Interplay between the cancer genome and epigenome

Cell

Volumn 153, Issue 1, 2013, Pages 38-55

  Shen, Hui ^a   Laird, Peter W ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CANCER CELL; CELL DIFFERENTIATION; CELL MATURATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; CPG ISLAND; DNA METHYLATION; DNA REPAIR; EPIGENETICS; GENE MUTATION; GENOME; GENOMIC INSTABILITY; HISTONE ACETYLATION; HISTONE METHYLATION; HUMAN; INSULATOR ELEMENT; NEOPLASM; NONHUMAN; NUCLEOSOME; PHENOTYPE; PRIORITY JOURNAL; REVIEW;

EID: 84875745673     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2013.03.008     Document Type: Review

References (199)

1. O. Abdel-Wahab, A. Mullally, C. Hedvat, G. Garcia-Manero, J. Patel, M. Wadleigh, S. Malinge, J. Yao, O. Kilpivaara, and R. Bhat Genetic characterization of TET1, TET2, and TET3 alterations in myeloid malignancies Blood 114 2009 144 147
2. O. Abdel-Wahab, M. Adli, L.M. LaFave, J. Gao, T. Hricik, A.H. Shih, S. Pandey, J.P. Patel, Y.R. Chung, and R. Koche ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression Cancer Cell 22 2012 180 193
3. D. Adams, L. Altucci, S.E. Antonarakis, J. Ballesteros, S. Beck, A. Bird, C. Bock, B. Boehm, E. Campo, and A. Caricasole BLUEPRINT to decode the epigenetic signature written in blood Nat. Biotechnol. 30 2012 224 226
4. C. Baer, R. Claus, and C. Plass Genome-wide epigenetic regulation of miRNAs in cancer Cancer Res. 73 2013 473 477
5. S.B. Baylin, and P.A. Jones A decade of exploring the cancer epigenome - biological and translational implications Nat. Rev. Cancer 11 2011 726 734
6. S.B. Baylin, J.W. Höppener, A. de Bustros, P.H. Steenbergh, C.J. Lips, and B.D. Nelkin DNA methylation patterns of the calcitonin gene in human lung cancers and lymphomas Cancer Res. 46 1986 2917 2922 (Pubitemid 16074305)
7. M.F. Berger, M.S. Lawrence, F. Demichelis, Y. Drier, K. Cibulskis, A.Y. Sivachenko, A. Sboner, R. Esgueva, D. Pflueger, and C. Sougnez The genomic complexity of primary human prostate cancer Nature 470 2011 214 220
8. B.P. Berman, D.J. Weisenberger, J.F. Aman, T. Hinoue, Z. Ramjan, Y. Liu, H. Noushmehr, C.P. Lange, C.M. van Dijk, and R.A. Tollenaar Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains Nat. Genet. 44 2012 40 46
9. B.E. Bernstein, T.S. Mikkelsen, X. Xie, M. Kamal, D.J. Huebert, J. Cuff, B. Fry, A. Meissner, M. Wernig, and K. Plath A bivalent chromatin structure marks key developmental genes in embryonic stem cells Cell 125 2006 315 326
10. A. Bird, M. Taggart, M. Frommer, O.J. Miller, and D. Macleod A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA Cell 40 1985 91 99 (Pubitemid 15169310)
11. E. Boyarchuk, R. Montes de Oca, and G. Almouzni Cell cycle dynamics of histone variants at the centromere, a model for chromosomal landmarks Curr. Opin. Cell Biol. 23 2011 266 276
12. A.P. Bracken, D. Pasini, M. Capra, E. Prosperini, E. Colli, and K. Helin EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer EMBO J. 22 2003 5323 5335 (Pubitemid 37279943)
13. Cancer Genome Atlas Research Network Integrated genomic analyses of ovarian carcinoma Nature 474 2011 609 615
14. Cancer Genome Atlas Research Network Comprehensive genomic characterization of squamous cell lung cancers Nature 489 2012 519 525
15. Cancer Genome Atlas Network Comprehensive molecular characterization of human colon and rectal cancer Nature 487 2012 330 337
16. Cancer Genome Atlas Network Comprehensive molecular portraits of human breast tumours Nature 490 2012 61 70
17. H. Cedar, and Y. Bergman Programming of DNA methylation patterns Annu. Rev. Biochem. 81 2012 97 117
18. G.A. Challen, D. Sun, M. Jeong, M. Luo, J. Jelinek, J.S. Berg, C. Bock, A. Vasanthakumar, H. Gu, and Y. Xi Dnmt3a is essential for hematopoietic stem cell differentiation Nat. Genet. 44 2012 23 31
19. P. Chi, C.D. Allis, and G.G. Wang Covalent histone modifications - miswritten, misinterpreted and mis-erased in human cancers Nat. Rev. Cancer 10 2010 457 469
20. S.J. Clark Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis Hum. Mol. Genet. 16 Spec No 1 2007 R88 R95
21. P.A. Cloos, J. Christensen, K. Agger, A. Maiolica, J. Rappsilber, T. Antal, K.H. Hansen, and K. Helin The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3 Nature 442 2006 307 311 (Pubitemid 44114906)
22. N.M. Cohen, E. Kenigsberg, and A. Tanay Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection Cell 145 2011 773 786
23. M.W. Coolen, C. Stirzaker, J.Z. Song, A.L. Statham, Z. Kassir, C.S. Moreno, A.N. Young, V. Varma, T.P. Speed, and M. Cowley Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity Nat. Cell Biol. 12 2010 235 246
24. L. Couronné, C. Bastard, and O.A. Bernard TET2 and DNMT3A mutations in human T-cell lymphoma N. Engl. J. Med. 366 2012 95 96
25. G.L. Dalgliesh, K. Furge, C. Greenman, L. Chen, G. Bignell, A. Butler, H. Davies, S. Edkins, C. Hardy, and C. Latimer Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes Nature 463 2010 360 363
26. M.A. Dawson, and T. Kouzarides Cancer epigenetics: from mechanism to therapy Cell 150 2012 12 27
