Cancer epigenetics: above and beyond

References

• Acharya MR, Sparreboom A, Venitz J, Figg WD. 2005. Rational development of histone deacetylase inhibitors as anticancer agents: a review. Mol Pharmacol 68:917–932.
   PubMed Web of Science ®Google Scholar
• Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP. 2008. The impact of microRNAs on protein output. Nature 455:64–71.
   PubMed Web of Science ®Google Scholar
• Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297.
   PubMed Web of Science ®Google Scholar
• Bartel DP. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136:215–233.
   PubMed Web of Science ®Google Scholar
• Baylin SB, Herman JG, Graff JR, Vertino PM, Issa JP. 1998. Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res 72:141–196.
   PubMed Web of Science ®Google Scholar
• Baylin SB, Ohm JE. 2006. Epigenetic gene silencing in cancer—a mechanism for early oncogenic pathway addiction? Nat Rev Cancer 6:107–116.
   PubMed Web of Science ®Google Scholar
• Bedford MT, van Helden PD. 1987. Hypomethylation of DNA in pathological conditions of the human prostate. Cancer Res 47:5274–5276.
   PubMed Web of Science ®Google Scholar
• Bhasin M, Reinherz EL, Reche PA. 2006. Recognition and classification of histones using support vector machine. J Comput Biol 13:102–112.
   PubMedGoogle Scholar
• Bird A. 1992. The essentials of DNA methylation. Cell 70:5–8.
   PubMed Web of Science ®Google Scholar
• Boyerinas B, Park SM, Hau A, Murmann AE, Peter ME. 2010. The role of let-7 in cell differentiation and cancer. Endocr Relat Cancer 17:F19–F36.
   PubMed Web of Science ®Google Scholar
• Brait M, Begum S, Carvalho AL, Dasgupta S, Vettore AL, Czerniak B, Caballero OL, Westra WH, Sidransky D, Hoque MO. 2008. Aberrant promoter methylation of multiple genes during pathogenesis of bladder cancer. Cancer Epidemiol Biomarkers Prev 17:2786–2794.
   PubMed Web of Science ®Google Scholar
• Brueckner B, Stresemann C, Kuner R, Mund C, Musch T, Meister M, Sültmann H, Lyko F. 2007. The human let-7a-3 locus contains an epigenetically regulated microRNA gene with oncogenic function. Cancer Res 67:1419–1423.
   PubMed Web of Science ®Google Scholar
• Cairns P. 2007. Gene methylation and early detection of genitourinary cancer: the road ahead. Nat Rev Cancer 7:531–543.
   PubMedGoogle Scholar
• Calin GA, Croce CM. 2006. MicroRNA signatures in human cancers. Nat Rev Cancer 6:857–866.
   PubMed Web of Science ®Google Scholar
• Cameron EE, Bachman KE, Myöhänen S, Herman JG, Baylin SB. 1999. Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nat Genet 21:103–107.
   PubMed Web of Science ®Google Scholar
• Cang S, Ma Y, Liu D. 2009. New clinical developments in histone deacetylase inhibitors for epigenetic therapy of cancer. J Hematol Oncol 2:22.
   Google Scholar
• Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, Jones RS, Zhang Y. 2002. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298:1039–1043.
   PubMed Web of Science ®Google Scholar
• Chang SS, Jiang WW, Smith I, Poeta LM, Begum S, Glazer C, Shan S, Westra W, Sidransky D, Califano JA. 2008. MicroRNA alterations in head and neck squamous cell carcinoma. Int J Cancer 123:2791–2797.
   PubMed Web of Science ®Google Scholar
• Cheng JC, Yoo CB, Weisenberger DJ, Chuang J, Wozniak C, Liang G, Marquez VE, Greer S, Orntoft TF, Thykjaer T, Jones PA. 2004. Preferential response of cancer cells to zebularine. Cancer Cell 6:151–158.
   PubMed Web of Science ®Google Scholar
• Chi P, Allis CD, Wang GG. 2010. Covalent histone modifications—miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer 10:457–469.
