Genome - Epigenome interactions in cancer

Human Molecular Genetics

Volumn 16, Issue R1, 2007, Pages

  Brena, Romulo M ^a   Costello, Joseph F ^b  

^a OHIO STATE UNIVERSITY   (United States)

^b Department of Neurological Surgery ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE 3A; DNA METHYLTRANSFERASE 3B; METHYLATED DNA PROTEIN CYSTEINE METHYLTRANSFERASE; PROMYELOCYTIC LEUKEMIA PROTEIN; PROTEIN MLH1; PROTEIN P53; RETINOIC ACID RECEPTOR; TRANSCRIPTION FACTOR PAX7; TRANSCRIPTION FACTOR PAX9;

BACTERIAL ARTIFICIAL CHROMOSOME; CANCER GENETICS; CARCINOGENESIS; COLON CANCER; CPG ISLAND; DISEASE COURSE; DNA METHYLATION; DNA MICROARRAY; EPIGENETICS; GENE IDENTIFICATION; GENE INTERACTION; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENE SILENCING; GENETIC MODEL; GENOME ANALYSIS; GENOMIC INSTABILITY; HEAD AND NECK CANCER; HETEROZYGOSITY LOSS; HUMAN; HYPOTHESIS; LEUKEMIA; LUNG CANCER; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; TUMOR SUPPRESSOR GENE;

EID: 34547824239     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddm073     Document Type: Review

References (156)

1. Garber, K. (2006) Momentum building for human epigenome project. J. Natl. Cancer Inst., 98, 84-86.
2. Higgins, M.E., Claremont, M., Major, J.E., Sander, C. and Lash, A.E. (2007) CancerGenes: A gene selection resource for cancer genome projects. Nucleic Acids Res., 35, D721-D726.
3. Jones, P.A. and Martienssen, R. (2005) A blueprint for a Human Epigenome Project: The AACR Human Epigenome Workshop. Cancer Res., 65, 11241-11246.
4. Okano, M., Bell, D.W., Haber, D.A. and Li, E. (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell, 99, 247-257.
5. Trasler, J.M., Trasler, D.G., Bestor, T.H., Li, E. and Ghibu, F. (1996) DNA methyltransferase in normal and Dnmtn/Dnmtn mouse embryos. Dev. Dyn., 206, 239-247.
6. Chen, R.Z., Pettersson, U., Beard, C., Jackson-Grusby, L. and Jaenisch, R. (1998) DNA hypomethylation leads to elevated mutation rates. Nature, 395, 89-93.
7. Maraschio, P., Zuffardi, O., Dalla Fior, T. and Tiepolo, L. (1988) Immunodeficiency, centromeric heterochromatin instability of chromosomes 1, 9 and 16, and facial anomalies: The ICF syndrome. J. Med. Genet. 25, 173-180.
8. Hansen, R.S., Wijmenga, C., Luo, P., Stanek, A.M., Canfield, T.K., Weemaes, C.M.R. and Gartler, S.M. (1999) The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc. Natl. Acad. Sci. USA, 96, 14412-14417.
9. Xu, G.L., Bestor, T.H., Bourc'his, D., Hsieh, C.L., Tommerup, N., Bugge, M., Hulten, M., Qu, X.Y., Russo, J.J. and Viegas-Pequignot, E. (1999) Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature, 402, 187-191.
10. Gonzalo, S., Jaco, I., Fraga, M.F., Chen, T., Li, E., Esteller, M. and Blasco, M.A. (2006) DNA methyltransferases control telomere length and telomere recombination in mammalian cells. Nat. Cell Biol., 8 416-424.
11. Li, E., Bestor, T.H. and Jaenisch, R. (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell, 69, 915-926.
12. Fan, G.P., Beard, C., Chen, R.Z., Csankovszki, G., Sun, Y., Siniaia, M., Biniszkiewicz, D., Bates, B., Lee, P.P., Kuhn, R. et al. (2001) DNA hypomethylation perturbs the function and survival of CNS neurons in postnatal animals. J. Neurosci., 21, 788-797.
13. Takizawa, T., Nakashima, K., Namihira, M., Ochiai, W., Uemura, A., Yanagisawa, M., Fujita, N., Nakao, M. and Taga, T. (2001) DNA methylation is a critical cell-intrinsic determinant of astrocyte differentiation in the fetal brain. Dev. Cell, 1, 749-758.
14. Kawai, J., Hirotsune, S., Hirose, K., Fushiki, S., Watanabe, S. and Hayashizaki, Y. (1993) Methylation profiles of genomic DNA of mouse developmental brain detected by restriction landmark genomic scanning (Rlgs) method. Nucleic Acids Res., 21, 5604-5608.
15. Kazazian, H.H. and Moran, J.V. (1998) The impact of L1 retrotransposons on the human genome. Nat. Genet., 19, 19-24.
16. Costello, J.F. (2003) DNA methylation in brain development and gliomagenesis. Front. Biosci., 8, S175-S184.
17. Rollins, R.A., Haghighi, F., Edwards, J.R., Das, R., Zhang, M.Q., Ju, J. and Bestor, T.H. (2006) Large-scale structure of genomic methylation patterns. Genome Res., 16, 157-163.
