Histone profiles in cancer

Pharmacology and Therapeutics

Volumn 154, Issue , 2015, Pages 87-109

  Riedel, Simone S ^a   Neff, Tobias ^a   Bernt, Kathrin M ^a  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

Author keywords

Cancer; Chromatin; Epigenetic modifiers; Histone profiles; Therapy

Indexed keywords

DEOXYRIBONUCLEASE; HISTONE; HISTONE DEMETHYLASE; MIXED LINEAGE LEUKEMIA PROTEIN; POLYCOMB REPRESSIVE COMPLEX 2; PROTAMINE KINASE; TRANSCRIPTION FACTOR; CHROMATIN;

ARTICLE; CANCER GENETICS; CANCER PROGNOSIS; CHROMATIN; ENHANCER REGION; EPIGENETICS; GENE EXPRESSION; GENE LOCUS; GENE MUTATION; HETEROCHROMATIN; HISTONE ACETYLATION; HISTONE METHYLATION; HISTONE MODIFICATION; HUMAN; IMMUNOHISTOCHEMISTRY; NEOPLASM; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN PROCESSING; SOMATIC MUTATION; TRANSCRIPTION REGULATION; BIOLOGICAL MODEL; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENETIC EPIGENESIS; GENETIC TRANSCRIPTION; GENETICS; MASS SPECTROMETRY; METABOLISM; PHYSIOLOGY; SEQUENCE ANALYSIS;

CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; EPIGENESIS, GENETIC; GENE EXPRESSION; HISTONES; HUMANS; IMMUNOHISTOCHEMISTRY; MASS SPECTROMETRY; MODELS, BIOLOGICAL; NEOPLASMS; POLYCOMB REPRESSIVE COMPLEX 2; SEQUENCE ANALYSIS, PROTEIN; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84941415266     PISSN: 01637258     EISSN: 1879016X     Source Type: Journal    
DOI: 10.1016/j.pharmthera.2015.07.004     Document Type: Review

References (349)

1. W. Al Sarakbi, W. Sasi, W.G. Jiang, T. Roberts, R.F. Newbold, and K. Mokbel The mRNA expression of SETD2 in human breast cancer: correlation with clinico-pathological parameters BMC Cancer 9 2009 290
2. L. Alland, R. Muhle, H. Hou, J. Potes, L. Chin, N. Schreiber-Agus, and et al. Role for N-CoR and histone deacetylase in Sin3-mediated transcriptional repression Nature 387 6628 1997 49 55
3. G. Allfrey, R. Faulkner, and A.E. Mirsky Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis Proc Natl Acad Sci U S A 315 1938 1964 786 794
4. C.D. Allis, C.V.C. Glover, J.K. Bowen, and M.A. Gorovsky Histone variants specific to the transcriptionally active, amitotically dividing macronucleus of the unicellular eucaryote, tetrahymena thermophila Cell 20 3 1980 609 617
5. R. Alpatov, B.J. Lesch, M. Nakamoto-Kinoshita, A. Blanco, S. Chen, A. Stützer, and et al. A chromatin-dependent role of the fragile X mental retardation protein FMRP in the DNA damage response Cell 157 4 2014 869 881
6. P.O. Angrand, F. Apiou, A.F. Stewart, B. Dutrillaux, R. Losson, and P. Chambon NSD3, a new SET domain-containing gene, maps to 8p12 and is amplified in human breast cancer cell lines Genomics 74 1 2001 79 88
7. S.A. Armstrong, J.E. Staunton, L.B. Silverman, R. Pieters, M.L. den Boer, M.D. Minden, and et al. MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia Nat Genet 30 1 2002 41 47
8. P.M. Ayton, and M.L. Cleary Transformation of myeloid progenitors by MLL oncoproteins is dependent on Hoxa7 and Hoxa9 Genes Dev 17 18 2003 2298 2307
9. A. Balakrishnan, F.E. Bleeker, S. Lamba, M. Rodolfo, M. Daniotti, A. Scarpa, and et al. Novel somatic and germline mutations in cancer candidate genes in glioblastoma, melanoma, and pancreatic carcinoma Cancer Res 67 8 2007 3545 3550
10. A.J. Bannister, and T. Kouzarides The CBP co-activator is a histone acetyltransferase Nature 384 6610 1996 641 643
