Cancer-epigenetics comes of age (original) (raw)

• Yang, A.S., Jones, P.A. & Shibata, A. The mutational burden of 5–methylcytosine. in Epigenetic Mechanisms of Gene Regulation (eds Riggs, A.D., Martienssen, R.A., and Russo, V.E.A.) 77–94 (Cold Spring Harbor Laboratory Press, Cold Spring Harbour, 1996).
  Google Scholar
• Razin, A. & Cedar, H. DNA methylation and gene expression. Microbiol. Rev. 55, 451– 458 (1991).
  CAS PubMed PubMed Central Google Scholar
• Yeivin, A. & Razin, A. Gene methylation patterns and expression. in DNA Methylation: Molecular Biology and Biological Significance (eds Jost, J.P. & Saluz, H.P.) 523–568 (Birkhauser Verlag, Basel, 1993).
  Chapter Google Scholar
• Kass, S.U., Pruss, D. & Wolffe, A.P. How does DNA methylation repress transcription? Trends Genet. 13, 444–449 (1997).
  Article CAS Google Scholar
• Jones, P.A. The methylation paradox. Trends Genet. (in press).
• Razin, A. & Riggs, A.D. DNA methylation and gene function. Science 210, 604–610 (1980).
  Article CAS Google Scholar
• Stoger, R. et al. Maternal–specific methylation of the imprinted mouse Igf2r locus identifies the expressed locus as carrying the imprinting signal. Cell 73, 61–71 (1993).
  Article CAS Google Scholar
• Larsen, F., Solheim, J. & Prydz, H. A methylated CpG island 3' in the apolipoprotein–E gene does not repress its transcription. Hum. Mol. Genet. 2, 775–780 (1993).
  Article CAS Google Scholar
• Barry, C., Faugeron, G. & Rossignol, J.–L. Methylation induced premeiotically in Ascobolus : coextension with DNA repeat lengths and effect on transcript elongation. Proc. Natl Acad. Sci. USA 90, 4557– 4561 (1993).
  Article CAS Google Scholar
• Rountree, M.R. & Selker, E.U. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa . Genes Dev. 11, 2383– 2395 (1997).
  Article CAS Google Scholar
• Clark, S.J., Harrison, J. & Molloy, P.L. Sp1 binding is inhibited by (m)Cp(m)CpG methylation. Gene 195, 67–71 (1997).
  Article CAS Google Scholar
• Prendergast, G.C. & Ziff, E.B. Methylation–sensitive sequence–specific DNA binding by the c–Myc basic region. Science 251, 186–189 ( 1991).
  Article CAS Google Scholar
• Zhang, X.Y., Ehrlich, K.C., Wang, R.Y. & Ehrlich, M. Effect of site–specific DNA methylation and mutagenesis on recognition by methylated DNA–binding protein from human placenta. Nucleic Acids Res. 14, 8387–8397 (1986).
  Article CAS Google Scholar
• Asiedu, C.K., Scotto, L., Assoian, R.K. & Ehrlich, M. Binding of AP–1/CREB proteins and of MDBP to contiguous sites downstream of the human TGF–β 1 gene. Biochim. Biophys. Acta 1219, 55–63 (1994).
  Article CAS Google Scholar
• Bestor, T.H. Gene silencing. Methylation meets acetylation. Nature 393, 311–312 (1998).
  Article CAS Google Scholar
• Nan, X., Campoy, F.J. & Bird, A. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell 88, 471 –481 (1997).
  Article CAS Google Scholar
• Nan, X. et al. Transcriptional repression by the methyl–CpG–binding protein MeCP2 involves a histone deacetylase complex. Nature 393, 386–389 (1998).
  Article CAS Google Scholar
• Jones, P.L. et al. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nature Genet. 19, 187– 191 (1998).
  Article CAS Google Scholar
• Bird, A.P. CpG–rich islands and the function of DNA methylation. Nature 321, 209–213 ( 1986).
  Article CAS Google Scholar
• Gardiner–Garden, M. & Frommer, M. CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261 –282 (1987).
