Impact of aging on DNA methylation

Ageing Research Reviews

Volumn 2, Issue 3, 2003, Pages 245-261

  Richardson, Bruce ^a,b  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b VETERANS AFFAIRS MEDICAL CENTER   (United States)

Author keywords

Aging; Autoimmunity; Cancer; Chromatin structure; DNA methylation

Indexed keywords

ANTIARRHYTHMIC AGENT; ANTIHYPERTENSIVE AGENT; CYTARABINE DERIVATIVE; CYTOSINE DERIVATIVE; HETEROCYCLIC COMPOUND; HYDRALAZINE; HYDROXYUREA; METHYL GROUP; PROCAINAMIDE; RETINOIC ACID;

AGING; AUTOIMMUNITY; CELL DIFFERENTIATION; CHROMATIN STRUCTURE; CPG ISLAND; DISEASE COURSE; DNA METHYLATION; DNA SEQUENCE; GENE EXPRESSION; GENE MAPPING; GENOME IMPRINTING; HEART ARRHYTHMIA; HUMAN; MALIGNANT NEOPLASTIC DISEASE; NONHUMAN; PATHOGENESIS; PROTEIN BINDING; PROTEIN FUNCTION; REVIEW; SCIENCE; X CHROMOSOME; ANIMAL; GENETICS; NEOPLASM;

AGING; ANIMALS; AUTOIMMUNITY; DNA METHYLATION; GENE EXPRESSION; HUMANS; NEOPLASMS;

EID: 0344321897     PISSN: 15681637     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1568-1637(03)00010-2     Document Type: Review

References (89)