27. L. Daxinger, and E. Whitelaw Understanding transgenerational epigenetic inheritance via the gametes in mammals Nat. Rev. Genet. 13 2012 153 162
28. S. De, and F. Michor DNA secondary structures and epigenetic determinants of cancer genome evolution Nat. Struct. Mol. Biol. 18 2011 950 955
29. D.D. De Carvalho, S. Sharma, J.S. You, S.F. Su, P.C. Taberlay, T.K. Kelly, X. Yang, G. Liang, and P.A. Jones DNA methylation screening identifies driver epigenetic events of cancer cell survival Cancer Cell 21 2012 655 667
30. B. De Craene, and G. Berx Regulatory networks defining EMT during cancer initiation and progression Nat. Rev. Cancer 13 2013 97 110
31. A. Dey, D. Seshasayee, R. Noubade, D.M. French, J. Liu, M.S. Chaurushiya, D.S. Kirkpatrick, V.C. Pham, J.R. Lill, and C.E. Bakalarski Loss of the tumor suppressor BAP1 causes myeloid transformation Science 337 2012 1541 1546
32. E.S. Diala, and R.M. Hoffman Hypomethylation of HeLa cell DNA and the absence of 5-methylcytosine in SV40 and adenovirus (type 2) DNA: analysis by HPLC Biochem. Biophys. Res. Commun. 107 1982 19 26 (Pubitemid 13166611)
33. V. Dion, Y. Lin, L. Hubert Jr., R.A. Waterland, and J.H. Wilson Dnmt1 deficiency promotes CAG repeat expansion in the mouse germline Hum. Mol. Genet. 17 2008 1306 1317 (Pubitemid 351566967)
34. A. Dolnik, J.C. Engelmann, M. Scharfenberger-Schmeer, J. Mauch, S. Kelkenberg-Schade, B. Haldemann, T. Fries, J. Krönke, M.W. Kühn, and P. Paschka Commonly altered genomic regions in acute myeloid leukemia are enriched for somatic mutations involved in chromatin remodeling and splicing Blood 120 2012 e83 e92
35. I. Dunham, A. Kundaje, S.F. Aldred, P.J. Collins, C.A. Davis, F. Doyle, C.B. Epstein, S. Frietze, J. Harrow, R. Kaul ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome Nature 489 2012 57 74
36. H. Easwaran, S.E. Johnstone, L. Van Neste, J. Ohm, T. Mosbruger, Q. Wang, M.J. Aryee, P. Joyce, N. Ahuja, and D. Weisenberger A DNA hypermethylation module for the stem/progenitor cell signature of cancer Genome Res. 22 2012 837 849
37. A. Eden, F. Gaudet, A. Waghmare, and R. Jaenisch Chromosomal instability and tumors promoted by DNA hypomethylation Science 300 2003 455 (Pubitemid 36444319)
38. M. Ehrlich, and R.Y. Wang 5-Methylcytosine in eukaryotic DNA Science 212 1981 1350 1357
39. M. Ehrlich, M.A. Gama-Sosa, L.H. Huang, R.M. Midgett, K.C. Kuo, R.A. McCune, and C. Gehrke Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells Nucleic Acids Res. 10 1982 2709 2721
40. T. Ernst, A.J. Chase, J. Score, C.E. Hidalgo-Curtis, C. Bryant, A.V. Jones, K. Waghorn, K. Zoi, F.M. Ross, and A. Reiter Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders Nat. Genet. 42 2010 722 726
41. J. Ernst, P. Kheradpour, T.S. Mikkelsen, N. Shoresh, L.D. Ward, C.B. Epstein, X. Zhang, L. Wang, R. Issner, and M. Coyne Mapping and analysis of chromatin state dynamics in nine human cell types Nature 473 2011 43 49
42. M.R. Estécio, J. Gallegos, C. Vallot, R.J. Castoro, W. Chung, S. Maegawa, Y. Oki, Y. Kondo, J. Jelinek, and L. Shen Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer Genome Res. 20 2010 1369 1382
43. M. Esteller, J. Garcia-Foncillas, E. Andion, S.N. Goodman, O.F. Hidalgo, V. Vanaclocha, S.B. Baylin, and J.G. Herman Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents N. Engl. J. Med. 343 2000 1350 1354
44. M. Esteller, M. Toyota, M. Sanchez-Cespedes, G. Capella, M.A. Peinado, D.N. Watkins, J.P. Issa, D. Sidransky, S.B. Baylin, and J.G. Herman 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 2000 2368 2371 (Pubitemid 30262424)
45. M. Esteller, R.A. Risques, M. Toyota, G. Capella, V. Moreno, M.A. Peinado, S.B. Baylin, and J.G. Herman 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 2001 4689 4692 (Pubitemid 32691877)
46. M. Fabbri, and G.A. Calin Epigenetics and miRNAs in human cancer Adv. Genet. 70 2010 87 99
47. A.P. Feinberg, and B. Vogelstein Hypomethylation distinguishes genes of some human cancers from their normal counterparts Nature 301 1983 89 92 (Pubitemid 13154475)
48. R. Fenouil, P. Cauchy, F. Koch, N. Descostes, J.Z. Cabeza, C. Innocenti, P. Ferrier, S. Spicuglia, M. Gut, I. Gut, and J.C. Andrau CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters Genome Res. 22 2012 2399 2408
49. M.E. Figueroa, O. Abdel-Wahab, C. Lu, P.S. Ward, J. Patel, A. Shih, Y. Li, N. Bhagwat, A. Vasanthakumar, and H.F. Fernandez Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation Cancer Cell 18 2010 553 567
50. P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W.B. Smith, O. Fedorov, E.M. Morse, T. Keates, T.T. Hickman, and I. Felletar Selective inhibition of BET bromodomains Nature 468 2010 1067 1073
51. G.N. Filippova, A. Lindblom, L.J. Meincke, E.M. Klenova, P.E. Neiman, S.J. Collins, N.A. Doggett, and V.V. Lobanenkov A widely expressed transcription factor with multiple DNA sequence specificity, CTCF, is localized at chromosome segment 16q22.1 within one of the smallest regions of overlap for common deletions in breast and prostate cancers Genes Chromosomes Cancer 22 1998 26 36 (Pubitemid 28217803)
