Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band (original) (raw)

• Jones, P.A. & Baylin, S.B. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3, 415–428 (2002).
  Article CAS Google Scholar
• Laird, P.W. Cancer epigenetics. Hum. Mol. Genet. 14, R65–R76 (2005).
  Article CAS Google Scholar
• Gardiner-Garden, M. & Frommer, M. CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261–282 (1987).
  Article CAS Google Scholar
• Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
  Article CAS Google Scholar
• Clark, S.J. & Melki, J. DNA methylation and gene silencing in cancer: which is the guilty party? Oncogene 21, 5380–5387 (2002).
  Article CAS Google Scholar
• Song, J.Z., Stirzaker, C., Harrison, J., Melki, J.R. & Clark, S.J. Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells. Oncogene 21, 1048–1061 (2002).
  Article CAS Google Scholar
• Baylin, S. & Bestor, T.H. Altered methylation patterns in cancer cell genomes: cause or consequence? Cancer Cell 1, 299–305 (2002).
  Article CAS Google Scholar
• Bachman, K.E. et al. Histone modifications and silencing prior to DNA methylation of a tumor suppressor gene. Cancer Cell 3, 89–95 (2003).
  Article CAS Google Scholar
• Melki, J.R., Vincent, P.C. & Clark, S.J. Concurrent DNA hypermethylation of multiple genes in acute myeloid leukaemia. Cancer Res. 59, 3730–3740 (1999).
  CAS PubMed Google Scholar
• Costello, J.F. et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat. Genet. 24, 132–138 (2000).
  Article CAS Google Scholar
• Rush, L.J. et al. Epigenetic profiling in chronic lymphocytic leukemia reveals novel methylation targets. Cancer Res. 64, 2424–2433 (2004).
  Article CAS Google Scholar
• Feltus, F.A., Lee, E.K., Costello, J.F., Plass, C. & Vertino, P.M. Predicting aberrant CpG island methylation. Proc. Natl. Acad. Sci. USA 100, 12253–12258 (2003).
  Article CAS Google Scholar
• Ushijima, T. Detection and interpretation of altered methylation patterns in cancer cells. Nat. Rev. Cancer 5, 223–231 (2005).
  Article CAS Google Scholar
• Frigola, J., Ribas, M., Risques, R.A. & Peinado, M.A. Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS). Nucleic Acids Res. 30, e28 (2002).
  Article Google Scholar
• Stirzaker, C., Song, J.Z., Davidson, B. & Clark, S.J. Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells. Cancer Res. 64, 3871–3877 (2004).
  Article CAS Google Scholar
• Kondo, Y., Shen, L., Yan, P.S., Huang, T.H. & Issa, J.P. Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylation. Proc. Natl. Acad. Sci. USA 101, 7398–7403 (2004).
  Article CAS Google Scholar
• Frigola, J. et al. Differential DNA hypermethylation and hypomethylation signatures in colorectal cancer. Hum. Mol. Genet. 14, 319–326 (2005).
  Article CAS Google Scholar
• Kangas, M. et al. Structure and chromosomal localization of the human and murine genes for the macrophage MARCO receptor. Genomics 58, 82–89 (1999).
  Article CAS Google Scholar
• Gui, C.Y., Ngo, L., Xu, W.S., Richon, V.M. & Marks, P.A. Histone deacetylase (HDAC) inhibitor activation of p21WAF1 involves changes in promoter-associated proteins, including HDAC1. Proc. Natl. Acad. Sci. USA 101, 1241–1246 (2004).
  Article CAS Google Scholar
• Archer, S.Y., Meng, S., Shei, A. & Hodin, R.A. p21(WAF1) is required for butyrate-mediated growth inhibition of human colon cancer cells. Proc. Natl. Acad. Sci. USA 95, 6791–6796 (1998).
  Article CAS Google Scholar
• Zhu, W.G. et al. 5-aza-2′-deoxycytidine activates the p53/p21Waf1/Cip1 pathway to inhibit cell proliferation. J. Biol. Chem. 279, 15161–15166 (2004).
  Article CAS Google Scholar
• Huschtscha, L.I. et al. Loss of p16INK4 expression by methylation is associated with lifespan extension of human mammary epithelial cells. Cancer Res. 58, 3508–3512 (1998).
  CAS PubMed Google Scholar
• Weber, M. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37, 853–862 (2005).
  Article CAS Google Scholar
• Nie, Y. et al. DNA hypermethylation is a mechanism for loss of expression of the HLA class I genes in human esophageal squamous cell carcinomas. Carcinogenesis 22, 1615–1623 (2001).
  Article CAS Google Scholar
• van Noesel, M.M. et al. Clustering of hypermethylated genes in neuroblastoma. Genes Chromosom. Cancer 38, 226–233 (2003).