   PubMed Web of Science ®Google Scholar
• Cimmino A, Calin GA, Fabbri M, Iorio MV, Ferracin M, Shimizu M, Wojcik SE, Aqeilan RI, Zupo S, Dono M, Rassenti L, Alder H, Volinia S, Liu CG, Kipps TJ, Negrini M, Croce CM. 2005. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci USA 102:13944–13949.
   PubMed Web of Science ®Google Scholar
• Clapier CR, Cairns BR. 2009. The biology of chromatin remodeling complexes. Annu Rev Biochem 78:273–304.
   PubMed Web of Science ®Google Scholar
• Costa FF. 2010a. Epigenomics in cancer management. Cancer Manag Res 2:255–265.
   PubMedGoogle Scholar
• Costa FF. 2010b. Non-coding RNAs: meet thy masters. Bioessays 32:599–608.
   PubMed Web of Science ®Google Scholar
• Costello JF, Frühwald MC, Smiraglia DJ, Rush LJ, Robertson GP, Gao X, Wright FA, Feramisco JD, Peltomäki P, Lang JC, Schuller DE, Yu L, Bloomfield CD, Caligiuri MA, Yates A, Nishikawa R, Su Huang H, Petrelli NJ, Zhang X, O’Dorisio MS, Held WA, Cavenee WK, Plass C. 2000. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet 24:132–138.
   PubMed Web of Science ®Google Scholar
• Di Croce L, Raker VA, Corsaro M, Fazi F, Fanelli M, Faretta M, Fuks F, Lo Coco F, Kouzarides T, Nervi C, Minucci S, Pelicci PG. 2002. Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science 295:1079–1082.
   PubMed Web of Science ®Google Scholar
• Ehrlich M. 2002. DNA hypomethylation, cancer, the immunodeficiency, centromeric region instability, facial anomalies syndrome and chromosomal rearrangements. J Nutr 132:2424S–2429S.
   PubMed Web of Science ®Google Scholar
• Ehrlich M, Jiang G, Fiala E, Dome JS, Yu MC, Long TI, Youn B, Sohn OS, Widschwendter M, Tomlinson GE, Chintagumpala M, Champagne M, Parham D, Liang G, Malik K, Laird PW. 2002. Hypomethylation and hypermethylation of DNA in Wilms tumors. Oncogene 21:6694–6702.
   PubMed Web of Science ®Google Scholar
• Esquela-Kerscher A, Slack FJ. 2006. Oncomirs—microRNAs with a role in cancer. Nat Rev Cancer 6:259–269.
   PubMed Web of Science ®Google Scholar
• Esteller M. 2007. Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum Mol Genet 16 (Spec No 1):R50–R59.
   Google Scholar
• Esteller M, Almouzni G. 2005. How epigenetics integrates nuclear functions. Workshop on epigenetics and chromatin: transcriptional regulation and beyond. EMBO Rep 6:624–628.
   PubMedGoogle Scholar
• Esteller M, Corn PG, Baylin SB, Herman JG. 2001. A gene hypermethylation profile of human cancer. Cancer Res 61:3225–3229.
   PubMed Web of Science ®Google Scholar
• Esteller M, Toyota M, Sanchez-Cespedes M, Capella G, Peinado MA, Watkins DN, Issa JP, Sidransky D, Baylin SB, Herman JG. 2000. Inactivation of the DNA repair gene O6-methylguanine–DNA methyltransferase by promoter hypermethylation is associated with G to A mutations in K-ras in colorectal tumorigenesis. Cancer Res 60:2368–2371.
   PubMed Web of Science ®Google Scholar
• Feinberg AP, Vogelstein B. 1983. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:89–92.
   PubMed Web of Science ®Google Scholar
• Ferguson-Smith AC, Reik W, Surani MA. 1990. Genomic imprinting and cancer. Cancer Surv 9:487–503.
   Google Scholar
• Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suñer D, Cigudosa JC, Urioste M, Benitez J, Boix-Chornet M, Sanchez-Aguilera A, Ling C, Carlsson E, Poulsen P, Vaag A, Stephan Z, Spector TD, Wu YZ, Plass C, Esteller M. 2005. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 102:10604–10609.