1. Agarwal S., Rao A. Modulation of chromatin structure regulates cytokine gene expression during T cell differentiation. Immunity. 9:1998;765-775.
2. Amir R.E., Van den Veyver I.B., Wan M., Tran C.Q., Francke U., Zoghbi H.Y. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat. Genet. 23:1999;185-188.
3. Antequera F., Bird A. Number of CpG islands and genes in human and mouse. Proc. Natl. Acad. Sci. U.S.A. 90:1993;11995-11999.
4. Antequera, F., Bird, A., 1993b. CpG islands. In: Jost, J.P., Saluz, H.P. (Eds.), DNA Methylation: Molecular Biology and Biological Significance. Birkhauser Verlag, Basel, pp. 169-185.
5. Bachman K.E., Rountree M.R., Baylin S.B. Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin. J. Biol. Chem. 276:2001;32282-32287.
6. Barbot W., Dupressoir A., Lazar V., Heidmann T. Epigenetic regulation of an IAP retrotransposon in the aging mouse: progressive demethylation and de-silencing of the element by its repetitive induction. Nucleic Acids Res. 30:2002;2365-2373.
7. Baylin S. Mechanisms underlying epigenetically mediated gene silencing in cancer. Semin. Cancer Biol. 12:2002;331.
8. Bestor T., Laudano A., Mattaliano R., Ingram V. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. J. Mol. Biol. 203:1988;971-983.
9. Bhattacharya S.K., Ramchandani S., Cervoni N., Szyf M. A mammalian protein with specific demethylase activity for mCpG DNA. Nature. 397:1999;579-583.
10. Bird A. The essentials of DNA methylation. Cell. 70:1992;5-8.
11. Bird A.P. Gene number, noise reduction and biological complexity. Trends Genet. 11:1995;94-100.
12. Bird A.P., Wolffe A.P. Methylation-induced repression - belts, braces, and chromatin. Cell. 99:1999;451-454.
13. Chan A.O., Broaddus R.R., Houlihan P.S., Issa J.P., Hamilton S.R., Rashid A. CpG island methylation in aberrant crypt foci of the colorectum. Am. J. Pathol. 160:2002;1823-1830.
14. Chen R.Z., Pettersson U., Beard C., Jackson-Grusby L., Jaenisch R. DNA hypomethylation leads to elevated mutation rates. Nature. 395:1998;89-93.
15. Clark S.J., Harrison J., Paul C.L., Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22:1994;2990-2997.
16. Comb M., Goodman H.M. CpG methylation inhibits proenkephalin gene expression and binding of the transcription factor AP-2. Nucleic Acids Res. 18:1990;3975-3982.
17. Cooney C.A. Dietary selenium and arsenic affect DNA methylation. J. Nutr. 131:2001;1871-1872.
18. Cornacchia E., Golbus J., Maybaum J., Strahler J., Hanash S., Richardson B. Hydralazine and procainamide inhibit T cell DNA methylation and induce autoreactivity. J. Immunol. 140:1988;2197-2200.
19. Counts J.L., Sarmiento J.I., Harbison M.L., Downing J.C., McClain R.M., Goodman J.L. Cell proliferation and global methylation status changes in mouse liver after phenobarbital and/or choline-devoid, methionine-deficient diet administration. Carcinogenesis. 17:1996;1251-1257.
20. Deng C., Yang J., Scott J., Hanash S., Richardson B.C. Role of the Ras-MAPK signaling pathway in the DNA methyltransferase response to DNA hypomethylation. Biol. Chem. 379:1998;1113-1120.
21. Deng C., Kaplan M.J., Yang J., Ray D., Zhang Z., McCune W.J., Hanash S.M., Richardson B.C. Decreased Ras-mitogen-activated protein kinase signaling may cause DNA hypomethylation in T lymphocytes from lupus patients. Arthritis Rheum. 44:2001;397-407.
22. Duan W., Ladenheim B., Cutler R.G., Kruman I.I., Cadet J.L., Mattson M.P. Dietary folate deficiency and elevated homocysteine levels endanger dopaminergic neurons in models of Parkinson's disease. J. Neurochem. 80:2002;101-110.
23. Ehrlich M. DNA methylation in cancer: too much, but also too little. Oncogene. 21:2002;5400-5413.