52. G.N. Filippova, C.F. Qi, J.E. Ulmer, J.M. Moore, M.D. Ward, Y.J. Hu, D.I. Loukinov, E.M. Pugacheva, E.M. Klenova, and P.E. Grundy Tumor-associated zinc finger mutations in the CTCF transcription factor selectively alter tts DNA-binding specificity Cancer Res. 62 2002 48 52 (Pubitemid 34073984)
53. M.F. Fraga, E. Ballestar, A. Villar-Garea, M. Boix-Chornet, J. Espada, G. Schotta, T. Bonaldi, C. Haydon, S. Ropero, and K. Petrie Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer Nat. Genet. 37 2005 391 400
54. C.A. French, C.L. Ramirez, J. Kolmakova, T.T. Hickman, M.J. Cameron, M.E. Thyne, J.L. Kutok, J.A. Toretsky, A.K. Tadavarthy, and U.R. Kees BRD-NUT oncoproteins: a family of closely related nuclear proteins that block epithelial differentiation and maintain the growth of carcinoma cells Oncogene 27 2008 2237 2242 (Pubitemid 351483375)
55. A. Fujimoto, Y. Totoki, T. Abe, K.A. Boroevich, F. Hosoda, H.H. Nguyen, M. Aoki, N. Hosono, M. Kubo, and F. Miya Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators Nat. Genet. 44 2012 760 764
56. D.J. Gaffney, G. McVicker, A.A. Pai, Y.N. Fondufe-Mittendorf, N. Lewellen, K. Michelini, J. Widom, Y. Gilad, and J.K. Pritchard Controls of nucleosome positioning in the human genome PLoS Genet. 8 2012 e1003036
57. E.N. Gal-Yam, G. Egger, L. Iniguez, H. Holster, S. Einarsson, X. Zhang, J.C. Lin, G. Liang, P.A. Jones, and A. Tanay Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line Proc. Natl. Acad. Sci. USA 105 2008 12979 12984
58. S.A. Gayther, S.J. Batley, L. Linger, A. Bannister, K. Thorpe, S.F. Chin, Y. Daigo, P. Russell, A. Wilson, and H.M. Sowter Mutations truncating the EP300 acetylase in human cancers Nat. Genet. 24 2000 300 303 (Pubitemid 30132203)
59. M. Gerlinger, A.J. Rowan, S. Horswell, J. Larkin, D. Endesfelder, E. Gronroos, P. Martinez, N. Matthews, A. Stewart, and P. Tarpey Intratumor heterogeneity and branched evolution revealed by multiregion sequencing N. Engl. J. Med. 366 2012 883 892
60. J. Gertz, K.E. Varley, T.E. Reddy, K.M. Bowling, F. Pauli, S.L. Parker, K.S. Kucera, H.F. Willard, and R.M. Myers Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation PLoS Genet. 7 2011 e1002228
61. M. Gessi, G.H. Gielen, J. Hammes, E. Dörner, A.Z. Mühlen, A. Waha, and T. Pietsch H3.3 G34R mutations in pediatric primitive neuroectodermal tumors of central nervous system (CNS-PNET) and pediatric glioblastomas: possible diagnostic and therapeutic implications? J. Neurooncol. 112 2013 67 72
62. P.A. Ginno, P.L. Lott, H.C. Christensen, I. Korf, and F. Chédin R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters Mol. Cell 45 2012 814 825
63. S. Gonzalo, I. Jaco, M.F. Fraga, T. Chen, E. Li, M. Esteller, and M.A. Blasco DNA methyltransferases control telomere length and telomere recombination in mammalian cells Nat. Cell Biol. 8 2006 416 424
64. J.R. Graff, E. Gabrielson, H. Fujii, S.B. Baylin, and J.G. Herman Methylation patterns of the E-cadherin 5′ CpG island are unstable and reflect the dynamic, heterogeneous loss of E-cadherin expression during metastatic progression J. Biol. Chem. 275 2000 2727 2732 (Pubitemid 30082043)
65. C.S. Grasso, Y.M. Wu, D.R. Robinson, X. Cao, S.M. Dhanasekaran, A.P. Khan, M.J. Quist, X. Jing, R.J. Lonigro, and J.C. Brenner The mutational landscape of lethal castration-resistant prostate cancer Nature 487 2012 239 243
66. B. Guan, T.L. Mao, P.K. Panuganti, E. Kuhn, R.J. Kurman, D. Maeda, E. Chen, Y.M. Jeng, T.L. Wang, and IeM. Shih Mutation and loss of expression of ARID1A in uterine low-grade endometrioid carcinoma Am. J. Surg. Pathol. 35 2011 625 632
67. Y. Gui, G. Guo, Y. Huang, X. Hu, A. Tang, S. Gao, R. Wu, C. Chen, X. Li, and L. Zhou Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder Nat. Genet. 43 2011 875 878
68. G. Guo, W. Wang, and A. Bradley Mismatch repair genes identified using genetic screens in Blm-deficient embryonic stem cells Nature 429 2004 891 895 (Pubitemid 38843302)
69. D. Hanahan, and R.A. Weinberg Hallmarks of cancer: the next generation Cell 144 2011 646 674
70. K.D. Hansen, W. Timp, H.C. Bravo, S. Sabunciyan, B. Langmead, O.G. McDonald, B. Wen, H. Wu, Y. Liu, and D. Diep Increased methylation variation in epigenetic domains across cancer types Nat. Genet. 43 2011 768 775
71. R.D. Hawkins, G.C. Hon, L.K. Lee, Q. Ngo, R. Lister, M. Pelizzola, L.E. Edsall, S. Kuan, Y. Luu, and S. Klugman Distinct epigenomic landscapes of pluripotent and lineage-committed human cells Cell Stem Cell 6 2010 479 491
72. C.M. Heaphy, R.F. de Wilde, Y. Jiao, A.P. Klein, B.H. Edil, C. Shi, C. Bettegowda, F.J. Rodriguez, C.G. Eberhart, and S. Hebbar Altered telomeres in tumors with ATRX and DAXX mutations Science 333 2011 425
73. M.E. Hegi, A.C. Diserens, T. Gorlia, M.F. Hamou, N. de Tribolet, M. Weller, J.M. Kros, J.A. Hainfellner, W. Mason, and L. Mariani MGMT gene silencing and benefit from temozolomide in glioblastoma N. Engl. J. Med. 352 2005 997 1003 (Pubitemid 40349502)
