Cancer Genetics and Epigenetics: Two Sides of the Same Coin?

Cancer Cell

Volumn 22, Issue 1, 2012, Pages 9-20

  You, Jueng Soo ^a   Jones, Peter A ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 AZA 2' DEOXYCYTIDINE; 5 METHYLCYTOSINE; ANTINEOPLASTIC AGENT; AZACITIDINE; BRCA1 PROTEIN; BRCA2 PROTEIN; BRG1 PROTEIN; BRM PROTEIN; BROMODOMAIN INHIBITOR; CYCLIN DEPENDENT KINASE INHIBITOR 2B; DNA; DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE 3A; DNA METHYLTRANSFERASE 3B; DOT1L INHIBITOR; EPZ004777; GSK525762; HISTONE ACETYLTRANSFERASE; HISTONE DEACETYLASE; HISTONE DEACETYLASE INHIBITOR; HISTONE DEMETHYLASE; K RAS PROTEIN; METHYLATED DNA PROTEIN CYSTEINE METHYLTRANSFERASE; MICRORNA; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PROTEIN P53; TRANSCRIPTION FACTOR EZH2; UNCLASSIFIED DRUG;

ACUTE GRANULOCYTIC LEUKEMIA; ANTINEOPLASTIC ACTIVITY; BRAIN CANCER; BREAST CANCER; CANCER CELL; CANCER CHEMOTHERAPY; CANCER GENETICS; CANCER RISK; CANCER THERAPY; CARCINOGENESIS; CELL CYCLE; COLON CANCER; COLORECTAL CANCER; DISEASE COURSE; DNA METHYLATION; DNA REPAIR; DNA REPLICATION; DOWN REGULATION; ENDOMETRIUM CANCER; EPIGENETICS; ESOPHAGUS CANCER; EWING SARCOMA; GENE EXPRESSION; GENE FUNCTION; GENE MUTATION; GENE SILENCING; GENETIC ASSOCIATION; GENOTYPE; GLIOMA; HEAD AND NECK CANCER; HISTONE MODIFICATION; HUMAN; IN VITRO STUDY; KIDNEY CARCINOMA; LIVER CANCER; LUNG ADENOMA; LUNG CANCER; LUNG NON SMALL CELL CANCER; MANTLE CELL LYMPHOMA; MELANOMA; MERKEL CELL TUMOR; MYELODYSPLASTIC SYNDROME; NEUROBLASTOMA; NONHODGKIN LYMPHOMA; NUCLEOSOME; OVARY CANCER; PANCREAS CANCER; PHENOTYPE; PRIORITY JOURNAL; PROSTATE CANCER; REVIEW; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; STOMACH CANCER; TESTIS CANCER; TRANSITIONAL CELL CARCINOMA; UTERINE CERVIX CANCER; UTERUS CANCER;

EID: 84863770814     PISSN: 15356108     EISSN: 18783686     Source Type: Journal    
DOI: 10.1016/j.ccr.2012.06.008     Document Type: Review

References (131)

1. Bagchi A., Papazoglu C., Wu Y., Capurso D., Brodt M., Francis D., Bredel M., Vogel H., Mills A.A. CHD5 is a tumor suppressor at human 1p36. Cell 2007, 128:459-475.
2. Balakrishnan A., Bleeker F.E., Lamba S., Rodolfo M., Daniotti M., Scarpa A., van Tilborg A.A., Leenstra S., Zanon C., Bardelli A. Novel somatic and germline mutations in cancer candidate genes in glioblastoma, melanoma, and pancreatic carcinoma. Cancer Res. 2007, 67:3545-3550.
3. Balgobind B.V., Zwaan C.M., Pieters R., Van den Heuvel-Eibrink M.M. The heterogeneity of pediatric MLL-rearranged acute myeloid leukemia. Leukemia 2011, 25:1239-1248.
4. Barretina J., Caponigro G., Stransky N., Venkatesan K., Margolin A.A., Kim S., Wilson C.J., Lehár J., Kryukov G.V., Sonkin D., et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012, 483:603-607.
5. Baylin S.B., Ohm J.E. Epigenetic gene silencing in cancer - a mechanism for early oncogenic pathway addiction?. Nat. Rev. Cancer 2006, 6:107-116.