   PubMed Web of Science ®Google Scholar
• Gal-Yam EN, Saito Y, Egger G, Jones PA. 2008. Cancer epigenetics: modifications, screening, and therapy. Annu Rev Med 59:267–280.
   PubMed Web of Science ®Google Scholar
• Georgel PT, Hansen JC. 2001. Linker histone function in chromatin: dual mechanisms of action. Biochem Cell Biol 79:313–316.
   PubMedGoogle Scholar
• Glazer CA, Smith IM, Ochs MF, Begum S, Westra W, Chang SS, Sun W, Bhan S, Khan Z, Ahrendt S, Califano JA. 2009. Integrative discovery of epigenetically derepressed cancer testis antigens in NSCLC. PLoS ONE 4:e8189.
   Google Scholar
• Goffin J, Eisenhauer E. 2002. DNA methyltransferase inhibitors-state of the art. Ann Oncol 13:1699–1716.
   PubMed Web of Science ®Google Scholar
• Gonzalez S, Pisano DG, Serrano M. 2008. Mechanistic principles of chromatin remodeling guided by siRNAs and miRNAs. Cell Cycle 7:2601–2608.
   PubMed Web of Science ®Google Scholar
• Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. 2007. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27:91–105.
   PubMed Web of Science ®Google Scholar
• Hayashita Y, Osada H, Tatematsu Y, Yamada H, Yanagisawa K, Tomida S, Yatabe Y, Kawahara K, Sekido Y, Takahashi T. 2005. A polycistronic microRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res 65:9628–9632.
   PubMed Web of Science ®Google Scholar
• Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W, Walter J, Surani MA. 2002. Epigenetic reprogramming in mouse primordial germ cells. Mech Dev 117:15–23.
   PubMed Web of Science ®Google Scholar
• Hanke M, Hoefig K, Merz H, Feller AC, Kausch I, Jocham D, Warnecke JM, Sczakiel G. 2010. A robust methodology to study urine microRNA as tumor marker: microRNA-126 and microRNA-182 are related to urinary bladder cancer. Urol Oncol 28:655–661.
   PubMed Web of Science ®Google Scholar
• Hellman A, Chess A. 2007. Gene body-specific methylation on the active X chromosome. Science 315:1141–1143.
   PubMed Web of Science ®Google Scholar
• Hoque MO. 2009. DNA methylation changes in prostate cancer: current developments and future clinical implementation. Expert Rev Mol Diagn 9:243–257.
   PubMed Web of Science ®Google Scholar
• Hoque MO, Kim MS, Ostrow KL, Liu J, Wisman GB, Park HL, Poeta ML, Jeronimo C, Henrique R, Lendvai A, Schuuring E, Begum S, Rosenbaum E, Ongenaert M, Yamashita K, Califano J, Westra W, van der Zee AG, Van Criekinge W, Sidransky D. 2008. Genome-wide promoter analysis uncovers portions of the cancer methylome. Cancer Res 68:2661–2670.
   PubMed Web of Science ®Google Scholar
• Huang Y, Greene E, Murray Stewart T, Goodwin AC, Baylin SB, Woster PM, Casero RA Jr. 2007. Inhibition of lysine-specific demethylase 1 by polyamine analogues results in reexpression of aberrantly silenced genes. Proc Natl Acad Sci USA 104:8023–8028.
   PubMed Web of Science ®Google Scholar
• Isharwal S, Miller MC, Marlow C, Makarov DV, Partin AW, Veltri RW. 2008. p300 (histone acetyltransferase) biomarker predicts prostate cancer biochemical recurrence and correlates with changes in epithelia nuclear size and shape. Prostate 68:1097–1104.
   Google Scholar
• Issa JP. 2004. CpG island methylator phenotype in cancer. Nat Rev Cancer 4:988–993.
   PubMed Web of Science ®Google Scholar
• Issa JP. 2007. DNA methylation as a therapeutic target in cancer. Clin Cancer Res 13:1634–1637.