74. J.G. Herman, A. Umar, K. Polyak, J.R. Graff, N. Ahuja, J.P. Issa, S. Markowitz, J.K. Willson, S.R. Hamilton, and K.W. Kinzler Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma Proc. Natl. Acad. Sci. USA 95 1998 6870 6875 (Pubitemid 28278073)
75. T. Hinoue, D.J. Weisenberger, F. Pan, M. Campan, M. Kim, J. Young, V.L. Whitehall, B.A. Leggett, and P.W. Laird Analysis of the association between CIMP and BRAF in colorectal cancer by DNA methylation profiling PLoS ONE 4 2009 e8357
76. T. Hinoue, D.J. Weisenberger, C.P. Lange, H. Shen, H.M. Byun, D. Van Den Berg, S. Malik, F. Pan, H. Noushmehr, and C.M. van Dijk Genome-scale analysis of aberrant DNA methylation in colorectal cancer Genome Res. 22 2012 271 282
77. M.P. Hitchins, R.W. Rapkins, C.T. Kwok, S. Srivastava, J.J. Wong, L.M. Khachigian, P. Polly, J. Goldblatt, and R.L. Ward Dominantly inherited constitutional epigenetic silencing of MLH1 in a cancer-affected family is linked to a single nucleotide variant within the 5'UTR Cancer Cell 20 2011 200 213
78. A. Hodgkinson, and A. Eyre-Walker Variation in the mutation rate across mammalian genomes Nat. Rev. Genet. 12 2011 756 766
79. E. Hodis, I.R. Watson, G.V. Kryukov, S.T. Arold, M. Imielinski, J.P. Theurillat, E. Nickerson, D. Auclair, L. Li, and C. Place A landscape of driver mutations in melanoma Cell 150 2012 251 263
80. L. Holmfeldt, L. Wei, E. Diaz-Flores, M. Walsh, J. Zhang, L. Ding, D. Payne-Turner, M. Churchman, A. Andersson, and S.C. Chen The genomic landscape of hypodiploid acute lymphoblastic leukemia Nat. Genet. 45 2013 242 252
81. G.C. Hon, R.D. Hawkins, O.L. Caballero, C. Lo, R. Lister, M. Pelizzola, A. Valsesia, Z. Ye, S. Kuan, and L.E. Edsall Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer Genome Res. 22 2012 246 258
82. J. Hussin, D. Sinnett, F. Casals, Y. Idaghdour, V. Bruat, V. Saillour, J. Healy, J.C. Grenier, T. de Malliard, and S. Busche Rare allelic forms of PRDM9 associated with childhood leukemogenesis Genome Res. 23 2013 419 430
83. E.M. Hyland, H. Molina, K. Poorey, C. Jie, Z. Xie, J. Dai, J. Qian, S. Bekiranov, D.T. Auble, A. Pandey, and J.D. Boeke An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae Genes Dev. 25 2011 1306 1319
84. M. Imielinski, A.H. Berger, P.S. Hammerman, B. Hernandez, T.J. Pugh, E. Hodis, J. Cho, J. Suh, M. Capelletti, and A. Sivachenko Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing Cell 150 2012 1107 1120
85. A. Inthal, P. Zeitlhofer, M. Zeginigg, M. Morak, R. Grausenburger, E. Fronkova, B. Fahrner, G. Mann, O.A. Haas, and R. Panzer-Grümayer CREBBP HAT domain mutations prevail in relapse cases of high hyperdiploid childhood acute lymphoblastic leukemia Leukemia 26 2012 1797 1803
86. R.A. Irizarry, C. Ladd-Acosta, B. Wen, Z. Wu, C. Montano, P. Onyango, H. Cui, K. Gabo, M. Rongione, and M. Webster The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores Nat. Genet. 41 2009 178 186
87. S. Ito, L. Shen, Q. Dai, S.C. Wu, L.B. Collins, J.A. Swenberg, C. He, and Y. Zhang Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine Science 333 2011 1300 1303
88. Y. Jiao, C. Shi, B.H. Edil, R.F. de Wilde, D.S. Klimstra, A. Maitra, R.D. Schulick, L.H. Tang, C.L. Wolfgang, and M.A. Choti DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors Science 331 2011 1199 1203
89. C. Jin, C. Zang, G. Wei, K. Cui, W. Peng, K. Zhao, and G. Felsenfeld H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions Nat. Genet. 41 2009 941 945
90. D.G. Johnson, and S.Y.R. Dent Chromatin: receiver and quarterback for cellular signals Cell 152 2013 685 689
91. P.A. Jones Functions of DNA methylation: islands, start sites, gene bodies and beyond Nat. Rev. Genet. 13 2012 484 492
92. P.A. Jones, and P.W. Laird Cancer epigenetics comes of age Nat. Genet. 21 1999 163 167 (Pubitemid 29070360)
93. P.A. Jones, and S.B. Baylin The fundamental role of epigenetic events in cancer Nat. Rev. Genet. 3 2002 415 428 (Pubitemid 34587077)
94. P.A. Jones, and G. Liang Rethinking how DNA methylation patterns are maintained Nat. Rev. Genet. 10 2009 805 811
95. S. Jones, T.L. Wang, IeM. Shih, T.L. Mao, K. Nakayama, R. Roden, R. Glas, D. Slamon, L.A. Diaz Jr., and B. Vogelstein Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma Science 330 2010 228 231
96. D.T. Jones, N. Jäger, M. Kool, T. Zichner, B. Hutter, M. Sultan, Y.J. Cho, T.J. Pugh, V. Hovestadt, and A.M. Stütz Dissecting the genomic complexity underlying medulloblastoma Nature 488 2012 100 105
97. R.T. Kamakaka, and S. Biggins Histone variants: deviants? Genes Dev. 19 2005 295 310 (Pubitemid 40189292)
98. K. Kerkel, A. Spadola, E. Yuan, J. Kosek, L. Jiang, E. Hod, K. Li, V.V. Murty, N. Schupf, and E. Vilain Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation Nat. Genet. 40 2008 904 908
99. M. Kim, B.N. Trinh, T.I. Long, S. Oghamian, and P.W. Laird Dnmt1 deficiency leads to enhanced microsatellite instability in mouse embryonic stem cells Nucleic Acids Res. 32 2004 5742 5749 (Pubitemid 39619157)