6. Baylin S.B., Jones P.A. A decade of exploring the cancer epigenome - biological and translational implications. Nat. Rev. Cancer 2011, 11:726-734.
7. Bernt K.M., Zhu N., Sinha A.U., Vempati S., Faber J., Krivtsov A.V., Feng Z., Punt N., Daigle A., Bullinger L., et al. MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L. Cancer Cell 2011, 20:66-78.
8. Bhaskara S., Knutson S.K., Jiang G., Chandrasekharan M.B., Wilson A.J., Zheng S., Yenamandra A., Locke K., Yuan J.L., Bonine-Summers A.R., et al. Hdac3 is essential for the maintenance of chromatin structure and genome stability. Cancer Cell 2010, 18:436-447.
9. Bhutani N., Burns D.M., Blau H.M. DNA demethylation dynamics. Cell 2011, 146:866-872.
10. Bogdanović O., Veenstra G.J. DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma 2009, 118:549-565.
11. Challen G.A., Sun D., Jeong M., Luo M., Jelinek J., Berg J.S., Bock C., Vasanthakumar A., Gu H., Xi Y., et al. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat. Genet. 2012, 44:23-31.
12. Chase A., Cross N.C. Aberrations of EZH2 in cancer. Clin. Cancer Res. 2011, 17:2613-2618.
13. Cimmino L., Abdel-Wahab O., Levine R.L., Aifantis I. TET family proteins and their role in stem cell differentiation and transformation. Cell Stem Cell 2011, 9:193-204.
14. Clapier C.R., Cairns B.R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 2009, 78:273-304.
15. Conerly M.L., Teves S.S., Diolaiti D., Ulrich M., Eisenman R.N., Henikoff S. Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis. Genome Res. 2010, 20:1383-1390.
16. Daigle S.R., Olhava E.J., Therkelsen C.A., Majer C.R., Sneeringer C.J., Song J., Johnston L.D., Scott M.P., Smith J.J., Xiao Y., et al. Selective killing of mixed lineage leukemia cells by a potent small-molecule DOT1L inhibitor. Cancer Cell 2011, 20:53-65.
17. De Carvalho D.D., You J.S., Jones P.A. DNA methylation and cellular reprogramming. Trends Cell Biol. 2010, 20:609-617.
18. De Carvalho D.D., Sharma S., You J.S., Su S.F., Taberlay P.C., Kelly T.K., Yang X., Liang G., Jones P.A. DNA methylation screening identifies driver epigenetic events of cancer cell survival. Cancer Cell 2012, 21:655-667.
19. de Zwaan S.E., Haass N.K. Genetics of basal cell carcinoma. Australas J Dermatol. 2010, 51:81-92. quiz 93-84.
20. Degner J.F., Pai A.A., Pique-Regi R., Veyrieras J.B., Gaffney D.J., Pickrell J.K., De Leon S., Michelini K., Lewellen N., Crawford G.E., et al. DNasecI sensitivity QTLs are a major determinant of human expression variation. Nature 2012, 482:390-394.
21. Delmore J.E., Issa G.C., Lemieux M.E., Rahl P.B., Shi J., Jacobs H.M., Kastritis E., Gilpatrick T., Paranal R.M., Qi J., et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 2011, 146:904-917.
22. Drost J., Mantovani F., Tocco F., Elkon R., Comel A., Holstege H., Kerkhoven R., Jonkers J., Voorhoeve P.M., Agami R., Del Sal G. BRD7 is a candidate tumour suppressor gene required for p53 function. Nat. Cell Biol. 2010, 12:380-389.
23. Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat. Rev. Genet. 2007, 8:286-298.
24. Fabbri M., Calin G.A. Epigenetics and miRNAs in human cancer. Adv. Genet. 2010, 70:87-99.
25. Fabbri M., Garzon R., Cimmino A., Liu Z., Zanesi N., Callegari E., Liu S., Alder H., Costinean S., Fernandez-Cymering C., et al. MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proc. Natl. Acad. Sci. USA 2007, 104:15805-15810.
26. Figueroa M.E., Abdel-Wahab O., Lu C., Ward P.S., Patel J., Shih A., Li Y., Bhagwat N., Vasanthakumar A., Fernandez H.F., et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 2010, 18:553-567.