24. Feinberg A.P. DNA methylation, genomic imprinting and cancer. Curr. Top. Microbiol. Immunol. 249:2000;87-99.
25. Feinberg A., Cui H., Ohlsson R. DNA methylation and genomic imprinting: insights from cancer into epigenetic mechanisms. Semin. Cancer Biol. 12:2002;389.
26. Ferguson-Smith A.C., Surani M.A. Imprinting and the epigenetic asymmetry between parental genomes. Science. 293:2001;1086-1089.
27. Golbus J., Palella T.D., Richardson B.C. Quantitative changes in T cell DNA methylation occur during differentiation and ageing. Eur. J. Immunol. 20:1990;1869-1872.
28. Hansen R.S., Wijmenga C., Luo P., Stanek A.M., Canfield T.K., Weemaes C.M., Gartler S.M. The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc. Natl. Acad. Sci. U.S.A. 96:1999;14412-14417.
29. Hatada I., Hayashizaki Y., Hirotsune S., Komatsubara H., Mukai T. A genomic scanning method for higher organisms using restriction sites as landmarks. Proc. Natl. Acad. Sci. U.S.A. 88:1991;9523-9527.
30. Hendrich B., Hardeland U., Ng H.H., Jiricny J., Bird A. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature. 401:1999;301-304.
31. Issa J.P. CpG-island methylation in aging and cancer. Curr. Top. Microbiol. Immunol. 249:2000;101-118.
32. Issa J.P., Ottaviano Y.L., Celano P., Hamilton S.R., Davidson N.E., Baylin S.B. Methylation of the oestrogen receptor CpG island links ageing and neoplasia in human colon. Nat. Genet. 7:1994;536-540.
33. Issa J.P., Vertino P.M., Boehm C.D., Newsham I.F., Baylin S.B. Switch from monoallelic to biallelic human IGF2 promoter methylation during aging and carcinogenesis. Proc. Natl. Acad. Sci. U.S.A. 93:1996;11757-11762.
34. Jones P.A. Altering gene expression with 5-azacytidine. Cell. 40:1985;485-486.
35. Jones P.A., Takai D. The role of DNA methylation in mammalian epigenetics. Science. 293:2001;1068-1070.
36. Jost J.P., Schwarz S., Hess D., Angliker H., Fuller-Pace F.V., Stahl H., Thiry S., Siegmann M. A chicken embryo protein related to the mammalian DEAD box protein p68 is tightly associated with the highly purified protein-RNA complex of 5-MeC-DNA glycosylase. Nucleic Acids Res. 27:1999;3245-3252.
37. Kawai J., Suzuki H., Taga C., Hara A., Watanabe S. Correspondence of RLGS-M spot behavior with tissue expression on mouse homologue of DP1/TB2 gene. Biochem. Biophys. Res. Commun. 213:1995;967-974.
38. Klein C.B., Costa M. DNA methylation, heterochromatin and epigenetic carcinogens. Mutat. Res. 386:1997;163-180.
39. Kruman I.I., Kumaravel T.S., Lohani A., Pedersen W.A., Cutler R.G., Kruman Y., Haughey N., Lee J., Evans M., Mattson M.P. Folic acid deficiency and homocysteine impair DNA repair in hippocampal neurons and sensitize them to amyloid toxicity in experimental models of Alzheimer's disease. J. Neurosci. 22:2002;1752-1762.
40. Laird, P.W., Jaenisch, R., 1994. DNA methylation and cancer. Hum. Mol. Genet. 3, 1487-1495.
41. Lengauer C., Kinzler K.W., Vogelstein B. DNA methylation and genetic instability in colorectal cancer cells. Proc. Natl. Acad. Sci. U.S.A. 94:1997;2545-2550.
42. Li E., Bestor T.H., Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell. 69:1992;915-926.
43. Lindsay S., Bird A.P. Use of restriction enzymes to detect potential gene sequences in mammalian DNA. Nature. 327:1987;336-338.
44. Lopatina N., Haskell J.F., Andrews L.G., Poole J.C., Saldanha S., Tollefsbol T. Differential maintenance and de novo methylating activity by three DNA methyltransferases in aging and immortalized fibroblasts. J. Cell. Biochem. 84:2002;324-334.
45. Lu Q., Kaplan M., Ray D., Zacharek S., Gutsch D., Richardson B. Demethylation of ITGAL (CD11a) regulatory sequences in systemic lupus erythematosus. Arthritis Rheum. 46:2002a;1282-1291.