100. T.H. Kim, Z.K. Abdullaev, A.D. Smith, K.A. Ching, D.I. Loukinov, R.D. Green, M.Q. Zhang, V.V. Lobanenkov, and B. Ren Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome Cell 128 2007 1231 1245 (Pubitemid 46427876)
101. M. Ko, Y. Huang, A.M. Jankowska, U.J. Pape, M. Tahiliani, H.S. Bandukwala, J. An, E.D. Lamperti, K.P. Koh, and R. Ganetzky Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2 Nature 468 2010 839 843
102. Y. Kondo, L. Shen, A.S. Cheng, S. Ahmed, Y. Boumber, C. Charo, T. Yamochi, T. Urano, K. Furukawa, and B. Kwabi-Addo Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation Nat. Genet. 40 2008 741 750 (Pubitemid 351748874)
103. M. Ku, R.P. Koche, E. Rheinbay, E.M. Mendenhall, M. Endoh, T.S. Mikkelsen, A. Presser, C. Nusbaum, X. Xie, and A.S. Chi Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains PLoS Genet. 4 2008 e1000242
104. A.Y. Lai, and P.A. Wade Cancer biology and NuRD: a multifaceted chromatin remodelling complex Nat. Rev. Cancer 11 2011 588 596
105. P.W. Laird Principles and challenges of genomewide DNA methylation analysis Nat. Rev. Genet. 11 2010 191 203
106. P.W. Laird, L. Jackson-Grusby, A. Fazeli, S.L. Dickinson, W.E. Jung, E. Li, R.A. Weinberg, and R. Jaenisch Suppression of intestinal neoplasia by DNA hypomethylation Cell 81 1995 197 205
107. S.M. Langemeijer, R.P. Kuiper, M. Berends, R. Knops, M.G. Aslanyan, M. Massop, E. Stevens-Linders, P. van Hoogen, A.G. van Kessel, and R.A. Raymakers Acquired mutations in TET2 are common in myelodysplastic syndromes Nat. Genet. 41 2009 838 842
108. M. Le Gallo, A.J. O'Hara, M.L. Rudd, M.E. Urick, N.F. Hansen, N.J. O'Neil, J.C. Price, S. Zhang, B.M. England, A.K. Godwin NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes Nat. Genet. 44 2012 1310 1315
109. J.T. Lee Epigenetic regulation by long noncoding RNAs Science 338 2012 1435 1439
110. E. Lee, R. Iskow, L. Yang, O. Gokcumen, P. Haseley, L.J. Luquette 3rd, J.G. Lohr, C.C. Harris, L. Ding, R.K. Wilson Cancer Genome Atlas Research Network Landscape of somatic retrotransposition in human cancers Science 337 2012 967 971
111. T.J. Ley, L. Ding, M.J. Walter, M.D. McLellan, T. Lamprecht, D.E. Larson, C. Kandoth, J.E. Payton, J. Baty, and J. Welch DNMT3A mutations in acute myeloid leukemia N. Engl. J. Med. 363 2010 2424 2433
112. J. Li, R.A. Harris, S.W. Cheung, C. Coarfa, M. Jeong, M.A. Goodell, L.D. White, A. Patel, S.H. Kang, and C. Shaw Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome PLoS Genet. 8 2012 e1002692
113. F. Lienert, C. Wirbelauer, I. Som, A. Dean, F. Mohn, and D. Schübeler Identification of genetic elements that autonomously determine DNA methylation states Nat. Genet. 43 2011 1091 1097
114. M.J. Ligtenberg, R.P. Kuiper, T.L. Chan, M. Goossens, K.M. Hebeda, M. Voorendt, T.Y. Lee, D. Bodmer, E. Hoenselaar, and S.J. Hendriks-Cornelissen Heritable somatic methylation and inactivation of MSH2 in families with Lynch syndrome due to deletion of the 3′ exons of TACSTD1 Nat. Genet. 41 2009 112 117
115. R. Lister, M. Pelizzola, R.H. Dowen, R.D. Hawkins, G. Hon, J. Tonti-Filippini, J.R. Nery, L. Lee, Z. Ye, and Q.M. Ngo Human DNA methylomes at base resolution show widespread epigenomic differences Nature 462 2009 315 322
116. G. Liu, A. Bollig-Fischer, B. Kreike, M.J. van de Vijver, J. Abrams, S.P. Ethier, and Z.Q. Yang Genomic amplification and oncogenic properties of the GASC1 histone demethylase gene in breast cancer Oncogene 28 2009 4491 4500
117. J.G. Lohr, P. Stojanov, M.S. Lawrence, D. Auclair, B. Chapuy, C. Sougnez, P. Cruz-Gordillo, B. Knoechel, Y.W. Asmann, and S.L. Slager Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing Proc. Natl. Acad. Sci. USA 109 2012 3879 3884
118. J.E. Loughery, P.D. Dunne, K.M. O'Neill, R.R. Meehan, J.R. McDaid, and C.P. Walsh DNMT1 deficiency triggers mismatch repair defects in human cells through depletion of repair protein levels in a process involving the DNA damage response Hum. Mol. Genet. 20 2011 3241 3255
119. C. Love, Z. Sun, D. Jima, G. Li, J. Zhang, R. Miles, K.L. Richards, C.H. Dunphy, W.W. Choi, and G. Srivastava The genetic landscape of mutations in Burkitt lymphoma Nat. Genet. 44 2012 1321 1325
120. C. Lu, P.S. Ward, G.S. Kapoor, D. Rohle, S. Turcan, O. Abdel-Wahab, C.R. Edwards, R. Khanin, M.E. Figueroa, and A. Melnick IDH mutation impairs histone demethylation and results in a block to cell differentiation Nature 483 2012 474 478
121. W. Meuleman, D. Peric-Hupkes, J. Kind, J.B. Beaudry, L. Pagie, M. Kellis, M. Reinders, L. Wessels, and B. van Steensel Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence Genome Res. 23 2013 270 280
122. A.A. Mills Throwing the cancer switch: reciprocal roles of polycomb and trithorax proteins Nat. Rev. Cancer 10 2010 669 682
123. S. Minucci, and P.G. Pelicci Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer Nat. Rev. Cancer 6 2006 38 51 (Pubitemid 43054973)
124. F. Mohn, M. Weber, M. Rebhan, T.C. Roloff, J. Richter, M.B. Stadler, M. Bibel, and D. Schübeler Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors Mol. Cell 30 2008 755 766