18. Das, R., Dimitrova, N., Xuan, Z., Rollins, R.A., Haghighi, F., Edwards, J.R., Ju, J., Bestor, T.H. and Zhang, M.Q. (2006) Computational prediction of methylation status in human genomic sequences. Proc. Natl. Acad. Sci. USA, 103, 10713-10716.
19. Ehrlich, M. (2000) DNA methylation: Normal development, inherited diseases, and cancer. J. Clin. Ligand Assay, 23, 144-146.
20. Ehrlich, M., Gama-Sosa, M.A., Huang, L.-H., Midgett, R.M., Kuo, K.C., McCune, R.A. and Gehrke, C. (1982) Amount and distribution of 5-methylcytosine in human DNA from different types of tissues and cells. Nucleic Acids Res., 10, 2709-2721.
21. Song, F., Smith, J.F., Kimura, M.T., Morrow, A.D., Matsuyama, T., Nagase, H. and Held, W.A. (2005) Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proc. Natl. Acad. Sci. USA., 102, 3336-3341.
22. Ching, T.T., Maunakea, A.K., Jun, P., Hong, C., Zardo, G., Pinkel, D., Albertson, D.G., Fridlyand, J., Mao, J.H., Shchors, K. et al. (2005) Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat. Genet, 37, 645-651.
23. Fraga, M.F., Ballestar, E., Paz, M.F., Ropero, S., Setien, F., Ballestar, M.L., Heine-Suner, D., Cigudosa, J.C., Urioste, M., Benitez, J. et al. (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proc. Natl. Acad. Sci. USA., 102, 10604-10609.
24. Sandovici, I., Kassovska-Bratinova, S., Loredo-Osti, J.C., Leppert, M., Suarez, A., Stewart, R., Bautista, F.D., Schiraldi, M. and Sapienza, C. (2005) Interindividual variability and parent of origin DNA methylation differences at specific human Alu elements. Hum. Mol. Genet., 14, 2135-2143.
25. Wong, A.H., Gottesman, I.I. and Petronis, A. (2005) Phenotypic differences in genetically identical organisms: The epigenetic perspective. Hum. Mol. Genet., 14(Spec No. 1), R11-R18.
26. Gartner, K. (1990) A third component causing random variability beside environment and genotype. A reason for the limited success of a 30 year long effort to standardize laboratory animals? Lab. Anim., 24 71-77.
27. Cardno, A.G., Rijsdijk, F.V., Sham, P.C., Murray, R.M. and McGuffin, P. (2002) A twin study of genetic relationships between psychotic symptoms. Am. J. Psychiatry, 159, 539-545.
28. Feinberg, A.P. (2005) Cancer epigenetics is no Mickey Mouse. Cancer Cell, 8, 267-268.
29. Baylin, S. and Bestor, T.H. (2002) Altered methylation patterns in cancer cell genomes: Cause or consequence? Cancer Cell, 1, 299-305.
30. Costello, J.F. and Plass, C. (2001) Methylation matters. J. Med. Genet., 38, 285-303.
31. Jones, P.A. and Baylin, S.B. (2007) The epigenomics of cancer. Cell 128, 683-692.
32. Feinberg, A.P. and Vogelstein, B. (1983) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301, 89-92.
33. Feinberg, A.P., Gehrke, C.W., Kuo, K.C. and Ehrlich, M. (1988) Reduced genomic 5-methylcytosine content in human colonic neoplasia. Cancer Res., 48, 1159-1161.
34. Gama-Sosa, M.A., Slagel, V.A., Trewyn, R.W., Oxenhandler, R., Kuo, K.C., Gehrke, C.W. and Ehrlich, M. (1983) The 5-methylcytosine content of DNA from human tumors. Nucleic Acids Res., 11, 6883-6894.
35. Gaudet, F., Hodgson, J.G., Eden, A., Jackson-Grusby, L., Dausman, J., Gray, J.W., Leonhardt, H. and Jaenisch, R. (2003) Induction of tumors in mice by genomic hypomethylation. Science, 300, 489-492.
36. Feinberg, A.P. and Tycko, B. (2004) The history of cancer epigenetics. Nat. Rev. Cancer, 4, 143-153.
37. Sakai, T., Toguchida, J., Ohtani, N., Yandell, D.W., Rapaport, J.M. and Dryja, T.P. (1991) Allele-specific hypermethylation of the retinoblastoma tumor-suppressor gene. Am. J. Hum. Genet., 48 880-888.
38. Greger, V., Passarge, E., Höpping, W., Messmer, E. and Horsthemke, B. (1989) Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma. Hum. Genet., 83, 155-158.
39. Merlo, A., Herman, J.G., Mao, L., Lee, D.J., Gabrielson, E., Burger, P.C., Baylin, S.B. and Sidransky, D. (1995) 50 CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/ CDKN2/MTS1 in human cancers. Nat. Med., 1, 686-692.
40. Liang, G.N., Robertson, K.D., Talmadge, C., Sumegi, J. and Jones, P.A. (2000) The gene for a novel transmembrane protein containing epidermal growth factor and follistatin domains is frequently hypermethylated in human tumor cells. Cancer Res., 60, 4907-4912.