46. Lu Q., Ray D., Gutsch D., Richardson B. Effect of DNA methylation and chromatin structure on ITGAL expression. Blood. 99:2002b;4503-4508.
47. MacLeod A.R., Rouleau J., Szyf M. Regulation of DNA methylation by the Ras signaling pathway. J. Biol. Chem. 270:1995;11327-11337.
48. Maher E.R., Reik W. Beckwith-Wiedemann syndrome: imprinting in clusters revisited. J. Clin. Invest. 105:2000;247-252.
49. Matzke M.A., Mette M.F., Aufsatz W., Jakowitsch J., Matzke A.J. Host defenses to parasitic sequences and the evolution of epigenetic control mechanisms. Genetica. 107:1999;271-287.
50. Mays-Hoopes L., Chao W., Butcher H.C., Huang R.C. Decreased methylation of the major mouse long interspersed repeated DNA during aging and in myeloma cells. Dev. Genet. 7:1986;65-73.
51. Nan X., Ng H.H., Johnson C.A., Laherty C.D., Turner B.M., Eisenman R.N., Bird A. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature. 393:1998;386-389.
52. Nyce J., Liu L., Jones P.A. Variable effects of DNA-synthesis inhibitors upon DNA methylation in mammalian cells. Nucleic Acids Res. 14:1986;4353-4367.
53. Okano M., Xie S., Li E. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nat. Genet. 19:1998;219-220.
54. Okano M., Bell D.W., Haber D.A., Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 99:1999;247-257.
55. Ono T., Shinya K., Uehara Y., Okada S. Endogenous virus genomes become hypomethylated tissue - specifically during aging process of C57BL mice. Mech. Ageing Dev. 50:1989;27-36.
56. Ono T., Uehara Y., Kurishita A., Tawa R., Sakurai H. Biological significance of DNA methylation in the ageing process. Age Ageing. 22:1993;S34-43.
57. Ottaviano Y.L., Issa J.P., Parl F.F., Smith H.S., Baylin S.B., Davidson N.E. Methylation of the estrogen receptor gene CpG island marks loss of estrogen receptor expression in human breast cancer cells. Cancer Res. 54:1994;2552-2555.
58. Pallis M., Robins A., Powell R. Quantitative analysis of lymphocyte CD11a using standardized flow cytometry. Scand. J. Immunol. 38:1993;559-564.
59. Park C.W., Chung J.H. Age-dependent changes of p57(Kip2) and p21(Cip1/Waf1) expression in skeletal muscle and lung of mice. Biochim. Biophys. Acta. 1520:2001;163-168.
60. Park Y., Kuroda M.I. Epigenetic aspects of X-chromosome dosage compensation. Science. 293:2001;1083-1085.
61. Poirier L.A. The effects of diet, genetics and chemicals on toxicity and aberrant DNA methylation: an introduction. J. Nutr. 132:2002;2336S-2339S.
62. Rath P.C., Kanungo M.S. Methylation of repetitive DNA sequences in the brain during aging of the rat. FEBS Lett. 244:1989;193-198.
63. Reik W., Dean W., Walter J. Epigenetic reprogramming in mammalian development. Science. 293:2001;1089-1093.
64. Richardson B.C. Role of DNA methylation in the regulation of cell function: autoimmunity, aging and cancer. J. Nutr. 132:2002;2401S-2405S.
65. Richardson B., Scheinbart L., Strahler J., Gross L., Hanash S., Johnson M. Evidence for impaired T cell DNA methylation in systemic lupus erythematosus and rheumatoid arthritis. Arthritis Rheum. 33:1990;1665-1673.
66. Richardson B., Powers D., Hooper F., Yung R.L., O'Rourke K. Lymphocyte function-associated antigen 1 overexpression and T cell autoreactivity. Arthritis Rheum. 37:1994;1363-1372.
67. Romanov G.A., Vanyushin B.F. Methylation of reiterated sequences in mammalian DNAs. Effects of the tissue type, age, malignancy and hormonal induction. Biochim. Biophys. Acta. 653:1981;204-218.
68. Rouleau J., MacLeod A.R., Szyf M. Regulation of the DNA methyltransferase by the Ras-AP-1 signaling pathway. J. Biol. Chem. 270:1995;1595-1601.
69. Rowling M.J., McMullen M.H., Schalinske K.L. Vitamin A and its derivatives induce hepatic glycine N-methyltransferase and hypomethylation of DNA in rats. J. Nutr. 132:2002;365-369.