  Article Google Scholar
• Larsen, F., Gundersen, G., Lopez, R. & Prydz, H. CpG islands as gene markers in the human genome. Genomics 13, 1095–1107 (1992).
  Article CAS Google Scholar
• Wutz, A. et al. Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 389, 745– 749 (1997).
  Article CAS Google Scholar
• Singer–Sam, J. & Riggs, A.D. X chromosome inactivation and DNA methylation. in DNA Methylation: Molecular Biology and Biological Significance (eds Jost, J.P. & Saluz, H.P.) 358 –384 (Birkhauser Verlag, Basel, 1993 ).
  Chapter Google Scholar
• Issa, J.P. et al. Methylation of the oestrogen receptor CpG island links ageing and neoplasia in human colon. Nature Genet. 7, 536–540 (1994).
  Article CAS Google Scholar
• 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. USA 93, 11757– 11762 (1996).
  Article CAS Google Scholar
• Jones, P.A. et al. De novo methylation of the MyoD1 CpG island during the establishment of immortal cell lines. Proc. Natl Acad. Sci. USA 87, 6117–6121 ( 1990).
  Article CAS Google Scholar
• Antequera, F., Boyes, J. & Bird, A. High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines. Cell 62, 503– 514 (1990).
  Article CAS Google Scholar
• Feinberg, A.P., Gehrke, C.W., Kuo, K.C. & Ehrlich, M. Reduced genomic 5–methylcytosine content in human colonic neoplasia. Cancer Res. 48, 1159–1161 ( 1988).
  CAS PubMed Google Scholar
• Jones, P.A. DNA methylation errors and cancer. Cancer Res. 56, 2463–2467 (1996).
  CAS PubMed Google Scholar
• Baylin, S.B., Herman, J.G., Graff, J.R., Vertino, P.M. & Issa, J.P. Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv. Cancer Res. 72 , 141–196 (1998).
  Article CAS Google Scholar
• Okano, M., Xie, S. & Li, E. Cloning and characterization of a family of novel mammalian DNA (cytosine–5) methyltransferases. Nature Genet. 19, 219 –220 (1998).
  Article CAS Google Scholar
• Gonzalez–Zuleta, M. et al. Methylation of the 5´ CpG island of the p16/CDKN2 tumor suppressor gene in normal and transformed human tissues correlates with gene silencing. Cancer Res. 55, 4531– 4535 (1995).
  Google Scholar
• Gonzalgo, M.L. et al. The role of DNA methylation in expression of the p19/p16 locus in human bladder cancer cell lines. Cancer Res. 58, 1245–1252 (1998).
  CAS PubMed Google Scholar
• Ohtani–Fujita, N. et al. Hypermethylation in the retinoblastoma gene is associated with unilateral, sporadic retinoblastoma. Cancer Genet. Cytogenet. 98, 43–49 ( 1997).
  Article Google Scholar
• Prowse, A.H. et al. Somatic inactivation of the VHL gene in Von Hippel–Lindau disease tumors. Am. J. Hum. Genet. 60, 765 –771 (1997).
  CAS PubMed PubMed Central Google Scholar
• Herman, J.G. et al. Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma. Proc. Natl Acad. Sci. USA 95, 6870–6875 ( 1998).
  Article CAS Google Scholar
• Lock, L.F., Takagi, N. & Martin, G.R. Methylation of the Hprt gene on the inactive X occurs after chromosome inactivation. Cell 48, 39–46 (1987).
  Article CAS Google Scholar
• Grant, M., Zuccotti, M. & Monk, M. Methylation of CpG sites of two X–linked genes coincides with X–inactivation in the female mouse embryo but not in the germ line. Nature Genet. 2, 161– 166 (1992).
  Article CAS Google Scholar
• Singer–Sam, J. et al. Use of a HpaII–polymerase chain reaction assay to study DNA methylation in the Pgk–1 CpG island of mouse embryos at the time of X–chromosome inactivation. Mol. Cell. Biol. 10, 4987–4989 (1990).