41. Ferguson, A.T., Evron, E., Umbricht, C.B., Pandita, T.K., Chan, T.A., Hermeking, H., Marks, J.R., Lambers, A.R., Futreal, P.A., Stampfer, M.R. et al. (2000) High frequency of hypermethylation at the 14-3-3 sigma locus leads to gene silencing in breast cancer. Proc. Natl. Acad. Sci. USA, 97, 6049-6054.
42. Stirzaker, C., Millar, D.S., Paul, C.L., Warnecke, P.M., Harrison, J., Vincent, P.C., Frommer, M. and Clark, S.J. (1997) Extensive DNA methylation spanning the Rb promoter in retinoblastoma tumors. Cancer Res., 57, 2229-2237.
43. Kissil, J.L., Feinstein, E., Cohen, O., Jones, P.A., Tsai, Y.C., Knowles, M.A., Eydmann, M.E. and Kimchi, A. (1997) DAP-kinase loss of expression in various carcinoma and B-cell lymphoma cell lines: Possible implications for role as tumor suppressor gene. Oncogene, 15 403-407.
44. Katzenellenbogen, R.A., Baylin, S.B. and Herman, J.G. (1999) Hypermethylation of the DAP-Kinase CpG island is a common alteration in B-cell malignancies. Blood, 93, 4347-4353.
45. Teitz, T., Wei, T., Valentine, M.B., Vanin, E.F., Grenet, J., Valentine, V.A., Behm, F.G., Look, A.T., Lahti, J.M. and Kidd, V.J. (2000) Caspase 8 is deleted or silenced preferentially in childhood neuroblastomas with amplification of MYCN. Nat. Med., 6, 529-535.
46. Conway, K.E., McConnell, B.B., Bowring, C.E., Donald, C.D., Warren, S.T. and Vertino, P.M. (2000) TMS1, a novel proapoptotic caspase recruitment domain protein, is a target of methylation-induced gene silencing in human breast cancers. Cancer Res., 60, 6236-6242.
47. Costello, J.F., Futscher, B.W., Kroes, R.A. and Pieper, R.O. (1994) Methylation-related chromatin structure is associated with exclusion of transcription factors from and suppressed expression of the O-6-methylguanine DNA methyltransferase gene in human glioma cell lines. Mol. Cell. Biol., 14, 6515-6521.
48. Costello, J.F., Futscher, B.W., Tano, K., Graunke, D.M. and Pieper, R.O. (1994) Graded methylation in the promoter and body of the O6-methylguanine DNA methyltransferase (MGMT) gene correlates with MGMT expression in human glioma cells. J. Biol. Chem., 269, 17228-17237.
49. Esteller, M., Garcia-Foncillas, J., Andion, E., Goodman, S.N., Hidalgo, O.F., Vanaclocha, V., Baylin, S.B. and Herman, J.G. (2000) Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N. Engl. J. Med., 343, 1350-1354.
50. Esteller, M., Silva, J.M., Dominguez, G., Bonilla, F., Matias-Guiu, X., Lerma, E., Bussaglia, E., Prat, J., Harkes, I.C., Repasky, E.A. et al. (2000) Promoter hypermethylation and BRCA1 inactivation in sporadic brast and ovarian tumors. J. Natl. Cancer Inst., 92 564-569.
51. Hegi, M.E., Diserens, A.C., Gorlia, T., Hamou, M.F., de Tribolet, N., Weller, M., Kros, J.M., Hainfellner, J.A., Mason, W., Mariani, L. et al. (2005) MGMT gene silencing and benefit from temozolomide in glioblastoma. N. Engl. J. Med., 352, 997-1003.
52. Herman, J.G., Umar, A., Polyak, K., Graff, J.R., Ahuja, N., Issa, J.P., Markowitz, S., Willson, J.K., Hamilton, S.R., Kinzler, K.W. et al. (1998) Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma. Proc. Natl. Acad. Sci. USA. 95, 6870-6875.
53. Kane, M.F., Loda, M., Gaida, G.M., Lipman, J., Mishra, R., Goldman, H., Jessup, J.M. and Kolodner, R. (1997) Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines. Cancer Res., 57, 808-811.
54. Akama, T.O., Okazaki, Y., Ito, M., Okuizumi, H., Konno, H., Muramatsu, M., Plass, C., Held, W.A. and Hayashizaki, Y. (1997) Restriction landmark genomic scanning (RLGS-M)-based genome-wide scanning of mouse liver tumors for alterations in DNA methylation status. Cancer Res. 57, 3294-3299.
55. Zardo, G., Tiirikainen, M.I.A., Hong, C., Misra, A., Feuerstein, B.G., Volik, S., Collins, C.C., Lamborn, K.R., Bollen, A., Pinkel, D. et al. (2002) Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. Nat. Genet, 32, 453-458.
56. Novak, P., Jensen, T., Oshiro, M.M., Wozniak, R.J., Nouzova, M., Watts, G.S., Klimecki, W.T., Kim, C. and Futscher, B.W. (2006) Epigenetic inactivation of the HOXA gene cluster in breast cancer. Cancer Res. 66, 10664-10670.
57. Smith, J.S. and Costello, J.F. (2006) A broad band of silence. Nat. Genet., 38, 504-506.
58. Frigola, J., Song, J., Stirzaker, C., Hinshelwood, R.A., Peinado, M.A. and Clark, S.J. (2006) Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat. Genet., 38, 540-549.