   PubMed Web of Science ®Google Scholar
• Jiang C, Pugh BF. 2009a. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol 10:R109.
   PubMedGoogle Scholar
• Jiang C, Pugh BF. 2009b. Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 10:161–172.
   PubMed Web of Science ®Google Scholar
• Johnstone RW. 2002. Histone-deacetylase inhibitors: novel drugs for the treatment of cancer. Nat Rev Drug Discov 1:287–299.
   PubMed Web of Science ®Google Scholar
• Jones PA, Baylin SB. 2007. The epigenomics of cancer. Cell 128:683–692.
   PubMed Web of Science ®Google Scholar
• Jones PA, Baylin SB. 2002. The fundamental role of epigenetic events in cancer. Nat Rev Genet 3:415–428.
   PubMed Web of Science ®Google Scholar
• Jones PA, Laird PW. 1999. Cancer epigenetics comes of age. Nat Genet 21:163–167.
   PubMed Web of Science ®Google Scholar
• Jones PA, Taylor SM. 1980. Cellular differentiation, cytidine analogs and DNA methylation. Cell 20:85–93.
   PubMed Web of Science ®Google Scholar
• Jost JP, Bruhat A. 1997. The formation of DNA methylation patterns and the silencing of genes. Prog Nucleic Acid Res Mol Biol 57:217–248.
   PubMedGoogle Scholar
• Kacem S, Feil R. 2009. Chromatin mechanisms in genomic imprinting. Mamm Genome 20:544–556.
   PubMed Web of Science ®Google Scholar
• Kim MS, Lee J, Sidransky D. 2010. DNA methylation markers in colorectal cancer. Cancer Metastasis Rev 29:181–206.
   PubMed Web of Science ®Google Scholar
• Kinzler KW, Vogelstein B. 1996. Lessons from hereditary colorectal cancer. Cell 87:159–170.
   PubMed Web of Science ®Google Scholar
• Kleer CG, Cao Q, Varambally S, Shen R, Ota I, Tomlins SA, Ghosh D, Sewalt RG, Otte AP, Hayes DF, Sabel MS, Livant D, Weiss SJ, Rubin MA, Chinnaiyan AM. 2003. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Sci USA 100:11606–11611.
   PubMed Web of Science ®Google Scholar
• Klose RJ, Bird AP. 2006. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31:89–97.
   PubMed Web of Science ®Google Scholar
• Knudson AG Jr. 1971. Mutation and cancer: statistical study of retinoblastoma. Proc Natl Acad Sci USA 68:820–823.
   PubMed Web of Science ®Google Scholar
• Kouzarides T. 2007. Chromatin modifications and their function. Cell 128:693–705.
   PubMed Web of Science ®Google Scholar
• Krichevsky AM, Gabriely G. 2009. miR-21: a small multi-faceted RNA. J Cell Mol Med 13:39–53.
   PubMed Web of Science ®Google Scholar
• Längst G, Becker PB. 2004. Nucleosome remodeling: one mechanism, many phenomena? Biochim Biophys Acta 1677:58–63.
   PubMedGoogle Scholar
• Le XF, Merchant O, Bast RC, Calin GA. 2010. The roles of microRNAs in the cancer invasion-metastasis cascade. Cancer Microenviron 3:137–147.
   Google Scholar
• le Sage C, Nagel R, Egan DA, Schrier M, Mesman E, Mangiola A, Anile C, Maira G, Mercatelli N, Ciafrè SA, Farace MG, Agami R. 2007. Regulation of the p27(Kip1) tumor suppressor by miR-221 and miR-222 promotes cancer cell proliferation. EMBO J 26:3699–3708.
   PubMed Web of Science ®Google Scholar
• Liu C, Kelnar K, Liu B, Chen X, Calhoun-Davis T, Li H, Patrawala L, Yan H, Jeter C, Honorio S, Wiggins JF, Bader AG, Fagin R, Brown D, Tang DG. 2011. The microRNA miR-34a inhibits prostate cancer stem cells and metastasis by directly repressing CD44. Nat Med 17:211–215.