11. G. Baujat, and V. Cormier-Daire Sotos syndrome Orphanet J Rare Dis 2 2007 36
12. H.C. Beck, E.C. Nielsen, R. Matthiesen, L.H. Jensen, M. Sehested, P. Finn, and et al. Quantitative proteomic analysis of post-translational modifications of human histones Mol Cell Proteomics 5 7 2006 1314 1325
13. D.B. Beck, H. Oda, S.S. Shen, and D. Reinberg PR-Set7 and H4K20me1: at the crossroads of genome integrity, cell cycle, chromosome condensation, and transcription Genes Dev 26 4 2012 325 337
14. W. Béguelin, R. Popovic, M. Teater, Y. Jiang, K.L. Bunting, M. Rosen, and et al. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation Cancer Cell 23 5 2013 677 692
15. O.R. Bereshchenko, W. Gu, and R. Dalla-Favera Acetylation inactivates the transcriptional repressor BCL6 Nat Genet 32 4 2002 606 613
16. S.L. Berger, W.D. Cress, A. Cress, S.J. Triezenberg, and L. Guarente Selective inhibition of activated but not basal transcription by the acidic activation domain of VP16: evidence for transcriptional adaptors Cell 61 7 1990 1199 1208
17. B.E. Bernstein, T.S. Mikkelsen, X. Xie, M. Kamal, D.J. Huebert, J. Cuff, and et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells Cell 125 2 2006 315 326
18. K.M. Bernt, N. Zhu, A.U. Sinha, S. Vempati, J. Faber, A.V. Krivtsov, and et al. MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L Cancer Cell 20 1 2011 66 78
19. J.A. Biegel, L. Tan, F. Zhang, L. Wainwright, P. Russo, and L.B. Rorke Alterations of the hSNF5/INI1 gene in central nervous system atypical teratoid/rhabdoid tumors and renal and extrarenal rhabdoid tumors Clin Cancer Res 8 11 2002 3461 3467
20. A. Biondi, G. Cimino, R. Pieters, and C.H. Pui Biological and therapeutic aspects of infant leukemia Blood 96 1 2000 24 33
21. E. Bitoun, P.L. Oliver, and K.E. Davies The mixed-lineage leukemia fusion partner AF4 stimulates RNA polymerase II transcriptional elongation and mediates coordinated chromatin remodeling Hum Mol Genet 16 1 2007 92 106
22. J.C. Black, A.L. Manning, C. Van Rechem, J. Kim, B. Ladd, J. Cho, and et al. KDM4A lysine demethylase induces site-specific copy gain and rereplication of regions amplified in tumors Cell 154 3 2013 541 555
23. C. Bödör, V. Grossmann, N. Popov, J. Okosun, C. O'Riain, K. Tan, and et al. EZH2 mutations are frequent and represent an early event in follicular lymphoma Blood 122 18 2013 3165 3168
24. S.D. Briggs, M. Bryk, B.D. Strahl, W.L. Cheung, J.K. Davie, S.Y. Dent, and et al. Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae Genes Dev 15 24 2001 3286 3295
25. A.E. Burrows, A. Smogorzewska, and S.J. Elledge Polybromo-associated BRG1-associated factor components BRD7 and BAF180 are critical regulators of p53 required for induction of replicative senescence Proc Natl Acad Sci U S A 107 32 2010 14280 14285
26. M. Caganova, C. Carrisi, G. Varano, F. Mainoldi, F. Zanardi, P.-L. Germain, and et al. Germinal center dysregulation by histone methyltransferase EZH2 promotes lymphomagenesis J Clin Invest 123 12 2013 5009 5022
27. R. Cao, L. Wang, H. Wang, L. Xia, H. Erdjument-Bromage, P. Tempst, and et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing Science 298 5595 2002 1039 1043
28. S. Carotta, L. Wu, and S.L. Nutt Surprising new roles for PU.1 in the adaptive immune response Immunol Rev 238 1 2010 63 75