59. Antequera, F. and Bird, A. (1993) Number of CpG islands and genes in human and mouse. Proc. Natl. Acad. Sci. USA., 90, 11995-11999.
60. Feinberg, A.P., Ohlsson, R. and Henikoff, S. (2006) The epigenetic progenitor origin of human cancer. Nat. Rev. Genet., 7, 21-33.
61. Gama-Sosa, M.A., Wang, R.Y., Kuo, K.C., Gehrke, C.W. and Ehrlich, M. (1983) The 5-methylcytosine content of highly repeated sequences in human DNA. Nucleic Acids Res., 11, 3087-3095.
62. Cadieux, B., Ching, T.T., Vandenberg, S.R. and Costello, J.F. (2006) Genome-wide Hypomethylation in Human Glioblastomas Associated with Specific Copy Number Alteration, Methylenetetrahydrofolate Reductase Allele Status, and Increased Proliferation. Cancer Res., 66, 8469-8476.
63. Iacobuzio-Donahue, C.A., Maitra, A., Olsen, M., Lowe, A.W., van Heek, N.T., Rosty, C., Walter, K., Sato, N., Parker, A., Ashfaq, R. et al. (2003) Exploration of global gene expression patterns in pancreatic adenocarcinoma using cDNA microarrays. Am. J. Pathol., 162, 1151-1162.
64. Sato, N., Fukushima, N., Matsubayashi, H. and Goggins, M. (2004) Identification of maspin and S100P as novel hypomethylation targets in pancreatic cancer using global gene expression profiling. Oncogene 23, 1531-1538.
65. Sato, N., Maitra, A., Fukushima, N., van Heek, N.T., Matsubayashi, H., Iacobuzio-Donahue, C.A., Rosty, C. and Goggins, M. (2003) Frequent hypomethylation of multiple genes overexpressed in pancreatic ductal adenocarcinoma. Cancer Res., 63, 4158-4166.
66. Wu, H., Chen, Y., Liang, J., Shi, B., Wu, G., Zhang, Y., Wang, D., Li, R., Yi, X., Zhang, H. et al. (2005) Hypomethylation-linked activation of PAX2 mediates tamoxifen-stimulated endometrial carcinogenesis. Nature, 438, 981-987.
67. Hoffmann, M.J. and Schulz, W.A. (2005) Causes and consequences of DNA hypomethylation in human cancer. Biochem. Cell Biol., 83, 296-321.
68. Cavenee, W.K., Dryja, T.P., Phillips, R.A., Benedict, W.F., Godbout, R., Gallie, B.L., Murphree, A.L., Strong, L.C. and White, R.L. (1983) Expression of recessive alleles by chromosomal mechanisms in retinoblastoma. Nature, 305, 779-784.
69. Knudson, A.G. (1971) Mutation and cancer: Statistical study of retinoblastoma. Proc. Natl. Acad. Sci. USA., 69, 820-823.
70. Davies, H., Bignell, G.R., Cox, C., Stephens, P., Edkins, S., Clegg, S., Teague, J., Woffendin, H., Garnett, M.J., Bottomley, W. et al. (2002) Mutations of the BRAF gene in human cancer. Nature, 417 949-954.
71. Davies, H., Hunter, C., Smith, R., Stephens, P., Greenman, C., Bignell, G., Teague, J., Butler, A., Edkins, S., Stevens, C. et al. (2005) Somatic mutations of the protein kinase gene family in human lung cancer. Cancer Res., 65, 7591-7595.
72. Sjoblom, T., Jones, S., Wood, L.D., Parsons, D.W., Lin, J., Barber, T.D., Mandelker, D., Leary, R.J., Ptak, J., Silliman, N. et al. (2006) The consensus coding sequences of human breast and colorectal cancers. Science, 314, 268-274.
73. Baylin, S.B. and Ohm, J.E. (2006) Epigenetic gene silencing in cancer - a mechanism for early oncogenic pathway addiction? Nat. Rev. Cancer 6, 107-116.
74. Costello, J.F., Fruhwald, M.C., Smiraglia, D.J., Rush, L.J., Robertson, G.P., Gao, X., Wright, F.A., Feramisco, J.D., Peltomaki, P., Lang, J.C. et al. (2000) Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat. Genet, 24, 132-138.
75. Jones, P.A. (2005) Overview of cancer epigenetics. Semin. Hematol. 42, S3-S8.
76. Rush, L.J., Dai, Z.Y., Smiraglia, D.J., Gao, X., Wright, F.A., Fruhwald, M., Costello, J.F., Held, W.A., Yu, L., Krahe, R. et al. (2001) Novel methylation targets in de novo acute myeloid leukemia with prevalence of chromosome 11 loci. Blood, 97, 3226-3233.
77. Hatada, I., Hayashizaki, Y., Hirotsune, S., Komatsubara, H. and Mukai, T. (1991) A genomic scanning method for higher organisms using restriction sites as landmarks. Proc. Natl. Acad. Sci. USA., 88 9523-9527.
78. Hong, C., Bollen, M.I.A. and Costello, J.F. (2003) The contribution of genetic and epigenetic mechanisms to gene silencing in oligodendrogliomas. Cancer Res., 63, 7600-7605.