   PubMed Web of Science ®Google Scholar
• Lopez-Serra L, Esteller M. 2008. Proteins that bind methylated DNA and human cancer: reading the wrong words. Br J Cancer 98:1881–1885.
   PubMed Web of Science ®Google Scholar
• Lucio-Eterovic AK, Cortez MA, Valera ET, Motta FJ, Queiroz RG, Machado HR, Carlotti CG Jr, Neder L, Scrideli CA, Tone LG. 2008. Differential expression of 12 histone deacetylase (HDAC) genes in astrocytomas and normal brain tissue: class II and IV are hypoexpressed in glioblastomas. BMC Cancer 8:243.
   PubMed Web of Science ®Google Scholar
• Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251–260.
   PubMed Web of Science ®Google Scholar
• Lujambio A, Calin GA, Villanueva A, Ropero S, Sánchez-Céspedes M, Blanco D, Montuenga LM, Rossi S, Nicoloso MS, Faller WJ, Gallagher WM, Eccles SA, Croce CM, Esteller M. 2008. A microRNA DNA methylation signature for human cancer metastasis. Proc Natl Acad Sci USA 105:13556–13561.
   PubMed Web of Science ®Google Scholar
• Ma L, Weinberg RA. 2008. Micromanagers of malignancy: role of microRNAs in regulating metastasis. Trends Genet 24:448–456.
   Google Scholar
• Maldonado L, Hoque MO. 2010. Epigenomics and ovarian carcinoma. Biomark Med 4:543–570.
   Google Scholar
• Martin C, Zhang Y. 2005. The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6:838–849.
   PubMed Web of Science ®Google Scholar
• Martinez-Garcia E, Licht JD. 2010. Deregulation of H3K27 methylation in cancer. Nat Genet 42:100–101.
   PubMed Web of Science ®Google Scholar
• Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. 2008. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18:1073–1083.
   PubMed Web of Science ®Google Scholar
• Melo SA, Ropero S, Moutinho C, Aaltonen LA, Yamamoto H, Calin GA, Rossi S, Fernandez AF, Carneiro F, Oliveira C, Ferreira B, Liu CG, Villanueva A, Capella G, Schwartz S Jr, Shiekhattar R, Esteller M. 2009. A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function. Nat Genet 41:365–370.
   PubMed Web of Science ®Google Scholar
• Merlo A, Herman JG, Mao L, Lee DJ, Gabrielson E, Burger PC, Baylin SB, Sidransky D. 1995. 5′ CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers. Nat Med 1:686–692.
   PubMed Web of Science ®Google Scholar
• Minucci S, Pelicci PG. 2006. Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat Rev Cancer 6:38–51.
   PubMed Web of Science ®Google Scholar
• Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O’Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, Tewari M. 2008. Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 105:10513–10518.
   PubMed Web of Science ®Google Scholar
• Momparler RL. 2003. Cancer epigenetics. Oncogene 22:6479–6483.
   PubMed Web of Science ®Google Scholar
• Morey L, Brenner C, Fazi F, Villa R, Gutierrez A, Buschbeck M, Nervi C, Minucci S, Fuks F, Di Croce L. 2008. MBD3, a component of the NuRD complex, facilitates chromatin alteration and deposition of epigenetic marks. Mol Cell Biol 28:5912–5923.
   PubMed Web of Science ®Google Scholar
• Morgan HD, Sutherland HG, Martin DI, Whitelaw E. 1999. Epigenetic inheritance at the agouti locus in the mouse. Nat Genet 23:314–318.
   PubMed Web of Science ®Google Scholar
• Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A. 1998. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393:386–389.
   PubMed Web of Science ®Google Scholar
• Natsume A, Kondo Y, Ito M, Motomura K, Wakabayashi T, Yoshida J. 2010. Epigenetic aberrations and therapeutic implications in gliomas. Cancer Sci 101:1331–1336.
   Web of Science ®Google Scholar
• Netto GJ, Nakai Y, Nakayama M, Jadallah S, Toubaji A, Nonomura N, Albadine R, Hicks JL, Epstein JI, Yegnasubramanian S, Nelson WG, De Marzo AM. 2008. Global DNA hypomethylation in intratubular germ cell neoplasia and seminoma, but not in nonseminomatous male germ cell tumors. Mod Pathol 21:1337–1344.