29. M. Casanova, A. Selicorni, and A. Ferrari Cancer predisposition in children with Kabuki syndrome Am J Med Genet A 155A 6 2011 1504
30. C.J. Ceol, Y. Houvras, J. Jane-Valbuena, S. Bilodeau, D.A. Orlando, V. Battisti, and et al. The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset Nature 471 7339 2011 513 517
31. A. Champhekar, S.S. Damle, G. Freedman, S. Carotta, S.L. Nutt, and E.V. Rothenberg Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1 Genes Dev 29 8 2015 832 848
32. F.T.M. Chang, F.L. Chan, R. McGhie, J.D. Udugama, M. Mayne, L. Collas, and et al. CHK1-driven histone H3.3 serine 31 phosphorylation is important for chromatin maintenance and cell survival in human ALT cancer cells Nucleic Acids Res 43 5 2015 2603 2614
33. M.A. Chapman, M.S. Lawrence, J.J. Keats, K. Cibulskis, C. Sougnez, A.C. Schinzel, and et al. Initial genome sequencing and analysis of multiple myeloma Nature 471 7339 2011 467 472
34. M.-K. Chen, M.-Y. Cai, R.-Z. Luo, X. Tian, Q.-M. Liao, X.-Y. Zhang, and et al. Overexpression of p300 correlates with poor prognosis in patients with cutaneous squamous cell carcinoma Br J Dermatol 172 1 2014 111 119
35. L. Chen, A.J. Deshpande, D. Banka, K.M. Bernt, S. Dias, C. Buske, and et al. Abrogation of MLL-AF10 and CALM-AF10-mediated transformation through genetic inactivation or pharmacological inhibition of the H3K79 methyltransferase Dot1l Leukemia 27 4 2013 813 822
36. L.-J. Chen, Y. Dong, S.-Y. Chen, L. Zhang, G.-B. Zhou, B. Chen, and et al. hCG-PLZF-RARalpha/hCG-RARalpha-PLZF transgenic mice developing into leukemia Zhongguo Shi Yan Xue Ye Xue Za Zhi 13 6 2005 924 931
37. C.-W. Chen, R.P. Koche, A.U. Sinha, A.J. Deshpande, N. Zhu, R. Eng, and et al. DOT1L inhibits SIRT1-mediated epigenetic silencing to maintain leukemic gene expression in MLL-rearranged leukemia Nat Med 21 4 2015 335 343
38. H. Chen, R.J. Lin, R.L. Schiltz, D. Chakravarti, A. Nash, L. Nagy, and et al. Nuclear receptor coactivator ACTR is a novel histone acetyltransferase and forms a multimeric activation complex with P/CAF and CBP/p300 Cell 90 3 1997 569 580
39. G.X. Cheng, X.H. Zhu, X.Q. Men, L. Wang, Q.H. Huang, X.L. Jin, and et al. Distinct leukemia phenotypes in transgenic mice and different corepressor interactions generated by promyelocytic leukemia variant fusion genes PLZF-RARalpha and NPM-RARalpha Proc Natl Acad Sci U S A 96 11 1999 6318 6323
40. Y. Chervona, and M. Costa Histone modifications and cancer: biomarkers of prognosis? Am J Cancer Res 2 5 2012 589 597
41. M. Chesi, G.M. Matthews, V.M. Garbitt, S.E. Palmer, J. Shortt, M. Lefebure, and et al. Drug response in a genetically engineered mouse model of multiple myeloma is predictive of clinical efficacy Blood 120 2 2012 376 385
42. M. Chesi, E. Nardini, R.S. Lim, K.D. Smith, W.M. Kuehl, and P.L. Bergsagel The t(4;14) translocation in myeloma dysregulates both FGFR3 and a novel gene, MMSET, resulting in IgH/MMSET hybrid transcripts Blood 92 9 1998 3025 3034
43. Y.-J. Cho, A. Tsherniak, P. Tamayo, S. Santagata, A. Ligon, H. Greulich, and et al. Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome J Clin Oncol 29 11 2011 1424 1430
44. C. Choudhary, C. Kumar, F. Gnad, M.L. Nielsen, M. Rehman, T.C. Walther, and et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions Science 325 5942 2009 834 840
45. L.A. Cirillo, F.R. Lin, I. Cuesta, D. Friedman, M. Jarnik, and K.S. Zaret Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4 Mol Cell 9 2 2002 279 289