79. Hong, C., Maunakea, A., Jun, P., Bollen, A.W., Hodgson, J.G., Goldenberg, D.D., Weiss, W.A. and Costello, J.F. (2005) Shared epigenetic mechanisms in human and mouse gliomas inactivate expression of the growth suppressor SLC5A8. Cancer Res., 65, 3617-3623.
80. Kochanek, S., Renz, D. and Doerfler, W. (1993) DNA methylation in the Alu sequences of diploid and haploid primary human cells. EMBO J., 12, 1141-1151.
81. Rein, T., DePamphilis, M.L. and Zorbas, H. (1998) Identifying 5-methylcytosine and related modifications in DNA genomes. Nucleic Acids Res., 26, 2255-2264.
82. Diala, E.S., Cheah, M.S., Rowitch, D. and Hoffman, R.M. (1983) Extent of DNA methylation in human tumor cells. J. Natl. Cancer Inst., 71 755-764.
83. Jones, P.A. and Baylin, S.B. (2002) The fundamental role of epigenetic events in cancer. Nat. Rev. Genet., 3, 415-428.
84. Hatada, I., Hayashizaki, Y., Hirotsune, S., Komatsubara, H. and Mukai, T. (1991) A genomic scanning method for higher organisms using restriction sites as landmarks. Proc. Natl. Acad. Sci. USA., 88, 9523-9527.
85. Rush, L.J. and Plass, C. (2002) Restriction landmark genomic scanning for DNA methylation in cancer: Past, present, and future applications. Anal. Biochem., 307, 191-201.
86. Lindsay, S. and Bird, A.P. (1987) Use of restriction enzymes to detect potential gene sequences in mammalian DNA. Nature, 327, 336-338.
87. Dai, Z., Weichenhan, D., Wu, Y.Z., Hall, J.L., Rush, L.J., Smith, L.T., Raval, A., Yu, L., Kroll, D., Muehlisch, J. et al. (2002) An AscI boundary library for the studies of genetic and epigenetic alterations in CpG islands. Genome Res., 12, 1591-1598.
88. Smiraglia, D.J., Fruhwald, M.C., Costello, J.F., McCormick, S.P., Dai, Z., Peltomaki, P., O'Dorisio, M.S., Cavenee, W.K. and Plass, C. (1999) A new tool for the rapid cloning of amplified and hypermethylated human DNA sequences from restriction landmark genome scanning gels. Genomics, 58, 254-262.
89. Dai, Z.Y., Lakshmanan, R.R., Zhu, W.G., Smiraglia, D.J., Rush, L.J., Fruhwald, M.C., Brena, R.M., Li, B., Wright, F.A., Ross, P. et al. (2001) Global methylation profiling of lung cancer identifies novel methylated genes. Neoplasia, 3, 314-323.
90. Smiraglia, D.J., Rush, L.J., Fruhwald, M.C., Dai, Z.Y., Held, W.A., Costello, J.F., Lang, J.C., Eng, C., Li, B., Wright, F.A. et al. (2001) Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies. Hum. Mol. Genet., 10, 1413-1419.
91. Kuromitsu, J., Kataoka, H., Yamashita, H., Muramatsu, M., Furuichi, Y., Sekine, T. and Hayashizaki, Y. (1995) Reproducible alterations of DNA methylation at a specific population of CpG islands during blast formation of peripheral blood lymphocytes. DNA Res., 2, 263-267.
92. Yoshikawa, H., de la Monte, S., Nagai, H., Wands, J.R., Matsubara, K. and Fujiyama, A. (1996) Chromosomal assignment of human genomic NotI restriction fragments in a two-dimensional electrophoresis profile. Genomics, 31, 28-35.
93. Dai, Z., Weichenhan, D., Wu, Y.Z., Hall, J.L., Rush, L.J., Smith, L.T., Raval, A., Yu, L., Kroll, D., Muehlisch, J. et al. (2002) An AscI boundary library for the studies of genetic and epigenetic alterations in CpG islands. Genome Res., 12, 1591-1598.
94. Plass, C., Weichenhan, D., Catanese, J., Costello, J.F., Yu, F., Yu, L., Smiraglia, D., Cavenee, W.K., Caligiuri, M.A., deJong, P. et al. (1997) An arrayed human not I-EcoRV boundary library as a tool for RLGS spot analysis. DNA Res., 4, 253-255.
95. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A. et al. (2001) The sequence of the human genome. Science, 291, 1304-1351.
96. Bibikova, M., Lin, Z., Zhou, L., Chudin, E., Garcia, E.W., Wu, B., Doucet, D., Thomas, N.J., Wang, Y., Vollmer, E. et al. (2006) High-throughput DNA methylation profiling using universal bead arrays. Genome Res., 16, 383-393.
97. Ehrich, M., Nelson, M.R., Stanssens, P., Zabeau, M., Liloglou, T., Xinarianos, G., Cantor, C.R., Field, J.K. and van den Boom, D. (2005) Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc. Natl. Acad. Sci. USA, 102, 15785-15790.