   PubMed Web of Science ®Google Scholar
• O’Day E, Lal A. 2010. MicroRNAs and their target gene networks in breast cancer. Breast Cancer Res 12:201.
   PubMed Web of Science ®Google Scholar
• Omoto S, Fujii YR. 2005. Regulation of human immunodeficiency virus 1 transcription by nef microRNA. J Gen Virol 86:751–755.
   PubMed Web of Science ®Google Scholar
• Oosterhuis JW, Looijenga LH. 2005. Testicular germ-cell tumours in a broader perspective. Nat Rev Cancer 5:210–222.
   PubMed Web of Science ®Google Scholar
• Passetti F, Ferreira CG, Costa FF. 2009. The impact of microRNAs and alternative splicing in pharmacogenomics. Pharmacogenomics J 9:1–13.
   PubMed Web of Science ®Google Scholar
• Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, Basyuk E, Bertrand E, Filipowicz W. 2005. Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science 309:1573–1576.
   PubMed Web of Science ®Google Scholar
• Portela A, Esteller M. 2010. Epigenetic modifications and human disease. Nat Biotechnol 28:1057–1068.
   PubMed Web of Science ®Google Scholar
• Rainier S, Johnson LA, Dobry CJ, Ping AJ, Grundy PE, Feinberg AP. 1993. Relaxation of imprinted genes in human cancer. Nature 362:747–749.
   PubMed Web of Science ®Google Scholar
• Reik W, Dean W, Walter J. 2001. Epigenetic reprogramming in mammalian development. Science 293:1089–1093.
   PubMed Web of Science ®Google Scholar
• Reik W, Surani MA. 1989. Cancer genetics. Genomic imprinting and embryonal tumours. Nature 338:112–113.
   PubMed Web of Science ®Google Scholar
• Riddihough G, Zahn LM. 2010. Epigenetics. What is epigenetics? Introduction. Science 330:611.
   PubMed Web of Science ®Google Scholar
• Riggs AD. 1975. X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet 14:9–25.
   PubMedGoogle Scholar
• Riggs AD, Jones PA. 1983. 5-Methylcytosine, gene regulation, and cancer. Adv Cancer Res 40:1–30.
   PubMed Web of Science ®Google Scholar
• Ropero S, Fraga MF, Ballestar E, Hamelin R, Yamamoto H, Boix-Chornet M, Caballero R, Alaminos M, Setien F, Paz MF, Herranz M, Palacios J, Arango D, Orntoft TF, Aaltonen LA, Schwartz S Jr, Esteller M. 2006. A truncating mutation of HDAC2 in human cancers confers resistance to histone deacetylase inhibition. Nat Genet 38:566–569.
   PubMed Web of Science ®Google Scholar
• Sawan C, Vaissière T, Murr R, Herceg Z. 2008. Epigenetic drivers and genetic passengers on the road to cancer. Mutat Res 642:1–13.
   PubMed Web of Science ®Google Scholar
• Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. 2008. Dynamic regulation of nucleosome positioning in the human genome. Cell 132:887–898.
   PubMed Web of Science ®Google Scholar
• Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Field Y, Moore IK, Wang JP, Widom J. 2006. A genomic code for nucleosome positioning. Nature 442:772–778.
   PubMed Web of Science ®Google Scholar
• Segura-Pacheco B, Trejo-Becerril C, Perez-Cardenas E, Taja-Chayeb L, Mariscal I, Chavez A, Acuña C, Salazar AM, Lizano M, Dueñas-Gonzalez A. 2003. Reactivation of tumor suppressor genes by the cardiovascular drugs hydralazine and procainamide and their potential use in cancer therapy. Clin Cancer Res 9:1596–1603.
   PubMed Web of Science ®Google Scholar
• Sharma S, Kelly TK, Jones PA. 2010. Epigenetics in cancer. Carcinogenesis 31:27–36.