27. Filippakopoulos P., Qi J., Picaud S., Shen Y., Smith W.B., Fedorov O., Morse E.M., Keates T., Hickman T.T., Felletar I., et al. Selective inhibition of BET bromodomains. Nature 2010, 468:1067-1073.
28. Friedman J.M., Liang G., Liu C.C., Wolff E.M., Tsai Y.C., Ye W., Zhou X., Jones P.A. The putative tumor suppressor microRNA-101 modulates the cancer epigenome by repressing the polycomb group protein EZH2. Cancer Res. 2009, 69:2623-2629.
29. Füllgrabe J., Kavanagh E., Joseph B. Histone onco-modifications. Oncogene 2011, 30:3391-3403.
30. Gelsi-Boyer V., Brecqueville M., Devillier R., Murati A., Mozziconacci M.J., Birnbaum D. Mutations in ASXL1 are associated with poor prognosis across the spectrum of malignant myeloid diseases. J. Hematol. Oncol. 2012, 5:12.
31. Greer E.L., Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat. Rev. Genet. 2012, 13:343-357.
32. Guan B., Mao T.L., Panuganti P.K., Kuhn E., Kurman R.J., Maeda D., Chen E., Jeng Y.M., Wang T.L., Shih IeM. Mutation and loss of expression of ARID1A in uterine low-grade endometrioid carcinoma. Am. J. Surg. Pathol. 2011, 35:625-632.
33. Gui Y., Guo G., Huang Y., Hu X., Tang A., Gao S., Wu R., Chen C., Li X., Zhou L., et al. Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat. Genet. 2011, 43:875-878.
34. Hanahan D., Weinberg R.A. Hallmarks of cancer: the next generation. Cell 2011, 144:646-674.
35. Hargreaves D.C., Crabtree G.R. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 2011, 21:396-420.
36. Hatziapostolou M., Iliopoulos D. Epigenetic aberrations during oncogenesis. Cell. Mol. Life Sci. 2011, 68:1681-1702.
37. Hawkins R.D., Hon G.C., Lee L.K., Ngo Q., Lister R., Pelizzola M., Edsall L.E., Kuan S., Luu Y., Klugman S., et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 2010, 6:479-491.
38. Hawkins R.D., Hon G.C., Yang C., Antosiewicz-Bourget J.E., Lee L.K., Ngo Q.M., Klugman S., Ching K.A., Edsall L.E., Ye Z., et al. Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Res. 2011, 21:1393-1409.
39. Hinoue T., Weisenberger D.J., Lange C.P., Shen H., Byun H.M., Van Den Berg D., Malik S., Pan F., Noushmehr H., van Dijk C.M., et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res. 2012, 22:271-282.
40. Hitchins M.P., Rapkins R.W., Kwok C.T., Srivastava S., Wong J.J., Khachigian L.M., Polly P., Goldblatt J., Ward R.L. 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 2011, 20:200-213.
41. Ho L., Crabtree G.R. Chromatin remodelling during development. Nature 2010, 463:474-484.
42. Hoischen A., van Bon B.W., Rodríguez-Santiago B., Gilissen C., Vissers L.E., de Vries P., Janssen I., van Lier B., Hastings R., Smithson S.F., et al. De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome. Nat. Genet. 2011, 43:729-731.
43. Hon G.C., Hawkins R.D., Ren B. Predictive chromatin signatures in the mammalian genome. Hum. Mol. Genet. 2009, 18(R2):R195-R201.
44. Iyer N.G., Ozdag H., Caldas C. p300/CBP and cancer. Oncogene 2004, 23:4225-4231.
45. Jagani Z., Mora-Blanco E.L., Sansam C.G., McKenna E.S., Wilson B., Chen D., Klekota J., Tamayo P., Nguyen P.T., Tolstorukov M., et al. Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway. Nat. Med. 2010, 16:1429-1433.
46. Jiang L., Li J., Song L. Bmi-1, stem cells and cancer. Acta Biochim. Biophys. Sin. (Shanghai) 2009, 41:527-534.
47. Jones P.A., Liang G. Rethinking how DNA methylation patterns are maintained. Nat. Rev. Genet. 2009, 10:805-811.
48. Jones S., Wang T.L., Shih IeM., Mao T.L., Nakayama K., Roden R., Glas R., Slamon D., Diaz L.A., Vogelstein B., et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 2010, 330:228-231.