70. Sherr C.J., DePinho R.A. Cellular senescence: mitotic clock or culture shock? Cell. 102:2000;407-410.
71. Slagboom P.E., de Leeuw W.J., Vijg J. Messenger RNA levels and methylation patterns of GAPDH and beta-actin genes in rat liver, spleen and brain in relation to aging. Mech. Ageing Dev. 53:1990;243-257.
72. Spotswood H.T., Turner B.M. An increasingly complex code. J. Clin. Invest. 110:2002;577-582.
73. Takatsu M., Uyeno S., Komura J., Watanabe M., Ono T. Age-dependent alterations in mRNA level and promoter methylation of collagen alpha1(I) gene in human periodontal ligament. Mech. Ageing Dev. 110:1999;37-48.
74. Tissenbaum H.A., Guarente L. Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans. Nature. 410:2001;227-230.
75. Toyota M., Ahuja N., Ohe-Toyota M., Herman J.G., Baylin S.B., Issa J.P. CpG island methylator phenotype in colorectal cancer. Proc. Natl. Acad. Sci. U.S.A. 96:1999;8681-8686.
76. Tra J.K.T., Lu Q., Kuick R., Hanash S., Richardson B. Infrequent occurrence of age-dependent changes in CpG island methylation as detected by restriction landmark genome scanning. Mech. Ageing Dev. 123:2002;1487-1503.
77. Vanyushin B.F., Tkacheva S.G., Belozersky A.N. Rare bases in animal DNA. Nature. 225:1970;948-949.
78. Vanyushin B.F., Nemirovsky L.E., Klimenko V.V., Vasiliev V.K., Belozersky A.N. The 5-methylcytosine in DNA of rats. Tissue and age specificity and the changes induced by hydrocortisone and other agents. Gerontologia. 19:1973;138-152.
79. Verkerk A.J., Pieretti M., Sutcliffe J.S., Fu Y.H., Kuhl D.P., Pizzuti A., Reiner O., Richards S., Victoria M.F., Zhang F.P.et al. Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in Fragile X syndrome. Cell. 65:1991;905-914.
80. Wade P.A., Gegonne A., Jones P.L., Ballestar E., Aubry F., Wolffe A.P. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat. Genet. 23:1999;62-66.
81. Wilson V.L., Smith R.A., Ma S., Cutler R.G. Genomic 5- methyldeoxycytidine decreases with age. J. Biol. Chem. 262:1987;9948-9951.
82. Wolffe A.P., Jones P.L., Wade P.A. DNA demethylation. Proc. Natl. Acad. Sci. U.S.A. 96:1999;5894-5896.
83. Wu J., Issa J.P., Herman J., Bassett D.E. Jr., Nelkin B.D., Baylin S.B. Expression of an exogenous eukaryotic DNA methyltransferase gene induces transformation of NIH 3T3 cells. Proc. Natl. Acad. Sci. U.S.A. 90:1993;8891-8895.
84. Yoder J.A., Walsh C.P., Bestor T.H. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13:1997;335-340.
85. Yung R.L., Quddus J., Chrisp C.E., Johnson K.J., Richardson B.C. Mechanism of drug-induced lupus. I. Cloned Th2 cells modified with DNA methylation inhibitors in vitro cause autoimmunity in vivo. J. Immunol. 154:1995;3025-3035.
86. Yung R., Powers D., Johnson K., Amento E., Carr D., Laing T., Yang J., Chang S., Hemati N., Richardson B. Mechanisms of drug-induced lupus. II. T cells overexpressing lymphocyte function-associated antigen 1 become autoreactive and cause a lupus-like disease in syngeneic mice. J. Clin. Invest. 97:1996;2866-2871.
87. Yung R., Chang S., Hemati N., Johnson K., Richardson B. Mechanisms of drug-induced lupus. IV. Comparison of procainamide and hydralazine with analogs in vitro and in vivo. Arthritis Rheum. 40:1997;1436-1443.
88. Yung R., Ray D., Eisenbraun J.K., Deng C., Attwood J., Eisenbraun M.D., Johnson K., Miller R.A., Hanash S., Richardson B. Unexpected effects of a heterozygous dnmt1 null mutation on age-dependent DNA hypomethylation and autoimmunity. J. Gerontol. A Biol. Sci. Med. Sci., B. 56:2001;268-276.
89. Zhang Z., Deng C., Lu Q., Richardson B. Age-dependent DNA methylation changes in the ITGAL (CD11a) promoter. Mech. Ageing Dev. 123:2002;1257-1268.