125. R.D. Morin, N.A. Johnson, T.M. Severson, A.J. Mungall, J. An, R. Goya, J.E. Paul, M. Boyle, B.W. Woolcock, and F. Kuchenbauer Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin Nat. Genet. 42 2010 181 185
126. R.D. Morin, M. Mendez-Lago, A.J. Mungall, R. Goya, K.L. Mungall, R.D. Corbett, N.A. Johnson, T.M. Severson, R. Chiu, and M. Field Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma Nature 476 2011 298 303
127. O. Mortusewicz, L. Schermelleh, J. Walter, M.C. Cardoso, and H. Leonhardt Recruitment of DNA methyltransferase I to DNA repair sites Proc. Natl. Acad. Sci. USA 102 2005 8905 8909 (Pubitemid 40881051)
128. C.G. Mullighan, J. Zhang, L.H. Kasper, S. Lerach, D. Payne-Turner, L.A. Phillips, S.L. Heatley, L. Holmfeldt, J.R. Collins-Underwood, and J. Ma CREBBP mutations in relapsed acute lymphoblastic leukaemia Nature 471 2011 235 239
129. S.K. Mummert, V.A. Lobanenkov, and A.P. Feinberg Association of chromosome arm 16q loss with loss of imprinting of insulin-like growth factor-II in Wilms tumor Genes Chromosomes Cancer 43 2005 155 161 (Pubitemid 40570735)
130. C.A. Musselman, M.E. Lalonde, J. Côté, and T.G. Kutateladze Perceiving the epigenetic landscape through histone readers Nat. Struct. Mol. Biol. 19 2012 1218 1227
131. G. Nikoloski, S.M. Langemeijer, R.P. Kuiper, R. Knops, M. Massop, E.R. Tönnissen, A. van der Heijden, T.N. Scheele, P. Vandenberghe, and T. de Witte Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes Nat. Genet. 42 2010 665 667
132. H. Noushmehr, D.J. Weisenberger, K. Diefes, H.S. Phillips, K. Pujara, B.P. Berman, F. Pan, C.E. Pelloski, E.P. Sulman, K.P. Bhat Cancer Genome Atlas Research Network Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma Cancer Cell 17 2010 510 522
133. P. Ntziachristos, A. Tsirigos, P. Van Vlierberghe, J. Nedjic, T. Trimarchi, M.S. Flaherty, D. Ferres-Marco, V. da Ros, Z. Tang, and J. Siegle Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia Nat. Med. 18 2012 298 301
134. J.E. Ohm, K.M. McGarvey, X. Yu, L. Cheng, K.E. Schuebel, L. Cope, H.P. Mohammad, W. Chen, V.C. Daniel, and W. Yu A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing Nat. Genet. 39 2007 237 242 (Pubitemid 46184356)
135. M. Okano, D.W. Bell, D.A. Haber, and E. Li DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development Cell 99 1999 247 257 (Pubitemid 29519904)
136. M. Olivier, M. Hollstein, and P. Hainaut TP53 mutations in human cancers: origins, consequences, and clinical use Cold Spring Harb. Perspect. Biol. 2 2010 a001008
137. M. Papamichos-Chronakis, and C.L. Peterson Chromatin and the genome integrity network Nat. Rev. Genet. 14 2013 62 75
138. D.W. Parsons, M. Li, X. Zhang, S. Jones, R.J. Leary, J.C. Lin, S.M. Boca, H. Carter, J. Samayoa, and C. Bettegowda The genetic landscape of the childhood cancer medulloblastoma Science 331 2011 435 439
139. L. Pasqualucci, V. Trifonov, G. Fabbri, J. Ma, D. Rossi, A. Chiarenza, V.A. Wells, A. Grunn, M. Messina, and O. Elliot Analysis of the coding genome of diffuse large B-cell lymphoma Nat. Genet. 43 2011 830 837
140. S. Petruk, Y. Sedkov, D.M. Johnston, J.W. Hodgson, K.L. Black, S.K. Kovermann, S. Beck, E. Canaani, H.W. Brock, and A. Mazo TrxG and PcG proteins but not methylated histones remain associated with DNA through replication Cell 150 2012 922 933
141. A. Prokhortchouk, O. Sansom, J. Selfridge, I.M. Caballero, S. Salozhin, D. Aithozhina, L. Cerchietti, F.G. Meng, L.H. Augenlicht, and J.M. Mariadason Kaiso-deficient mice show resistance to intestinal cancer Mol. Cell. Biol. 26 2006 199 208
142. T.J. Pugh, S.D. Weeraratne, T.C. Archer, D.A. Pomeranz Krummel, D. Auclair, J. Bochicchio, M.O. Carneiro, S.L. Carter, K. Cibulskis, and R.L. Erlich Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations Nature 488 2012 106 110
143. C. Quivoron, L. Couronné, V. Della Valle, C.K. Lopez, I. Plo, O. Wagner-Ballon, M. Do Cruzeiro, F. Delhommeau, B. Arnulf, and M.H. Stern TET2 inactivation results in pleiotropic hematopoietic abnormalities in mouse and is a recurrent event during human lymphomagenesis Cancer Cell 20 2011 25 38
144. G. Raddatz, Q. Gao, S. Bender, R. Jaenisch, and F. Lyko Dnmt3a protects active chromosome domains against cancer-associated hypomethylation PLoS Genet. 8 2012 e1003146
145. O. Ram, A. Goren, I. Amit, N. Shoresh, N. Yosef, J. Ernst, M. Kellis, M. Gymrek, R. Issner, and M. Coyne Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells Cell 147 2011 1628 1639
146. G. Robinson, M. Parker, T.A. Kranenburg, C. Lu, X. Chen, L. Ding, T.N. Phoenix, E. Hedlund, L. Wei, and X. Zhu Novel mutations target distinct subgroups of medulloblastoma Nature 488 2012 43 48
147. L. Rui, N.C. Emre, M.J. Kruhlak, H.J. Chung, C. Steidl, G. Slack, G.W. Wright, G. Lenz, V.N. Ngo, and A.L. Shaffer Cooperative epigenetic modulation by cancer amplicon genes Cancer Cell 18 2010 590 605
148. J. Sandoval, and M. Esteller Cancer epigenomics: beyond genomics Curr. Opin. Genet. Dev. 22 2012 50 55
149. O.J. Sansom, J. Berger, S.M. Bishop, B. Hendrich, A. Bird, and A.R. Clarke Deficiency of Mbd2 suppresses intestinal tumorigenesis Nat. Genet. 34 2003 145 147 (Pubitemid 36666922)