49. Juergens R.A., Wrangle J., Vendetti F.P., Murphy S.C., Zhao M., Coleman B., Sebree R., Rodgers K., Hooker C.M., Franco N., et al. Combination epigenetic therapy has efficacy in patients with refractory advanced non-small cell lung cancer. Cancer Discov. 2011, 1:598-607.
50. Kalari S., Pfeifer G.P. Identification of driver and passenger DNA methylation in cancer by epigenomic analysis. Adv. Genet. 2010, 70:277-308.
51. Kanai Y., Ushijima S., Nakanishi Y., Sakamoto M., Hirohashi S. Mutation of the DNA methyltransferase (DNMT) 1 gene in human colorectal cancers. Cancer Lett. 2003, 192:75-82.
52. Kasinski A.L., Slack F.J. Epigenetics and genetics. MicroRNAs en route to the clinic: progress in validating and targeting microRNAs for cancer therapy. Nat. Rev. Cancer 2011, 11:849-864.
53. Kelly T.K., De Carvalho D.D., Jones P.A. Epigenetic modifications as therapeutic targets. Nat. Biotechnol. 2010, 28:1069-1078.
54. Kim M.S., Chung N.G., Kang M.R., Yoo N.J., Lee S.H. Genetic and expressional alterations of CHD genes in gastric and colorectal cancers. Histopathology 2011, 58:660-668.
55. Kinney S.R., Pradhan S. Regulation of expression and activity of DNA (cytosine-5) methyltransferases in mammalian cells. Prog. Mol. Biol. Transl. Sci. 2011, 101:311-333.
56. Ko M., Huang Y., Jankowska A.M., Pape U.J., Tahiliani M., Bandukwala H.S., An J., Lamperti E.D., Koh K.P., Ganetzky R., et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 2010, 468:839-843.
57. Krivtsov A.V., Armstrong S.A. MLL translocations, histone modifications and leukaemia stem-cell development. Nat. Rev. Cancer 2007, 7:823-833.
58. Lao V.V., Darwanto A., Sowers L.C. Impact of base analogues within a CpG dinucleotide on the binding of DNA by the methyl-binding domain of MeCP2 and methylation by DNMT1. Biochemistry 2010, 49:10228-10236.
59. Lee Y.H., Stallcup M.R. Minireview: protein arginine methylation of nonhistone proteins in transcriptional regulation. Mol. Endocrinol. 2009, 23:425-433.
60. Ley T.J., Ding L., Walter M.J., McLellan M.D., Lamprecht T., Larson D.E., Kandoth C., Payton J.E., Baty J., Welch J., et al. DNMT3A mutations in acute myeloid leukemia. N. Engl. J. Med. 2010, 363:2424-2433.
61. Li M., Zhao H., Zhang X., Wood L.D., Anders R.A., Choti M.A., Pawlik T.M., Daniel H.D., Kannangai R., Offerhaus G.J., et al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat. Genet. 2011, 43:828-829.
62. Lin H., Wong R.P., Martinka M., Li G. Loss of SNF5 expression correlates with poor patient survival in melanoma. Clin. Cancer Res. 2009, 15:6404-6411.
63. Lu C., Ward P.S., Kapoor G.S., Rohle D., Turcan S., Abdel-Wahab O., Edwards C.R., Khanin R., Figueroa M.E., Melnick A., et al. IDH mutation impairs histone demethylation and results in a block to cell differentiation. Nature 2012, 483:474-478.
64. Luger K., Mäder A.W., Richmond R.K., Sargent D.F., Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997, 389:251-260.
65. Lukacs R.U., Memarzadeh S., Wu H., Witte O.N. Bmi-1 is a crucial regulator of prostate stem cell self-renewal and malignant transformation. Cell Stem Cell 2010, 7:682-693.
66. Marks P.A., Rifkind R.A., Richon V.M., Breslow R., Miller T., Kelly W.K. Histone deacetylases and cancer: causes and therapies. Nat. Rev. Cancer 2001, 1:194-202.
67. Matei D.E., Nephew K.P. Epigenetic therapies for chemoresensitization of epithelial ovarian cancer. Gynecol. Oncol. 2010, 116:195-201.