  Article Google Scholar
• Norris, D.P., Brockdorff, N. & Rastan, S. Methylation status of CpG–rich islands on active and inactive mouse X chromosomes. Mamm. Genome. 1, 78–83 (1991).
  Article CAS Google Scholar
• Li, E., Beard, C. & Jaenisch, R. Role for DNA methylation in genomic imprinting. Nature 366, 362–365 ( 1993).
  Article CAS Google Scholar
• Laird, P.W. et al. Suppression of intestinal neoplasia by DNA hypomethylation. Cell 81, 197–205 (1995).
  Article CAS Google Scholar
• Moulton, T. et al. Epigenetic lesions at the H19 locus in Wilms' tumour patients. Nature Genet. 7, 440– 447 (1994).
  Article CAS Google Scholar
• Steenman, M.J. et al. Loss of imprinting of IGF2 is linked to reduced expression and abnormal methylation of H19 in Wilms' tumour. Nature Genet. 7, 433–439 ( 1994).
  Article CAS Google Scholar
• Ohtani–Fujita, N. et al. CpG methylation inactivates the promoter activity of the human retinoblastoma tumor–suppressor gene. Oncogene 8, 1063–1067 (1993).
  PubMed Google Scholar
• Veigl, M.L. et al. Biallelic inactivation of hMLH1 by epigenetic gene silencing, a novel mechanism causing human MSI cancers. Proc. Natl Acad. Sci. USA 95, 8698–8702 (1998).
  Article CAS Google Scholar
• Cunningham, J.M. et al. Hypermethylation of the hMLH1 promoter in colon cancer with microsatellite instability. Cancer Res. 58, 3455–3460 (1998).
  CAS PubMed Google Scholar
• Lengauer, C., Kinzler, K.W. & Vogelstein, B. DNA methylation and genetic instability in colorectal cancer cells. Proc. Natl Acad. Sci. USA 94, 2545–2550 (1997).
  Article CAS Google Scholar
• Ahuja, N. et al. Association between CpG island methylation and microsatellite instability in colorectal cancer. Cancer Res. 57, 3370–3374 (1997).
  CAS PubMed Google Scholar
• Hussain, S.P. & Harris, C.C. Molecular epidemiology of human cancer: contribution of mutation spectra studies of tumor suppressor genes. Cancer Res. 58, 4023–4037 (1998).
  CAS PubMed Google Scholar
• Kamb, A. et al. A cell cycle regulator potentially involved in genesis of many tumor types. Science 264, 436– 440 (1994).
  Article CAS Google Scholar
• Hatada, I., Sugama, T. & Mukai, T. A new imprinted gene cloned by a methylation–sensitive genome scanning method. Nucleic Acids Res. 21, 5577–5582 (1993).
  Article CAS Google Scholar
• Ushijima, T. et al. Establishment of methylation–sensitive–representational difference analysis and isolation of hypo– and hypermethylated genomic fragments in mouse liver tumors. Proc. Natl Acad. Sci. USA 94, 2284–2289 (1997).
  Article CAS Google Scholar
• Gonzalgo, M.L. et al. Identification and characterization of differentially methylated regions of genomic DNA by methylation–sensitive arbitrarily primed PCR. Cancer Res. 57, 594–599 (1997).
  CAS PubMed Google Scholar
• Huang, T.H. et al. Identification of DNA methylation markers for human breast carcinomas using the methylation–sensitive restriction fingerprinting technique. Cancer Res. 57, 1030– 1034 (1997).
  CAS PubMed Google Scholar
• Toyota, M. et al. Identification of novel aberrantly methylated CpG islands in colorectal carcinoma. Proc. Am. Assoc. Cancer Res. 39, 95 (1998).
  Google Scholar
• Frommer, M. et al. 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 (1992).
  Article CAS Google Scholar
• Rein, T., DePamphilis, M.L. & Zorbas, H. Identifying 5–methylcytosine and related modifications in DNA genomes. Nucleic Acids Res. 26, 2255 –2264 (1998).