   PubMed Web of Science ®Google Scholar
• Sidransky D. 2002. Emerging molecular markers of cancer. Nat Rev Cancer 2:210–219.
   PubMed Web of Science ®Google Scholar
• Simpson AJ, Caballero OL, Jungbluth A, Chen YT, Old LJ. 2005. Cancer/testis antigens, gametogenesis and cancer. Nat Rev Cancer 5:615–625.
   PubMed Web of Science ®Google Scholar
• Smith IM, Glazer CA, Mithani SK, Ochs MF, Sun W, Bhan S, Vostrov A, Abdullaev Z, Lobanenkov V, Gray A, Liu C, Chang SS, Ostrow KL, Westra WH, Begum S, Dhara M, Califano J. 2009. Coordinated activation of candidate proto-oncogenes and cancer testes antigens via promoter demethylation in head and neck cancer and lung cancer. PLoS ONE 4:e4961.
   PubMedGoogle Scholar
• Smith IM, Mydlarz WK, Mithani SK, Califano JA. 2007. DNA global hypomethylation in squamous cell head and neck cancer associated with smoking, alcohol consumption and stage. Int J Cancer 121:1724–1728.
   PubMed Web of Science ®Google Scholar
• Straussman R, Nejman D, Roberts D, Steinfeld I, Blum B, Benvenisty N, Simon I, Yakhini Z, Cedar H. 2009. Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol 16:564–571.
   PubMed Web of Science ®Google Scholar
• Struhl K. 1998. Histone acetylation and transcriptional regulatory mechanisms. Genes Dev 12:599–606.
   PubMed Web of Science ®Google Scholar
• Taby R, Issa JP. 2010. Cancer epigenetics. CA Cancer J Clin 60:376–392.
   PubMed Web of Science ®Google Scholar
• Takai D, Jones PA. 2002. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 99:3740–3745.
   PubMed Web of Science ®Google Scholar
• Takamizawa J, Konishi H, Yanagisawa K, Tomida S, Osada H, Endoh H, Harano T, Yatabe Y, Nagino M, Nimura Y, Mitsudomi T, Takahashi T. 2004. Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res 64:3753–3756.
   PubMed Web of Science ®Google Scholar
• Tan J, Yang X, Zhuang L, Jiang X, Chen W, Lee PL, Karuturi RK, Tan PB, Liu ET, Yu Q. 2007. Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. Genes Dev 21:1050–1063.
   PubMed Web of Science ®Google Scholar
• Thomson JP, Skene PJ, Selfridge J, Clouaire T, Guy J, Webb S, Kerr AR, Deaton A, Andrews R, James KD, Turner DJ, Illingworth R, Bird A. 2010. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464:1082–1086.
   PubMed Web of Science ®Google Scholar
• Ting AH, McGarvey KM, Baylin SB. 2006. The cancer epigenome—components and functional correlates. Genes Dev 20:3215–3231.
   PubMed Web of Science ®Google Scholar
• Tsai WC, Hsu PW, Lai TC, Chau GY, Lin CW, Chen CM, Lin CD, Liao YL, Wang JL, Chau YP, Hsu MT, Hsiao M, Huang HD, Tsou AP. 2009. MicroRNA-122, a tumor suppressor microRNA that regulates intrahepatic metastasis of hepatocellular carcinoma. Hepatology 49:1571–1582.
   PubMed Web of Science ®Google Scholar
• Turker MS, Bestor TH. 1997. Formation of methylation patterns in the mammalian genome. Mutat Res 386:119–130.
   PubMed Web of Science ®Google Scholar
• van Haaften G, Agami R. 2010. Tumorigenicity of the miR-17-92 cluster distilled. Genes Dev 24:1–4.
   PubMed Web of Science ®Google Scholar
• Ventura A, Jacks T. 2009. MicroRNAs and cancer: short RNAs go a long way. Cell 136:586–591.
   PubMed Web of Science ®Google Scholar
• Vigushin DM, Ali S, Pace PE, Mirsaidi N, Ito K, Adcock I, Coombes RC. 2001. Trichostatin A is a histone deacetylase inhibitor with potent antitumor activity against breast cancer in vivo. Clin Cancer Res 7:971–976.