46. C.R. Clapier, and B.R. Cairns The biology of chromatin remodeling complexes Annu Rev Biochem 78 2009 273 304
47. M. Cockell, D. Rhodes, and A. Klug Location of the primary sites of micrococcal nuclease cleavage on the nucleosome core J Mol Biol 170 2 1983 423 446
48. A.S.A. Cohen, B. Tuysuz, Y. Shen, S.K. Bhalla, S.J.M. Jones, and W.T. Gibson A novel mutation in EED associated with overgrowth J Hum Genet 6 60 2015 339 342
49. B. Coiffier, B. Pro, H.M. Prince, F. Foss, L. Sokol, M. Greenwood, and et al. Romidepsin for the treatment of relapsed/refractory peripheral T-cell lymphoma: pivotal study update demonstrates durable responses J Hematol Oncol 7 1 2014 11
50. J. Côté, J. Quinn, J.L. Workman, and C.L. Peterson Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex Science 265 5168 1994 53 60
51. M.P. Creyghton, A.W. Cheng, G.G. Welstead, T. Kooistra, B.W. Carey, E.J. Steine, and et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state Proc Natl Acad Sci U S A 107 50 2010 21931 21936
52. A. Cuomo, S. Moretti, S. Minucci, and T. Bonaldi SILAC-based proteomic analysis to dissect the "histone modification signature" of human breast cancer cells Amino Acids 41 2 2011 387 399
53. J. Dai, S. Sultan, S.S. Taylor, and J.M.G. Higgins The kinase haspin is required for mitotic histone H3 Thr 3 phosphorylation and normal metaphase chromosome alignment Genes Dev 19 4 2005 472 488
54. S.R. Daigle, E.J. Olhava, C.A. Therkelsen, A. Basavapathruni, L. Jin, P.A. Boriack-Sjodin, and et al. Potent inhibition of DOT1L as treatment of MLL-fusion leukemia Blood 122 6 2013 1017 1025
55. G.L. Dalgliesh, K. Furge, C. Greenman, L. Chen, G. Bignell, A. Butler, and et al. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes Nature 463 7279 2010 360 363
56. M.A. Dawson, A.J. Bannister, B. Göttgens, S.D. Foster, T. Bartke, A.R. Green, and et al. JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin Nature 461 7265 2009 819 822
57. M.A. Dawson, S.D. Foster, A.J. Bannister, S.C. Robson, R. Hannah, X. Wang, and et al. Three distinct patterns of histone H3Y41 phosphorylation mark active genes Cell Rep 2 3 2012 470 477
58. M.A. Dawson, and T. Kouzarides Cancer epigenetics: from mechanism to therapy Cell 150 1 2012 12 27
59. M.A. Dawson, T. Kouzarides, and B.J.P. Huntly Targeting epigenetic readers in cancer N Engl J Med 367 7 2012 647 657
60. M.A. Dawson, R.K. Prinjha, A. Dittmann, G. Giotopoulos, M. Bantscheff, W.-I. Chan, and et al. Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia Nature 478 7370 2011 529 533
61. J.D.E. De Rooij, I.H.I.M. Hollink, S.T.C.J.M. Arentsen-Peters, J.F. van Galen, H. Berna Beverloo, A. Baruchel, and et al. NUP98/JARID1A is a novel recurrent abnormality in pediatric acute megakaryoblastic leukemia with a distinct HOX gene expression pattern Leukemia 27 12 2013 2280 2288
62. J.E. Delmore, G.C. Issa, M.E. Lemieux, P.B. Rahl, J. Shi, H.M. Jacobs, and et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc Cell 146 6 2011 904 917
63. A.J. Deshpande, L. Chen, M. Fazio, A.U. Sinha, K.M. Bernt, D. Banka, and et al. Leukemic transformation by the MLL-AF6 fusion oncogene requires the H3K79 methyltransferase Dot1l Blood 121 13 2013 1 3
64. A.J. Deshpande, A. Deshpande, A.U. Sinha, L. Chen, J. Chang, A. Cihan, and et al. AF10 regulates progressive H3K79 methylation and HOX gene expression in diverse AML subtypes Cancer Cell 26 6 2014 896 908