68. Mattera L., Escaffit F., Pillaire M.J., Selves J., Tyteca S., Hoffmann J.S., Gourraud P.A., Chevillard-Briet M., Cazaux C., Trouche D. The p400/Tip60 ratio is critical for colorectal cancer cell proliferation through DNA damage response pathways. Oncogene 2009, 28:1506-1517.
69. Meissner A., Mikkelsen T.S., Gu H., Wernig M., Hanna J., Sivachenko A., Zhang X., Bernstein B.E., Nusbaum C., Jaffe D.B., et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008, 454:766-770.
70. Mills A.A. Throwing the cancer switch: reciprocal roles of polycomb and trithorax proteins. Nat. Rev. Cancer 2010, 10:669-682.
71. Miremadi A., Oestergaard M.Z., Pharoah P.D., Caldas C. Cancer genetics of epigenetic genes. Hum. Mol. Genet. 2007, 16(Spec No 1):R28-R49.
72. Morin R.D., Mendez-Lago M., Mungall A.J., Goya R., Mungall K.L., Corbett R.D., Johnson N.A., Severson T.M., Chiu R., Field M., et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 2011, 476:298-303.
73. Mosammaparast N., Shi Y. Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases. Annu. Rev. Biochem. 2010, 79:155-179.
74. Nakayama T., Yamashita M. Critical role of the Polycomb and Trithorax complexes in the maintenance of CD4 T cell memory. Semin. Immunol. 2009, 21:78-83.
75. Network C.G.A.R. Integrated genomic analyses of ovarian carcinoma. Nature 2011, 474:609-615. Cancer Genome Atlas Research Network.
76. Nica A.C., Montgomery S.B., Dimas A.S., Stranger B.E., Beazley C., Barroso I., Dermitzakis E.T. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet. 2010, 6:e1000895.
77. Nicodeme E., Jeffrey K.L., Schaefer U., Beinke S., Dewell S., Chung C.W., Chandwani R., Marazzi I., Wilson P., Coste H., et al. Suppression of inflammation by a synthetic histone mimic. Nature 2010, 468:1119-1123.
78. Nicolae D.L., Gamazon E., Zhang W., Duan S., Dolan M.E., Cox N.J. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet. 2010, 6:e1000888.
79. Noushmehr H., Weisenberger D.J., Diefes K., Phillips H.S., Pujara K., Berman B.P., Pan F., Pelloski C.E., Sulman E.P., Bhat K.P., et al. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell 2010, 17:510-522. Cancer Genome Atlas Research Network.
80. Ocker M., Schneider-Stock R. Histone deacetylase inhibitors: signalling towards p21cip1/waf1. Int. J. Biochem. Cell Biol. 2007, 39:1367-1374.
81. Ooi S.K., Bestor T.H. The colorful history of active DNA demethylation. Cell 2008, 133:1145-1148.
82. Reisman D., Glaros S., Thompson E.A. The SWI/SNF complex and cancer. Oncogene 2009, 28:1653-1668.
83. Rideout W.M., Coetzee G.A., Olumi A.F., Jones P.A. 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science 1990, 249:1288-1290.
84. Roberts C.W., Orkin S.H. The SWI/SNF complex-chromatin and cancer. Nat. Rev. Cancer 2004, 4:133-142.
85. Rodríguez-Paredes M., Esteller M. Cancer epigenetics reaches mainstream oncology. Nat. Med. 2011, 17:330-339.
86. Ropero S., Fraga M.F., Ballestar E., Hamelin R., Yamamoto H., Boix-Chornet M., Caballero R., Alaminos M., Setien F., Paz M.F., et al. A truncating mutation of HDAC2 in human cancers confers resistance to histone deacetylase inhibition. Nat. Genet. 2006, 38:566-569.
87. Rotili D., Mai A. Targeting histone demethylases: a new avenue for the fight against cancer. Genes Cancer 2011, 2:663-679.
88. Ryan B.M., Robles A.I., Harris C.C. Genetic variation in microRNA networks: the implications for cancer research. Nat. Rev. Cancer 2010, 10:389-402.
89. Saito Y., Liang G., Egger G., Friedman J.M., Chuang J.C., Coetzee G.A., Jones P.A. Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell 2006, 9:435-443.