150. Y. Schlesinger, R. Straussman, I. Keshet, S. Farkash, M. Hecht, J. Zimmerman, E. Eden, Z. Yakhini, E. Ben-Shushan, and B.E. Reubinoff Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer Nat. Genet. 39 2007 232 236 (Pubitemid 46184355)
151. R. Schneppenheim, M.C. Frühwald, S. Gesk, M. Hasselblatt, A. Jeibmann, U. Kordes, M. Kreuz, I. Leuschner, J.I. Martin Subero, and T. Obser Germline nonsense mutation and somatic inactivation of SMARCA4/BRG1 in a family with rhabdoid tumor predisposition syndrome Am. J. Hum. Genet. 86 2010 279 284
152. B. Schuster-Böckler, and B. Lehner Chromatin organization is a major influence on regional mutation rates in human cancer cells Nature 488 2012 504 507
153. J. Schwartzentruber, A. Korshunov, X.Y. Liu, D.T. Jones, E. Pfaff, K. Jacob, D. Sturm, A.M. Fontebasso, D.A. Quang, and M. Tönjes Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma Nature 482 2012 226 231
154. D.B. Seligson, S. Horvath, T. Shi, H. Yu, S. Tze, M. Grunstein, and S.K. Kurdistani Global histone modification patterns predict risk of prostate cancer recurrence Nature 435 2005 1262 1266 (Pubitemid 40943093)
155. S. Sharma, D.D. De Carvalho, S. Jeong, P.A. Jones, and G. Liang Nucleosomes containing methylated DNA stabilize DNA methyltransferases 3A/3B and ensure faithful epigenetic inheritance PLoS Genet. 7 2011 e1001286
156. C. Simon, J. Chagraoui, J. Krosl, P. Gendron, B. Wilhelm, S. Lemieux, G. Boucher, P. Chagnon, S. Drouin, and R. Lambert A key role for EZH2 and associated genes in mouse and human adult T-cell acute leukemia Genes Dev. 26 2012 651 656
157. S.B. Simpkins, T. Bocker, E.M. Swisher, D.G. Mutch, D.J. Gersell, A.J. Kovatich, J.P. Palazzo, R. Fishel, and P.J. Goodfellow MLH1 promoter methylation and gene silencing is the primary cause of microsatellite instability in sporadic endometrial cancers Hum. Mol. Genet. 8 1999 661 666 (Pubitemid 29139981)
158. M.J. Smith, J. O'Sullivan, S.S. Bhaskar, K.D. Hadfield, G. Poke, J. Caird, S. Sharif, D. Eccles, D. Fitzpatrick, and D. Rawluk Loss-of-function mutations in SMARCE1 cause an inherited disorder of multiple spinal meningiomas Nat. Genet. 45 2013 295 298
159. D. Sproul, R.R. Kitchen, C.E. Nestor, J.M. Dixon, A.H. Sims, D.J. Harrison, B.H. Ramsahoye, and R.R. Meehan Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns Genome Biol. 13 2012 R84
160. N. Stransky, A.M. Egloff, A.D. Tward, A.D. Kostic, K. Cibulskis, A. Sivachenko, G.V. Kryukov, M.S. Lawrence, C. Sougnez, and A. McKenna The mutational landscape of head and neck squamous cell carcinoma Science 333 2011 1157 1160
161. D. Sturm, H. Witt, V. Hovestadt, D.A. Khuong-Quang, D.T. Jones, C. Konermann, E. Pfaff, M. Tönjes, M. Sill, and S. Bender Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma Cancer Cell 22 2012 425 437
162. J. Tan, M. Jones, H. Koseki, M. Nakayama, A.G. Muntean, I. Maillard, and J.L. Hess CBX8, a polycomb group protein, is essential for MLL-AF9-induced leukemogenesis Cancer Cell 20 2011 563 575
163. M. Tan, H. Luo, S. Lee, F. Jin, J.S. Yang, E. Montellier, T. Buchou, Z. Cheng, S. Rousseaux, and N. Rajagopal Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification Cell 146 2011 1016 1028
164. A. Tanay, A.H. O'Donnell, M. Damelin, and T.H. Bestor Hyperconserved CpG domains underlie Polycomb-binding sites Proc. Natl. Acad. Sci. USA 104 2007 5521 5526 (Pubitemid 47175713)
165. A.E. Teschendorff, U. Menon, A. Gentry-Maharaj, S.J. Ramus, D.J. Weisenberger, H. Shen, M. Campan, H. Noushmehr, C.G. Bell, and A.P. Maxwell Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer Genome Res. 20 2010 440 446
166. J.R. Testa, M. Cheung, J. Pei, J.E. Below, Y. Tan, E. Sementino, N.J. Cox, A.U. Dogan, H.I. Pass, and S. Trusa Germline BAP1 mutations predispose to malignant mesothelioma Nat. Genet. 43 2011 1022 1025
167. M. Toyota, and H. Suzuki Epigenetic drivers of genetic alterations Adv. Genet. 70 2010 309 323
168. M. Toyota, N. Ahuja, M. Ohe-Toyota, J.G. Herman, S.B. Baylin, and J.P. Issa CpG island methylator phenotype in colorectal cancer Proc. Natl. Acad. Sci. USA 96 1999 8681 8686 (Pubitemid 29354851)
169. S. Turcan, D. Rohle, A. Goenka, L.A. Walsh, F. Fang, E. Yilmaz, C. Campos, A.W. Fabius, C. Lu, and P.S. Ward IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype Nature 483 2012 479 483
170. A. Valouev, S.M. Johnson, S.D. Boyd, C.L. Smith, A.Z. Fire, and A. Sidow Determinants of nucleosome organization in primary human cells Nature 474 2011 516 520
171. G. van Haaften, G.L. Dalgliesh, H. Davies, L. Chen, G. Bignell, C. Greenman, S. Edkins, C. Hardy, S. O'Meara, and J. Teague Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer Nat. Genet. 41 2009 521 523
172. P. Van Vlierberghe, T. Palomero, H. Khiabanian, J. Van der Meulen, M. Castillo, N. Van Roy, B. De Moerloose, J. Philippé, S. González-García, and M.L. Toribio PHF6 mutations in T-cell acute lymphoblastic leukemia Nat. Genet. 42 2010 338 342