98. Ishkanian, A.S., Malloff, C.A., Watson, S.K., DeLeeuw, R.J., Chi, B., Coe, B.P., Snijders, A., Albertson, D.G., Pinkel, D., Marra, M.A. et al. (2004) A tiling resolution DNA microarray with complete coverage of the human genome. Nat. Genet, 36, 299-303.
99. Khulan, B., Thompson, R.F., Ye, K., Fazzari, M.J., Suzuki, M., Stasiek, E., Figueroa, M.E., Glass, J.L., Chen, Q., Montagna, C. et al. (2006) Comparative isoschizomer profiling of cytosine methylation: The HELP assay. Genome Res., 16, 1046-1055.
100. Schumacher, A., Kapranov, P., Kaminsky, Z., Flanagan, J., Assadzadeh, A., Yau, P., Virtanen, C., Winegarden, N., Cheng, J., Gingeras, T. et al. (2006) Microarray-based DNA methylation profiling: Technology and applications. Nucleic Acids Res., 34, 528-542.
101. Weber, M., Davies, J.J., Wittig, D., Oakeley, E.J., Haase, M., Lam, W.L. and Schubeler, D. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet, 37, 853-862.
102. Misawa, A., Inoue, J., Sugino, Y., Hosoi, H., Sugimoto, T., Hosoda, F., Ohki, M., Imoto, I. and Inazawa, J. (2005) Methylation-associated silencing of the nuclear receptor 1I2 gene in advanced-type neuroblastomas, identified by bacterial artificial chromosome array-based methylated CpG island amplification. Cancer Res., 65, 10233-10242.
103. Huang, T.H., Laux, D.E., Hamlin, B.C., Tran, P., Tran, H. and Lubahn, D.B. (1997) Identification of DNA methylation markers for human breast carcinomas using the methylation-sensitive restriction fingerprinting technique. Cancer Res., 57, 1030-1034.
104. Wang, Y., Hayakawa, J., Long, F., Yu, Q., Cho, A.H., Rondeau, G., Welsh, J., Mittal, S., De Belle, I., Adamson, E. et al. (2005) 'Promoter array' studies identify cohorts of genes directly regulated by methylation, copy number change, or transcription factor binding in human cancer cells. Ann. N.Y. Acad. Sci., 1058, 162-185.
105. Hellman, A. and Chess, A. (2007) Gene body-specific methylation on the active X chromosome. Science, 315, 1141-1143.
106. Khulan, B., Thompson, R.F., Ye, K., Fazzari, M.J., Suzuki, M., Stasiek, E., Figueroa, M.E., Glass, J.L., Chen, Q., Montagna, C. et al. (2006) Comparative isoschizomer profiling of cytosine methylation: The HELP assay. Genome Res., 16, 1046-1055.
107. Weber, M., Davies, J.J., Wittig, D., Oakeley, E.J., Haase, M., Lam, W.L. and Schubeler, D. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nature Genet., 37, 853-862.
108. Misawa, A., Inoue, J., Sugino, Y., Hosoi, H., Sugimoto, T., Hosoda, F., Ohki, M., Imoto, I. and Inazawa, J. (2005) Methylation-associated silencing of the nuclear receptor 1I2 gene in advanced-type neuroblastomas, identified by bacterial artificial chromosome array-based methylated CpG island amplification. Cancer Res., 65, 10233-10242.
109. Frommer, M., McDonald, L.E., Millar, D.S., Collis, C.M., Watt, F., Grigg, G.W., Molloy, P.L. and Paul, C.L. (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.
110. Herman, J.G., Graff, J.R., Myohanen, S., Nelkin, B.D. and Baylin, S.B. (1996) Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA., 93, 9821-9826.
111. Laird, P.W. (2003) The power and the promise of DNA methylation markers. Nat. Rev. Cancer, 3, 253-266.
112. Adorjan, P., Distler, J., Lipscher, E., Model, F., Muller, J., Pelet, C., Braun, A., Florl, A.R., Gutig, D., Grabs, G. et al. (2002) Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res., 30, e21.
113. Yan, P.S., Wei, S.H. and Huang, T.H. (2004) Methylation-specific oligonucleotide microarray. Methods Mol Biol, 287, 251-260.
114. Novak, P., Jensen, T., Oshiro, M.M., Wozniak, R.J., Nouzova, M., Watts, G.S., Klimecki, W.T., Kim, C. and Futscher, B.W. (2006) Epigenetic inactivation of the HOXA gene cluster in breast cancer. Cancer Res. 66, 10664-10670.
115. Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S., Chan, S.W., Chen, H., Henderson, I.R., Shinn, P., Pellegrini, M., Jacobsen, S.E. et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell, 126, 1189-1201.
116. Keshet, I., Schlesinger, Y., Farkash, S., Rand, E., Hecht, M., Segal, E., Pikarski, E., Young, R.A., Niveleau, A., Cedar, H. et al. (2006) Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat. Genet., 38, 149-153.
117. Rauch, T., Li, H., Wu, X. and Pfeifer, G.P. (2006) MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res., 66, 7939-7947.
118. Zilberman, D., Gehring, M., Tran, R.K., Ballinger, T. and Henikoff, S. (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet, 39, 61-69.
119. Lippman, Z., Gendrel, A.V., Black, M., Vaughn, M.W., Dedhia, N., McCombie, W.R., Lavine, K., Mittal, V., May, B., Kasschau, K.D. et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature, 430, 471-476.