90. Sandoval J., Esteller M. Cancer epigenomics: beyond genomics. Curr. Opin. Genet. Dev. 2012, 22:50-55.
91. Sansom O.J., Maddison K., Clarke A.R. Mechanisms of disease: methyl-binding domain proteins as potential therapeutic targets in cancer. Nat. Clin. Pract. Oncol. 2007, 4:305-315.
92. Santen G.W., Aten E., Sun Y., Almomani R., Gilissen C., Nielsen M., Kant S.G., Snoeck I.N., Peeters E.A., Hilhorst-Hofstee Y., et al. Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome. Nat. Genet. 2012, 44:379-380.
93. Sauvageau M., Sauvageau G. Polycomb group proteins: multi-faceted regulators of somatic stem cells and cancer. Cell Stem Cell 2010, 7:299-313.
94. Schepers A., Clevers H. Wnt signaling, stem cells, and cancer of the gastrointestinal tract. Cold Spring Harb. Perspect. Biol. 2012, 4:a007989.
95. Schuettengruber B., Martinez A.-M., Iovino N., Cavalli G. Trithorax group proteins: switching genes on and keeping them active. Nat. Rev. Mol. Cell Biol. 2011, 12:799-814.
96. Segal E., Widom J. What controls nucleosome positions?. Trends Genet. 2009, 25:335-343.
97. Shankar S., Srivastava R.K. Histone deacetylase inhibitors: mechanisms and clinical significance in cancer: HDAC inhibitor-induced apoptosis. Adv. Exp. Med. Biol. 2008, 615:261-298.
98. Sharma S., Kelly T.K., Jones P.A. Epigenetics in cancer. Carcinogenesis 2010, 31:27-36.
99. Shen H., Wang L., Spitz M.R., Hong W.K., Mao L., Wei Q. A novel polymorphism in human cytosine DNA-methyltransferase-3B promoter is associated with an increased risk of lung cancer. Cancer Res. 2002, 62:4992-4995.
100. Slany R.K. The molecular biology of mixed lineage leukemia. Haematologica 2009, 94:984-993.
101. Smith K.T., Workman J.L. Histone deacetylase inhibitors: anticancer compounds. Int. J. Biochem. Cell Biol. 2009, 41:21-25.
102. Song J., Teplova M., Ishibe-Murakami S., Patel D.J. Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation. Science 2012, 335:709-712.
103. Suganuma T., Workman J.L. Signals and combinatorial functions of histone modifications. Annu. Rev. Biochem. 2011, 80:473-499.
104. Sun A., Tawfik O., Gayed B., Thrasher J.B., Hoestje S., Li C., Li B. Aberrant expression of SWI/SNF catalytic subunits BRG1/BRM is associated with tumor development and increased invasiveness in prostate cancers. Prostate 2007, 67:203-213.
105. Tan A.Y., Manley J.L. The TET family of proteins: functions and roles in disease. J. Mol. Cell Biol. 2009, 1:82-92.
106. Teng L., Firpi H.A., Tan K. Enhancers in embryonic stem cells are enriched for transposable elements and genetic variations associated with cancers. Nucleic Acids Res. 2011, 39:7371-7379.
107. Trowbridge J.J., Orkin S.H. Dnmt3a silences hematopoietic stem cell self-renewal. Nat. Genet. 2012, 44:13-14.
108. Tsang D.P., Cheng A.S. Epigenetic regulation of signaling pathways in cancer: role of the histone methyltransferase EZH2. J. Gastroenterol. Hepatol. 2011, 26:19-27.
109. Tsurusaki Y., Okamoto N., Ohashi H., Kosho T., Imai Y., Hibi-Ko Y., Kaname T., Naritomi K., Kawame H., Wakui K., et al. Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome. Nat. Genet. 2012, 44:376-378.
110. Turcan S., Rohle D., Goenka A., Walsh L.A., Fang F., Yilmaz E., Campos C., Fabius A.W., Lu C., Ward P.S., et al. IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype. Nature 2012, 483:479-483.
111. Tycko B. Allele-specific DNA methylation: beyond imprinting. Hum. Mol. Genet. 2010, 19(R2):R210-R220.
112. Valouev A., Johnson S.M., Boyd S.D., Smith C.L., Fire A.Z., Sidow A. Determinants of nucleosome organization in primary human cells. Nature 2011, 474:516-520.
113. Varambally S., Cao Q., Mani R.S., Shankar S., Wang X., Ateeq B., Laxman B., Cao X., Jing X., Ramnarayanan K., et al. Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer. Science 2008, 322:1695-1699.