   PubMed Web of Science ®Google Scholar
• Visone R, Russo L, Pallante P, De Martino I, Ferraro A, Leone V, Borbone E, Petrocca F, Alder H, Croce CM, Fusco A. 2007. MicroRNAs (miR)-221 and miR-222, both overexpressed in human thyroid papillary carcinomas, regulate p27Kip1 protein levels and cell cycle. Endocr Relat Cancer 14:791–798.
   PubMed Web of Science ®Google Scholar
• Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, Visone R, Iorio M, Roldo C, Ferracin M, Prueitt RL, Yanaihara N, Lanza G, Scarpa A, Vecchione A, Negrini M, Harris CC, Croce CM. 2006. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci USA 103:2257–2261.
   PubMed Web of Science ®Google Scholar
• Vucic EA, Brown CJ, Lam WL. 2008. Epigenetics of cancer progression. Pharmacogenomics 9:215–234.
   PubMed Web of Science ®Google Scholar
• Waddington CH. 1942. The epigenotype. Endeavour 1:18–20.
   Google Scholar
• Wang QZ, Xu W, Habib N, Xu R. 2009. Potential uses of microRNA in lung cancer diagnosis, prognosis, and therapy. Curr Cancer Drug Targets 9:572–594.
   PubMed Web of Science ®Google Scholar
• Wang Y, Leung FC. 2004. An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics 20:1170–1177.
   PubMed Web of Science ®Google Scholar
• Weissman B, Knudsen KE. 2009. Hijacking the chromatin remodeling machinery: impact of SWI/SNF perturbations in cancer. Cancer Res 69:8223–8230.
   Google Scholar
• Wolff EM, Byun HM, Han HF, Sharma S, Nichols PW, Siegmund KD, Yang AS, Jones PA, Liang G. 2010. Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer. PLoS Genet 6:e1000917.
   PubMed Web of Science ®Google Scholar
• Wurdinger T, Costa FF. 2007. Molecular therapy in the microRNA era. Pharmacogenomics J 7:297–304.
   PubMed Web of Science ®Google Scholar
• Xie Y, Todd NW, Liu Z, Zhan M, Fang H, Peng H, Alattar M, Deepak J, Stass SA, Jiang F. 2010. Altered miRNA expression in sputum for diagnosis of non-small cell lung cancer. Lung Cancer 67:170–176.
   PubMed Web of Science ®Google Scholar
• Yan L, Nass SJ, Smith D, Nelson WG, Herman JG, Davidson NE. 2003. Specific inhibition of DNMT1 by antisense oligonucleotides induces re-expression of estrogen receptor-alpha (ER) in ER-negative human breast cancer cell lines. Cancer Biol Ther 2:552–556.
   PubMed Web of Science ®Google Scholar
• Yu J, Yu J, Rhodes DR, Tomlins SA, Cao X, Chen G, Mehra R, Wang X, Ghosh D, Shah RB, Varambally S, Pienta KJ, Chinnaiyan AM. 2007. A polycomb repression signature in metastatic prostate cancer predicts cancer outcome. Cancer Res 67:10657–10663.
   PubMed Web of Science ®Google Scholar
• Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. 2005. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309:626–630.
   PubMed Web of Science ®Google Scholar
• Zhang B, Pan X, Cobb GP, Anderson TA. 2007. microRNAs as oncogenes and tumor suppressors. Dev Biol 302:1–12.
   PubMed Web of Science ®Google Scholar
• Zhu J, Yao X. 2009. Use of DNA methylation for cancer detection: promises and challenges. Int J Biochem Cell Biol 41:147–154.
   Google Scholar
• Zhu P, Martin E, Mengwasser J, Schlag P, Janssen KP, Göttlicher M. 2004. Induction of HDAC2 expression upon loss of APC in colorectal tumorigenesis. Cancer Cell 5:455–463.
   PubMed Web of Science ®Google Scholar
• Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2007. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39:61–69.
   PubMed Web of Science ®Google Scholar