  Article CAS Google Scholar
• Gonzalgo, M.L. et al. Low frequency of p16/CDKN2A methylation in sporadic melanoma: comparative approaches for methylation analysis of primary tumors. Cancer Res. 57, 5336–5347 (1997).
  CAS PubMed Google Scholar
• Herman, J.G., Graff, J.R., Myohanen, S., Nelkin, B.D. & Baylin, S.B. Methylation–specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl Acad. Sci. USA 93, 9821–9826 (1996).
  Article CAS Google Scholar
• Gonzalgo, M.L. & Jones, P.A. Rapid quantitation of methylation differences at specific sites using methylation–sensitive single nucleotide primer extension (Ms–SNuPE). Nucleic Acids Res. 25, 2529–2531 ( 1997).
  Article CAS Google Scholar
• Xiong, Z. & Laird, P.W. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res. 25, 2532–2534 (1997).
  Article CAS Google Scholar
• Bender, C.M., Pao, M.M. & Jones, P.A. Inhibition of DNA methylation by 5–aza–2´–deoxycytidine suppresses the growth of human tumor cell lines. Cancer Res. 58, 95–101 (1998).
  CAS PubMed Google Scholar
• Lübbert, M. et al. Cytogenic response to low–dose 5–aza–2´–deoxycytidine (DAC) in poor–risk myelodysplastic syndromes (MDS)—phase II study results. Blood 90 (suppl. 1), 582a (1997).
  Google Scholar
• Silverman, L.R. et al. A randomized controlled trial of subcutaneous azacytidine (aza C) in patients with the myelodysplastic syndrome (MDS): a study of the cancer and leukemia group (CALGB). Proc. ASCO 17, 14a (1998).
  Google Scholar
• Jackson–Grusby, L., Laird, P.W., Magge, S.N., Moeller, B.J. & Jaenisch, R. Mutagenicity of 5–aza–2´–deoxycytidine is mediated by the mammalian DNA methyltransferase. Proc. Natl Acad. Sci. USA 94, 4681–4685 (1997).
  Article Google Scholar
• Ramchandani, S., MacLeod, A.R., Pinard, M., von Hofe, E. & Szyf, M. Inhibition of tumorigenesis by a cytosine–DNA, methyltransferase, antisense oligodeoxynucleotide. Proc. Natl Acad. Sci. USA 94, 684–689 ( 1997).
  Article CAS Google Scholar
• Sakai, T. et al. Allele–specific hypermethylation of the retinoblastoma tumor–suppressor gene. Am. J. Hum. Genet. 48, 880–888 (1991).
  CAS PubMed PubMed Central Google Scholar
• Greenblatt, M.S., Bennett, W.P., Hollstein, M. & Harris, C.C. Mutations in the p53 tumor suppressor gene: clues to cancer etiology and molecular pathogenesis. Cancer Res. 54, 4855–4878 (1994).
  CAS PubMed Google Scholar
• Myohanen, S.K., Baylin, S.B. & Herman, J.G. Hypermethylation can selectively silence individual p16ink4A alleles in neoplasia. Cancer Res. 58, 591–593 (1998).
  CAS PubMed Google Scholar
• Yeager, T.R. et al. Overcoming cellular senescence in human cancer pathogenesis. Genes Dev. 12, 163–174 (1998).
  Article CAS Google Scholar
• Flores, J.F. et al. Analysis of the CDKN2A, CDKN2B and CDK4 genes in 48 Australian melanoma kindreds. Oncogene 15, 2999–3005 (1997).
  Article CAS Google Scholar
• Batova, A. et al. Frequent and selective methylation of p15 and deletion of both p15 and p16 in T–cell acute lymphoblastic leukemia. Cancer Res. 57, 832–836 (1997).
  CAS PubMed Google Scholar
• Hiltunen, M.O. et al. Hypermethylation of the APC (adenomatous polyposis coli) gene promoter region in human colorectal carcinoma. Int. J. Cancer 70, 644–648 ( 1997).
  Article CAS Google Scholar