65. C. Dingwall, G.P. Lomonossoff, and R.A. Laskey High sequence specificity of micrococcal nuclease Nucleic Acids Res 9 12 1981 2659 2673
66. M.F. Dion, S.J. Altschuler, L.F. Wu, and O.J. Rando Genomic characterization reveals a simple histone H4 acetylation code Proc Natl Acad Sci U S A 102 15 2005 5501 5506
67. A. Dolnik, J.C. Engelmann, M. Scharfenberger-Schmeer, J. Mauch, S. Kelkenberg-Schade, B. Haldemann, and et al. Commonly altered genomic regions in acute myeloid leukemia are enriched for somatic mutations involved in chromatin remodeling and splicing Blood 120 18 2012 e83 e92
68. J. Drost, F. Mantovani, F. Tocco, R. Elkon, A. Comel, H. Holstege, and et al. BRD7 is a candidate tumour suppressor gene required for p53 function Nat Cell Biol 12 4 2010 380 389
69. S. Drouin, L. Laramée, P.-É. Jacques, A. Forest, M. Bergeron, and F. Robert DSIF and RNA polymerase II CTD phosphorylation coordinate the recruitment of Rpd3S to actively transcribed genes PLoS Genet 6 10 2010 e1001173
70. H. Duan, C.A. Heckman, and L.M. Boxer Histone deacetylase inhibitors down-regulate bcl-2 expression and induce apoptosis in t(14;18) lymphomas Mol Cell Biol 25 5 2005 1608 1619
71. A.M. Dubuc, M. Remke, A. Korshunov, P.A. Northcott, S.H. Zhan, M. Mendez-Lago, and et al. Aberrant patterns of H3K4 and H3K27 histone lysine methylation occur across subgroups in medulloblastoma Acta Neuropathol 125 3 2013 373 384
72. H.C. Eberl, M. Mann, and M. Vermeulen Quantitative proteomics for epigenetics Chembiochem 12 2 2011 224 234
73. T. Ernst, A.J. Chase, J. Score, C.E. Hidalgo-Curtis, C. Bryant, A.V. Jones, and et al. Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders Nat Genet 42 8 2010 722 726
74. Q. Feng, H. Wang, H.H. Ng, H. Erdjument-bromage, P. Tempst, K. Struhl, and et al. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain Curr Biol 12 02 2002 1052 1058
75. P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W.B. Smith, O. Fedorov, and et al. Selective inhibition of BET bromodomains Nature 468 7327 2010 1067 1073
76. A. Flaus, D.M.A. Martin, G.J. Barton, and T. Owen-Hughes Identification of multiple distinct Snf2 subfamilies with conserved structural motifs Nucleic Acids Res 34 10 2006 2887 2905
77. A.M. Fontebasso, J. Schwartzentruber, D.-A. Khuong-Quang, X.-Y. Liu, D. Sturm, A. Korshunov, and et al. Mutations in SETD2 and genes affecting histone H3K36 methylation target hemispheric high-grade gliomas Acta Neuropathol 125 5 2013 659 669
78. C.A. French, S. Rahman, E.M. Walsh, S. Kühnle, A.R. Grayson, M.E. Lemieux, and et al. NSD3-NUT fusion oncoprotein in NUT midline carcinoma: implications for a novel oncogenic mechanism Cancer Discov 4 8 2014 928 941
79. A. Fujimoto, Y. Totoki, T. Abe, K.A. Boroevich, F. Hosoda, H.H. Nguyen, and et al. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators Nat Genet 44 7 2012 760 764
80. M.J. Garcia, J.C.M. Pole, S.-F. Chin, A. Teschendorff, A. Naderi, H. Ozdag, and et al. A 1 Mb minimal amplicon at 8p11-12 in breast cancer identifies new candidate oncogenes Oncogene 24 33 2005 5235 5245
81. K.E. Gardner, C.D. Allis, and B.D. Strahl Operating on chromatin, a colorful language where context matters J Mol Biol 409(1) 2011 Elsevier Ltd. 36 46
