de novo methylation //Nature. 1994. V. 371. P. 435-438.
47. Bellacosa A., Cicchillitti L., Schepis F. et al. MED1, a novel human methyl-CpG-binding endonuclease, interacts with DNA mismatch repair protein MLH1 //Proc. Natl Acad. Sei. USA. 1999. V. 96. P. 3969-3974.
48. Nan X., Compoy J., Bird A. MeCP2 is a transcriptional represser with abundant binding sites in genomic chromatin//Cell. 1997. V. 88. P. 471-481.
49. Jones PL., Wolffe A. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription //Nature Genet. 1998. V. 19. P. 187-191.
50. Lewis I.D., Meehan R.R., Henzel WJ. et al. Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA //Cell. 1992. V. 69. P. 905-914.
51. Hundriss J., Lorenzi R., Purewal A., Monk M. A methylation-dependent DNA binding activity recognizing the methylated promoter region of the mouse Xist gene //Biochem. and Biophys. Res. Comm. 1997. V. 235. P. 730-738.
52. Nan X., Täte P., Li E., Bird A. DNA methylation specifies chromosomal localization of MeCp2 //Mol. and Cell. Biol. 1996. V. 16. P. 414-421.
53. Saluz H.P., Jiricny J., Jost J.P. Genomic sequencing reveals a positive correlation between the kinetics of strand-specific DNA demethylation of the overlapping estradiol/glucocorticoid-receptor binding sites and the rate of avian vitellogenin mRNA synthesis //Proc. Natl Acad. Sei. USA. 1986. V. 83. JNa 19. P. 7167-7171.
54. Hendrich B., Bird A. Identification and characterization of a family of mammalian methyl-CpG binding proteins //Mol. Cel. Biol. 1998. V. 18. P. 6538-6547.
55. Eden S., Hashimshony T., Keshetl., Cedar H. DNA methylation models histon acetilation //Nature. 1998. V. 394. P. 842.
56. Fiore B.D., Palena A., Felsani A. et al. Cytosine methylation transforms an E2F site in the retinoblastoma gene promoter into a binding site for the general repressor methylcytosine-binding protein 2 (MeCP2) //Nucl. Acids Res. 1999. V. 27. P. 2852-2859.
57. Zhang Y., Ng H., Erdjument-Bromage H. et al. Analysis of the NURD subunits reveal a histone deacetylase core complex and a connection with DNA methylation //Genes and Develop. 1999. V. 13. P. 1924-1936.
58. Daniel J.M., Reynolds A.B. The catenin p120ctn interacts with a novel BTB/POZ zinc finger transcription factor, Kaiso//Mol. Cell. Biol. 1999. V. 19. P. 3614-3623.
59. Ferguson-Smith S.H., Sasaki H., Cattanack B.M., Surani M.A. Parental-origin-specific epigenetic modification of the mouse H19 gene //Nature. 1993. V. 362. P. 751-755.
60. Bardwell VJ., Treisman R. The POZ domain: a conserved protein-protein interaction motif //Genes and Develop. 1994. V. 8. P. 1664-1677.
61. De la Luna S., Alien K.E., Mason S.L., La Tangue N.B. Integration of a growth-suppressing BTB/POZ domain protein with the DP component of the E2F transcription factor //EMBO J. 1999. V. 18. J 1. P. 212-228.
62. Dhordain P., Lin RJ., QuiefS. et al. The LAZ3(BCL-6) oncoprotein recruits a SMRT(mSIN3A) histon deacetylase containing complex to mediate transcriptional repression //Nucl. Acids Res. 1998. V. 26. -Ns 20. P. 4645-4651.
63. Bestor T.H., Gundersen G., Kolsto A.-B., Prydz H. CpG islands in mammalian gene promoters are inherently resistant to de novo methylation //Genet. Anal. Tech. Appl. 1992. V. 9. P. 48-53.
64. Razin A., Cedar H. DNA methylation and genomic imprinting //Cell. 1994. V. 77. P. 473-476.
65. Barlow D.P. Gametic imprinting in mammals //Science. 1995. V. 270. P. 1610-1613.
66. Li E., Bestor H., Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embrionic lethality //Cell. 1992. V. 69. P. 915-926.
67. Tucker K.L., Beard C., Dausmann J. et al. Germ-lene passage is required for esteblishment of methylation and expression patterns of imprinted but not of nonimprinted genes //Genes and Develop. 1996. V. 12. P. 321-324.
68. Surani M. Genomic imprinting: control of gene expression by epigenetic inheritance //Current Opinion in Cell Biol. 1994. V. 6. P. 390-395.
69. Leighton P.F., Ingram R.S., Eggeschwiler J. et al. Disruption of imprinting caused by deletion of the HI 9 gene region in mice //Nature. 1995. V. 375. P. 34-39.
70. Bestor T.H. DNA methylation: how a bacterial immune function has evolved into a regulatory of gene expression and genome structure in higher eukaryotes //Philos. Trans. R. Soc. Lond. (B) Biol. Sei. 1990. V. 326. P. 179-187.
71. Wines D.R., Talbert P.B., Clark D.V., HenikoffS. Introduction of a DNA methyltransferase into Drosophila to probe chromatin structure in vivo //Chromosoma. 1996. V. 104. P. 332-340.
72. Counts J.L., Goodman J.l. Alterations in DNA methylation may play a variety of roles in carcinogenesis //Cell. 1995. V. 83. P. 13-15.
73. Laird P.W., Jackson-Grusby L., Fazeli A. et al. Supression of intestinal neoplasia by DNA hypomethylation //Cell. 1995. V. 81. P. 197-205.
74. Baylin S.B. Abnormal patterns of DNA methylation in human neoplasia: potential consequences for tumor progression //Cancer Cell. 1991. V. 3. P. 383-390.
75. GreenblattM.S.,Bennett W.P., Harris C.C. Mutations in the p53 tumor suppressor gene: clues to cancer etiology and molecular pathogenesis //Cancer Res. 1994. V. 54. P. 4855-4878.
76. Liard P.W., Jaenisch R. DNA methylation and cancer //Hum. Mol. Genet. 1994. V. 3. P. 1487-1495.
77. GraffJ.R., Gabrielson E., Fujii H. et al. Methylation patterns of the E-cadherin 5'-CpG island are unstable and reflect the dynamic, heterogeneous loss of E-cadherin expression during metastatic progression //J. Biol. Chem. 2000. V. 275. Ma 4. P. 2727-2732.
78. Shivapurcar N. Hepatic DNA methylation and liver tumor formation in male C3H mice fed methionon - and cholin-deficient diets //J. Natl. Cancer Inst. 1987. V. 77. P. 213-217.
79. Rainier S., Johnson LA., Dobry CJ. etal. Relaxation of imprinted genes in human cancer //Nature. 1993. V. 362. P. 747-749.
80. Ogawa O., Eccles M.R., Szeto J. et al. Relaxation of insulin-like growth factor II gene imprinting implicated in Wilm's tumor //Nature. 1993. V. 362. P. 749-751.
81. Herman J.G., LatifF., Weng G. et al. Silencing of the VHL tumor-suppressor gene by DNA methylation in renal carcinoma//Proc. Natl Acad. Sei. USA. 1994. V. 91. P. 9700-9704.
82. Adams R.L.P., Lindsay H. What is hemimethylated DNA? //FEES Letters. 1993. V. 320. P. 243-245.