120. Hu, M., Yao, J., Cai, L., Bachman, K.E., van den Brule, F., Velculescu, V. and Polyak, K. (2005) Distinct epigenetic changes in the stromal cells of breast cancers. Nat. Genet, 37, 899-905.
121. Suzuki, H., Gabrielson, E., Chen, W., Anbazhagan, R., van Engeland, M., Weijenberg, M.P., Herman, J.G. and Baylin, S.B. (2002) A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat. Genet, 31, 141-149.
122. Karpf, A.R. and Jones, D.A. (2002) Reactivating the expression of methylation silenced genes in human cancer. Oncogene, 21, 5496-5503.
123. Karpf, A.R., Peterson, P.W., Rawlins, J.T., Dalley, B.K., Yang, Q., Albertsen, H. and Jones, D.A. (1999) Inhibition of DNA methyltransferase stimulates the expression of signal transducer and activator of transcription 1, 2 and 3 genes in colon tumor cells. Proc. Nat. Acad. Sci. USA, 96, 14007-14012.
124. Shames, D.S., Girard, L., Gao, B., Sato, M., Lewis, C.M., Shivapurkar, N., Jiang, A., Perou, C.M., Kim, Y.H., Pollack, J.R. et al. (2006) A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Med., 3, e486.
125. Meissner, A., Gnirke, A., Bell, G.W., Ramsahoye, B., Lander, E.S. and Jaenisch, R. (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res., 33, 5868-5877.
126. Eckhardt, F., Lewin, J., Cortese, R., Rakyan, V.K., Attwood, J., Burger, M., Burton, J., Cox, T.V., Davies, R., Down, T.A. et al. (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nature Genetics, 38, 1378-1385.
127. Jeltsch, A., Walter, J., Reinhardt, R. and Platzer, M. (2006) German human methylome project started. Cancer Research, 66, 7378.
128. Rakyan, V.K., Hildmann, T., Novik, K.L., Lewin, J., Tost, J., Cox, A.V., Andrews, T.D., Howe, K.L., Otto, T., Olek, A. et al. (2004) DNA methylation profiling of the human major histocompatibility complex: A pilot study for the human epigenome project. PLoS Biol, 2, e405.
129. Smith, L.T., Lin, M., Brena, R.M., Lang, J.C., Schuller, D.E., Otterson, G.A., Morrison, C.D., Smiraglia, D.J. and Plass, C. (2006) Epigenetic regulation of the tumor suppressor gene TCF21 on 6q23-q24 in lung and head and neck cancer. Proceedings of the National Academy of Sciences of the United States of America, 103, 982-987.
130. Welch, D.R., Chen, P., Miele, M.E., McGary, C.T., Bower, J.M., Stanbridge, E.J. and Weissman, B.E. (1994) Microcell-mediated transfer of chromosome 6 into metastatic human C8161 melanoma cells suppresses metastasis but does not inhibit tumorigenicity. Oncogene, 9, 255-262.
131. Brena, R.M., Morrison, C., Liyanarachchi, S., Jarjoura, D., Davuluri, R.V., Otterson, G.A., Reisman, D., Glaros, S., Rush, L.J. and Plass, C. (2007) Aberrant DNA Methylation of OLIG1, a Novel Prognostic Factor in Non-Small Cell Lung Cancer. PLoS Medicine, 4, e108.
132. Lee, E.B., Park, T.I., Park, S.H. and Park, J.Y. (2003) Loss of heterozygosity on the long arm of chromosome 21 in non-small cell lung cancer. Annals of Thoracic Surgery, 75, 1597-1600.
133. Wales, M.M., Biel, M.A., Eldeiry, W., Nelkin, B.D., Issa, P., Cavenee, W.K., Kuerbitz, S.J. and Baylin, S.B. (1995) P53 Activates Expression of Hic-1, a New Candidate Tumour Suppressor Gene On 17p13.3. Nat Med, 1, 570-577.
134. Rauch, T., Li, H., Wu, X. and Pfeifer, G.P. (2006) MIRA-Assisted Microarray Analysis, a New Technology for the Determination of DNA Methylation Patterns, Identifies Frequent Methylation of Homeodomain-Containing Genes in Lung Cancer Cells. Cancer Res., 66, 7939-7947.
135. Raval, A., Lucas, D.M., Matkovic, J.J., Bennett, K.L., Liyanarachchi, S., Young, D.C., Rassenti, L., Kipps, T.J., Grever, M.R., Byrd, J.C. et al. (2005) TWIST2 demonstrates differential methylation in immunoglobulin variable heavy chain mutated and unmutated chronic lymphocytic leukemia. J. Clin. Oncol., 23, 3877-3885.
136. Yan, P.S., Chen, C.M., Shi, H.D., Rahmatpanah, F., Wei, S.H., Caldwell, C.W. and Huang, T.H.M. (2001) Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. Cancer Res., 61 8375-8380.
137. Keshet, I., Schlesinger, Y., Farkash, S., Rand, E., Hecht, M., Segal, E., Pikarski, E., Young, R.A., Niveleau, A., Cedar, H. et al. (2006) Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat. Genet., 38, 149-153.