82. S.A. Gayther, S.J. Batley, L. Linger, A. Bannister, K. Thorpe, S.F. Chin, and et al. Mutations truncating the EP300 acetylase in human cancers Nat Genet 24 3 2000 300 303
83. N. Girard, M. Tremblay, M. Humbert, B. Grondin, A. Haman, J. Labrecque, and et al. RARα-PLZF oncogene inhibits C/EBPα function in myeloid cells Proc Natl Acad Sci U S A 110 33 2013 13522 13527
84. S. Glaser, J. Schaft, S. Lubitz, K. Vintersten, F. van der Hoeven, K.R. Tufteland, and et al. Multiple epigenetic maintenance factors implicated by the loss of Mll2 in mouse development Development 133 8 2006 1423 1432
85. H. Goto, Y. Yasui, E.A. Nigg, and M. Inagaki Aurora-B phosphorylates histone H3 at serine28 with regard to the mitotic chromosome condensation Genes Cells 7 1 2002 11 17
86. S.M. Gough, F. Lee, F. Yang, R.L. Walker, Y.J. Zhu, M. Pineda, and et al. NUP98-PHF23 is a chromatin-modifying oncoprotein that causes a wide array of leukemias sensitive to inhibition of PHD histone reader function Cancer Discov 4 5 2014 564 577
87. C.K. Govind, H. Qiu, D.S. Ginsburg, C. Ruan, K. Hofmeyer, C. Hu, and et al. Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes Mol Cell 39 2 2010 234 246
88. S. Grant, C. Easley, and P. Kirkpatrick Vorinostat Nat Rev Drug Discov 6 1 2007 21 22
89. I.V. Gregoretti, Y.-M. Lee, and H.V. Goodson Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis J Mol Biol 338 1 2004 17 31
90. M.G. Guenther, L.N. Lawton, T. Rozovskaia, G.M. Frampton, S.S. Levine, T.L. Volkert, and et al. Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia Genes Dev 22 24 2008 3403 3408
91. P. Guglielmelli, F. Biamonte, J. Score, C. Hidalgo-Curtis, F. Cervantes, M. Maffioli, and et al. EZH2 mutational status predicts poor survival in myelofibrosis Blood 118 19 2011 5227 5234
92. Y. Gui, G. Guo, Y. Huang, X. Hu, A. Tang, S. Gao, and et al. Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder Nat Genet 43 9 2011 875 878
93. B.J. Guppy, and K.J. McManus Mitotic accumulation of dimethylated lysine 79 of histone h3 is important for maintaining genome integrity during mitosis in human cells Genetics 199 2 2015 423 433
94. Y. Han, and B.A. Garcia Combining genomic and proteomic approaches for epigenetics research Epigenomics 5 4 2013 439 452
95. M.C. Hannibal, K.J. Buckingham, S.B. Ng, J.E. Ming, A.E. Beck, M.J. McMillin, and et al. Spectrum of MLL2 (ALR) mutations in 110 cases of Kabuki syndrome Am J Med Genet A 155A 7 2011 1511 1516
96. J.C. Hansen, C. Tse, and A.P. Wolffe Structure and function of the core histone N-termini: more than meets the eye Biochemistry 37 51 1998 17637 17641
97. S. Hardy, P.-E. Jacques, N. Gévry, A. Forest, M.-E. Fortin, L. Laflamme, and et al. The euchromatic and heterochromatic landscapes are shaped by antagonizing effects of transcription on H2A.Z deposition PLoS Genet 5 10 2009 e1000687
98. A.H. Hassan, P. Prochasson, K.E. Neely, S.C. Galasinski, M. Chandy, M.J. Carrozza, and et al. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes Cell 111 3 2002 369 379
99. C.A. Hassig, T.C. Fleischer, A.N. Billin, S.L. Schreiber, and D.E. Ayer Histone deacetylase activity is required for full transcriptional repression by mSin3A Cell 89 3 1997 341 347
100. H.H. He, C.A. Meyer, S.S. Hu, M.-W. Chen, C. Zang, Y. Liu, and et al. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification Nat Methods 11 1 2014 73 78