  Article CAS Google Scholar
• Palmisano, W.A. et al. Aberrant promoter methylation of the transcription factor genes PAX5 alpha and beta in human cancers. Cancer Res. 63, 4620–4625 (2003).
  CAS PubMed Google Scholar
• Brockdorff, N. X-chromosome inactivation: closing in on proteins that bind Xist RNA. Trends Genet. 18, 352–358 (2002).
  Article CAS Google Scholar
• Latham, K.E. X chromosome imprinting and inactivation in preimplantation mammalian embryos. Trends Genet. 21, 120–127 (2005).
  Article CAS Google Scholar
• Plath, K., Mlynarczyk-Evans, S., Nusinow, D.A. & Panning, B. Xist RNA and the mechanism of X chromosome inactivation. Annu. Rev. Genet. 36, 233–278 (2002).
  Article CAS Google Scholar
• Lippman, Z. & Martienssen, R. The role of RNA interference in heterochromatic silencing. Nature 431, 364–370 (2004).
  Article CAS Google Scholar
• O'Neill, M.J. The influence of non-coding RNAs on allele-specific gene expression in mammals. Hum. Mol. Genet. 14, R113–R120 (2005).
  Article CAS Google Scholar
• Jaffrey, R.G. et al. Genomic instability at the BUB1 locus in colorectal cancer, but not in non-small cell lung cancer. Cancer Res. 60, 4349–4352 (2000).
  CAS PubMed Google Scholar
• Moon, R.T., Kohn, A.D., De Ferrari, G.V. & Kaykas, A. WNT and beta-catenin signalling: diseases and therapies. Nat. Rev. Genet. 5, 691–701 (2004).
  Article CAS Google Scholar
• Adamska, M., MacDonald, B.T., Sarmast, Z.H., Oliver, E.R. & Meisler, M.H. En1 and Wnt7a interact with Dkk1 during limb development in the mouse. Dev. Biol. 272, 134–144 (2004).
  Article CAS Google Scholar
• Pang, R.T., Lee, L.T., Ng, S.S., Yung, W.H. & Chow, B.K. CpG methylation and transcription factors Sp1 and Sp3 regulate the expression of the human secretin receptor gene. Mol. Endocrinol. 18, 471–483 (2004).
  Article CAS Google Scholar
• Tang, C. et al. Expression of receptors for gut peptides in pancreata of BOP-treated and control hamsters. Carcinogenesis 17, 2171–2175 (1996).
  Article CAS Google Scholar
• Tang, C., Biemond, I. & Lamers, C.B. Expression of peptide receptors in human endocrine tumours of the pancreas. Gut 40, 267–271 (1997).
  Article CAS Google Scholar
• Reis, F.M. et al. Activin, inhibin and the human breast. Mol. Cell. Endocrinol. 225, 77–82 (2004).
  Article CAS Google Scholar
• Mylonas, I. et al. Inhibin/activin subunits (inhibin-alpha, -betaA and -betaB) are differentially expressed in human breast cancer and their metastasis. Oncol. Rep. 13, 81–88 (2005).
  CAS PubMed Google Scholar
• Sims, R.J., III, Nishioka, K. & Reinberg, D. Histone lysine methylation: a signature for chromatin function. Trends Genet. 19, 629–639 (2003).
  Article CAS Google Scholar
• Mutskov, V. & Felsenfeld, G. Silencing of transgene transcription precedes methylation of promoter DNA and histone H3 lysine 9. EMBO J. 23, 138–149 (2004).
  Article CAS Google Scholar
• Gius, D. et al. Distinct effects on gene expression of chemical and genetic manipulation of the cancer epigenome revealed by a multimodality approach. Cancer Cell 6, 361–371 (2004).
  Article CAS Google Scholar
• Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002).
  Article CAS Google Scholar
• Lorincz, M.C., Schubeler, D., Hutchinson, S.R., Dickerson, D.R. & Groudine, M. DNA methylation density influences the stability of an epigenetic imprint and Dnmt3a/b-independent de novo methylation. Mol. Cell. Biol. 22, 7572–7580 (2002).
  Article CAS Google Scholar
• Nguyen, C. et al. Susceptibility of nonpromoter CpG islands to de novo methylation in normal and neoplastic cells. J. Natl. Cancer Inst. 93, 1465–1472 (2001).
  Article CAS Google Scholar
• Lorincz, M.C., Dickerson, D.R., Schmitt, M. & Groudine, M. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat. Struct. Mol. Biol. 11, 1068–1075 (2004).
  Article CAS Google Scholar
• Clark, S.J., Harrison, J., Paul, C.L. & Frommer, M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22, 2990–2997 (1994).
  Article CAS Google Scholar