138. Bock, C., Paulsen, M., Tierling, S., Mikeska, T., Lengauer, T. and Walter, J. (2006) CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet, 2, e26.
139. Fang, F., Fan, S., Zhang, X. and Zhang, M.Q. (2006) Predicting methylation status of CpG islands in the human brain. Bioinformatics 22, 2204-2209.
140. Feltus, F.A., Lee, E.K., Costello, J.F., Plass, C. and Vertino, P.M. (2003) Predicting aberrant CpG island methylation. Proc. Nat. Acad. Sci. USA, 100, 12253-12258.
141. Feltus, F.A., Lee, E.K., Costello, J.F., Plass, C. and Vertino, P.M. (2006) DNA motifs associated with aberrant CpG island methylation. Genomics, 87, 572-579.
142. Ohm, J.E., McGarvey, K.M., Yu, X., Cheng, L., Schuebel, K.E., Cope, L., Mohammad, H.P., Chen, W., Daniel, V.C., Yu, W. et al. (2007) A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat. Genet, 39 237-242.
143. Schlesinger, Y., Straussman, R., Keshet, I., Farkash, S., Hecht, M., Zimmerman, J., Eden, E., Yakhini, Z., Ben-Shushan, E., Reubinoff, B.E. et al. (2007) Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat. Genet 39, 232-236.
144. Widschwendter, M., Fiegl, H., Egle, D., Mueller-Holzner, E., Spizzo, G., Marth, C., Weisenberger, D.J., Campan, M., Young, J., Jacobs, I. et al. (2007) Epigenetic stem cell signature in cancer. Nat. Genet 39, 157-158.
145. Vire, E., Brenner, C., Deplus, R., Blanchon, L., Fraga, M., Didelot, C., Morey, L., Van Eynde, A., Bernard, D., Vanderwinden, J.M. et al. (2006) The Polycomb group protein EZH2 directly controls DNA methylation. Nature, 439, 871-874.
146. Reynolds, P.A., Sigaroudinia, M., Zardo, G., Wilson, M.B., Benton, G.M., Miller, C.J., Hong, C., Fridlyand, J., Costello, J.F. and Tlsty, T.D. (2006) Tumor suppressor p16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cells. J. Biol. Chem. 281, 24790-24802.
147. Reilly, K.M., Broman, K.W., Bronson, R.T., Tsang, S., Loisel, D.A., Christy, E.S., Sun, Z., Diehl, J., Munroe, D.J. and Tuskan, R.G. (2006) An imprinted locus epistatically influences Nstr1 and Nstr2 to control resistance to nerve sheath tumors in a neurofibromatosis type 1 mouse model. Cancer Res., 66, 62-68.
148. Trinh, B.N., Long, T.I., Nickel, A.E., Shibata, D. and Laird, P.W. (2002) DNA methyltransferase deficiency modifies cancer susceptibility in mice lacking DNA mismatch repair. Mol. Cell. Biol., 22, 2906-2917.
149. Laird, P.W., Jackson-Grusby, L., Fazeli, A., Dickinson, S.L., Jung, W.E., Li, E., Weinberg, R.A. and Jaenisch, R. (1995) Suppression of intestinal neoplasia by DNA hypomethylation. Cell, 81, 197-205.
150. Holm, T.M., Jackson-Grusby, L., Brambrink, T., Yamada, Y., Rideout, W.M., 3rd. and Jaenisch, R. (2005) Global loss of imprinting leads to widespread tumorigenesis in adult mice. Cancer Cell, 8, 275-285.
151. Myöhänen, S.K., Baylin, S.B. and Herman, J.G. (1998) Hypermethylation can selectively silence individual p16ink4A alleles in neoplasia. Cancer Res., 58, 591-593.
152. Grady, W.M., Willis, J., Guilford, P.J., Dunbier, A.K., Toro, T.T., Lynch, H., Wiesner, G., Ferguson, K., Eng, C., Park, J.G. et al. (2000) Methylation of the CDH1 promoter as the second genetic hit in hereditary diffuse gastric cancer. Nat. Genet, 26, 16-17.
153. Esteller, M., Risques, R.A., Toyota, M., Capella, G., Moreno, V., Peinado, M.A., Baylin, S.B. and Herman, J.G. (2001) Promoter hypermethylation of the DNA repair gene O(6)-methylguanine-DNA methyltransferase is associated with the presence of G:C to A:T transition mutations in p53 in human colorectal tumorigenesis. Cancer Res., 61, 4689-4692.
154. Di Croce, L., Raker, V.A., Corsaro, M., Fazi, F., Fanelli, M., Faretta, M., Fuks, F., Lo Coco, F., Kouzarides, T., Nervi, C. et al. (2002) Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science, 295 1079-1082.
155. Toyota, M., Ahuja, N., Ohe-Toyota, M., Herman, J.G., Baylin, S.B. and Issa, J.P.J. (1999) CpG island methylator phenotype in colorectal cancer. Proc. Natl. Acad. Sci. USA., 96, 8681-8686.
156. Weisenberger, D.J., Siegmund, K.D., Campan, M., Young, J., Long, T.I., Faasse, M.A., Kang, G.H., Widschwendter, M., Weener, D., Buchanan, D. et al. (2006) CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat. Genet, 38, 787-793.