114. Varela I., Tarpey P., Raine K., Huang D., Ong C.K., Stephens P., Davies H., Jones D., Lin M.L., Teague J., et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 2011, 469:539-542.
115. Varier R.A., Timmers H.T. Histone lysine methylation and demethylation pathways in cancer. Biochim. Biophys. Acta 2011, 1815:75-89.
116. Wang G.G., Allis C.D., Chi P. Chromatin remodeling and cancer, Part II: ATP-dependent chromatin remodeling. Trends Mol. Med. 2007, 13:373-380.
117. Wang J., Chen H., Fu S., Xu Z.M., Sun K.L., Fu W.N. The involvement of CHD5 hypermethylation in laryngeal squamous cell carcinoma. Oral Oncol. 2011, 47:601-608.
118. Wang L., Gural A., Sun X.J., Zhao X., Perna F., Huang G., Hatlen M.A., Vu L., Liu F., Xu H., et al. The leukemogenicity of AML1-ETO is dependent on site-specific lysine acetylation. Science 2011, 333:765-769.
119. Wessels K., Bohnhorst B., Luhmer I., Morlot S., Bohring A., Jonasson J., Epplen J.T., Gadzicki D., Glaser S., Göhring G., et al. Novel CHD7 mutations contributing to the mutation spectrum in patients with CHARGE syndrome. Eur. J. Med. Genet. 2010, 53:280-285.
120. Wiegand K.C., Shah S.P., Al-Agha O.M., Zhao Y., Tse K., Zeng T., Senz J., McConechy M.K., Anglesio M.S., Kalloger S.E., et al. ARID1A mutations in endometriosis-associated ovarian carcinomas. N. Engl. J. Med. 2010, 363:1532-1543.
121. Wijmenga C., Hansen R.S., Gimelli G., Björck E.J., Davies E.G., Valentine D., Belohradsky B.H., van Dongen J.J., Smeets D.F., van den Heuvel L.P., et al. Genetic variation in ICF syndrome: evidence for genetic heterogeneity. Hum. Mutat. 2000, 16:509-517.
122. Wilson B.G., Roberts C.W. SWI/SNF nucleosome remodellers and cancer. Nat. Rev. Cancer 2011, 11:481-492.
123. Wu S.C., Zhang Y. Active DNA demethylation: many roads lead to Rome. Nat. Rev. Mol. Cell Biol. 2010, 11:607-620.
124. Wu Y., Strawn E., Basir Z., Halverson G., Guo S.W. Aberrant expression of deoxyribonucleic acid methyltransferases DNMT1, DNMT3A, and DNMT3B in women with endometriosis. Fertil. Steril. 2007, 87:24-32.
125. Yamashita Y., Yuan J., Suetake I., Suzuki H., Ishikawa Y., Choi Y.L., Ueno T., Soda M., Hamada T., Haruta H., et al. Array-based genomic resequencing of human leukemia. Oncogene 2010, 29:3723-3731.
126. Yan X.J., Xu J., Gu Z.H., Pan C.M., Lu G., Shen Y., Shi J.Y., Zhu Y.M., Tang L., Zhang X.W., et al. Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat. Genet. 2011, 43:309-315.
127. Yang G.F., He W.P., Cai M.Y., He L.R., Luo J.H., Deng H.X., Guan X.Y., Zeng M.S., Zeng Y.X., Xie D. Intensive expression of Bmi-1 is a new independent predictor of poor outcome in patients with ovarian carcinoma. BMC Cancer 2010, 10:133.
128. Yang X.J. The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases. Nucleic Acids Res. 2004, 32:959-976.
129. Young R.A. Control of the embryonic stem cell state. Cell 2011, 144:940-954.
130. Zhang X., Zhang Y., Yang Y., Niu M., Sun S., Ji H., Ma Y., Yao G., Jiang Y., Shan M., et al. Frequent low expression of chromatin remodeling gene ARID1A in breast cancer and its clinical significance. Cancer Epidemiol. 2011, 36:288-293.
131. Zuber J., Shi J., Wang E., Rappaport A.R., Herrmann H., Sison E.A., Magoon D., Qi J., Blatt K., Wunderlich M., et al. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 2011, 478:524-528.