173. P. Van Vlierberghe, J. Patel, O. Abdel-Wahab, C. Lobry, C.V. Hedvat, M. Balbin, C. Nicolas, A.R. Payer, H.F. Fernandez, and M.S. Tallman PHF6 mutations in adult acute myeloid leukemia Leukemia 25 2011 130 134
174. S. Varambally, Q. Cao, R.S. Mani, S. Shankar, X. Wang, B. Ateeq, B. Laxman, X. Cao, X. Jing, and K. Ramnarayanan Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer Science 322 2008 1695 1699
175. I. Varela, P. Tarpey, K. Raine, D. Huang, C.K. Ong, P. Stephens, H. Davies, D. Jones, M.L. Lin, and J. Teague Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma Nature 469 2011 539 542
176. I. Versteege, N. Sévenet, J. Lange, M.F. Rousseau-Merck, P. Ambros, R. Handgretinger, A. Aurias, and O. Delattre Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer Nature 394 1998 203 206 (Pubitemid 28325977)
177. Z.Y. Wang, and Z. Chen Acute promyelocytic leukemia: from highly fatal to highly curable Blood 111 2008 2505 2515
178. R.Y. Wang, K.C. Kuo, C.W. Gehrke, L.H. Huang, and M. Ehrlich Heat- and alkali-induced deamination of 5-methylcytosine and cytosine residues in DNA Biochim. Biophys. Acta 697 1982 371 377
179. D.J. Weisenberger, K.D. Siegmund, M. Campan, J. Young, T.I. Long, M.A. Faasse, G.H. Kang, M. Widschwendter, D. Weener, and D. Buchanan CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer Nat. Genet. 38 2006 787 793 (Pubitemid 43980599)
180. S. Weissmann, T. Alpermann, V. Grossmann, A. Kowarsch, N. Nadarajah, C. Eder, F. Dicker, A. Fasan, C. Haferlach, and T. Haferlach Landscape of TET2 mutations in acute myeloid leukemia Leukemia 26 2012 934 942
181. M. Widschwendter, H. Fiegl, D. Egle, E. Mueller-Holzner, G. Spizzo, C. Marth, D.J. Weisenberger, M. Campan, J. Young, I. Jacobs, and P.W. Laird Epigenetic stem cell signature in cancer Nat. Genet. 39 2007 157 158 (Pubitemid 46184343)
182. K.C. Wiegand, S.P. Shah, O.M. Al-Agha, Y. Zhao, K. Tse, T. Zeng, J. Senz, M.K. McConechy, M.S. Anglesio, and S.E. Kalloger ARID1A mutations in endometriosis-associated ovarian carcinomas N. Engl. J. Med. 363 2010 1532 1543
183. T. Wiesner, A.C. Obenauf, R. Murali, I. Fried, K.G. Griewank, P. Ulz, C. Windpassinger, W. Wackernagel, S. Loy, and I. Wolf Germline mutations in BAP1 predispose to melanocytic tumors Nat. Genet. 43 2011 1018 1021
184. K. Williams, J. Christensen, and K. Helin DNA methylation: TET proteins-guardians of CpG islands? EMBO Rep. 13 2012 28 35
185. B.G. Wilson, and C.W. Roberts SWI/SNF nucleosome remodellers and cancer Nat. Rev. Cancer 11 2011 481 492
186. G. Wu, A. Broniscer, T.A. McEachron, C. Lu, B.S. Paugh, J. Becksfort, C. Qu, L. Ding, R. Huether, M. Parker St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas Nat. Genet. 44 2012 251 253
187. W. Xu, H. Yang, Y. Liu, Y. Yang, P. Wang, S.H. Kim, S. Ito, C. Yang, P. Wang, and M.T. Xiao Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases Cancer Cell 19 2011 17 30
188. K. Xu, Z.J. Wu, A.C. Groner, H.H. He, C. Cai, R.T. Lis, X. Wu, E.C. Stack, M. Loda, and T. Liu EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent Science 338 2012 1465 1469
189. E. Yamamoto, H. Suzuki, H.O. Yamano, R. Maruyama, M. Nojima, S. Kamimae, T. Sawada, M. Ashida, K. Yoshikawa, and T. Kimura Molecular dissection of premalignant colorectal lesions reveals early onset of the CpG island methylator phenotype Am. J. Pathol. 181 2012 1847 1861
190. K. Yamashita, T. Dai, Y. Dai, F. Yamamoto, and M. Perucho Genetics supersedes epigenetics in colon cancer phenotype Cancer Cell 4 2003 121 131 (Pubitemid 37040828)
191. J. Yamazaki, M.R. Estecio, Y. Lu, H. Long, G.G. Malouf, D. Graber, Y. Huo, L. Ramagli, S. Liang, and S.M. Kornblau The epigenome of AML stem and progenitor cells Epigenetics 8 2013 92 104
192. X.J. Yan, J. Xu, Z.H. Gu, C.M. Pan, G. Lu, Y. Shen, J.Y. Shi, Y.M. Zhu, L. Tang, and X.W. Zhang Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia Nat. Genet. 43 2011 309 315
193. X.J. Yang The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases Nucleic Acids Res. 32 2004 959 976
194. A. Yokoyama, and M.L. Cleary Menin critically links MLL proteins with LEDGF on cancer-associated target genes Cancer Cell 14 2008 36 46 (Pubitemid 351885493)
195. J.S. You, and P.A. Jones Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell 22 2012 9 20
196. B.B. Zeisig, A.G. Kulasekararaj, G.J. Mufti, and C.W. So SnapShot: acute myeloid leukemia Cancer Cell 22 2012 698
197. J. Zhang, L. Ding, L. Holmfeldt, G. Wu, S.L. Heatley, D. Payne-Turner, J. Easton, X. Chen, J. Wang, and M. Rusch The genetic basis of early T-cell precursor acute lymphoblastic leukaemia Nature 481 2012 157 163
198. J. Zhu, M. Adli, J.Y. Zou, G. Verstappen, M. Coyne, X. Zhang, T. Durham, M. Miri, V. Deshpande, and P.L. De Jager Genome-wide chromatin state transitions associated with developmental and environmental cues Cell 152 2013 642 654
199. J.M. Zullo, I.A. Demarco, R. Piqué-Regi, D.J. Gaffney, C.B. Epstein, C.J. Spooner, T.R. Luperchio, B.E. Bernstein, J.K. Pritchard, K.L. Reddy, and H. Singh DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina Cell 149 2012 1474 1487