101. S. Heinz, C. Benner, N. Spann, E. Bertolino, Y.C. Lin, P. Laslo, and et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities Mol Cell 38 4 2010 576 589
102. R. Heit, J.B. Rattner, G.K.T. Chan, and M.J. Hendzel G2 histone methylation is required for the proper segregation of chromosomes J Cell Sci 122 Pt 16 2009 2957 2968
103. S. Henikoff, and A. Shilatifard Histone modification: cause or cog? Trends Genet 27 10 2011 389 396
104. A. Herry, N. Douet-Guilbert, N. Guéganic, F. Morel, M.-J. Le Bris, C. Berthou, and et al. Del(5q) and MLL amplification in homogeneously staining region in acute myeloblastic leukemia: a recurrent cytogenetic association Ann Hematol 85 4 2006 244 249
105. H.-M. Herz, D. Hu, and A. Shilatifard Enhancer malfunction in cancer Mol Cell 53 6 2014 859 866
106. H.-M. Herz, L.D. Madden, Z. Chen, C. Bolduc, E. Buff, R. Gupta, and et al. The H3K27me3 demethylase dUTX is a suppressor of Notch- and Rb-dependent tumors in Drosophila Mol Cell Biol 30 10 2010 2485 2497
107. T. Hideshima, and K.C. Anderson Histone deacetylase inhibitors in the treatment for multiple myeloma Int J Hematol 97 3 2013 324 332
108. D. Hnisz, B.J. Abraham, T.I. Lee, A. Lau, V. Saint-André, A.A. Sigova, and et al. Super-enhancers in the control of cell identity and disease Cell 155 4 2013 934 947
109. L. Ho, J.L. Ronan, J. Wu, B.T. Staahl, L. Chen, A. Kuo, and et al. An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency Proc Natl Acad Sci U S A 106 13 2009 5181 5186
110. K. Hochedlinger, and K. Plath Epigenetic reprogramming and induced pluripotency Development 136 4 2009 509 523
111. J.R. Horton, A.K. Upadhyay, H.H. Qi, X. Zhang, Y. Shi, and X. Cheng Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases Nat Struct Mol Biol 17 1 2010 38 43
112. W. Hörz, and W. Altenburger Sequence specific cleavage of DNA by micrococcal nuclease Nucleic Acids Res 9 12 1981 2643 2658
113. X. Hou, Y. Li, R.-Z. Luo, J.-H. Fu, J.-H. He, L.-J. Zhang, and et al. High expression of the transcriptional co-activator p300 predicts poor survival in resectable non-small cell lung cancers Eur J Surg Oncol 38 6 2012 523 530
114. R. Huether, L. Dong, X. Chen, G. Wu, M. Parker, L. Wei, and et al. The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes Nat Commun 5 2014 3630
115. J.L. Huret, P. Dessen, and A. Bernheim An atlas of chromosomes in hematological malignancies. Example: 11q23 and MLL partners Leukemia 15 6 2001 987 989
116. A. Insinga, S. Monestiroli, S. Ronzoni, V. Gelmetti, F. Marchesi, A. Viale, and et al. Inhibitors of histone deacetylases induce tumor-selective apoptosis through activation of the death receptor pathway Nat Med 11 1 2005 71 76
117. M. Iwafuchi-Doi, and K.S. Zaret Pioneer transcription factors in cell reprogramming Genes Dev 28 24 2014 2679 2692
118. R.H. Jacobson, A.G. Ladurner, D.S. King, and R. Tjian Structure and function of a human TAFII250 double bromodomain module Science 288 5470 2000 1422 1425
119. J.D. Jaffe, Y. Wang, H.M. Chan, J. Zhang, R. Huether, G.V. Kryukov, and et al. Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia Nat Genet 45 11 2013 1386 1391
120. L. Jiang, J.N. Smith, S.L. Anderson, P. Ma, C.A. Mizzen, and N.L. Kelleher Global assessment of combinatorial post-translational modification of core histones in yeast using contemporary mass spectrometry. LYS4 trimethylation correlates with degree of acetylation on the same H3 tail J Biol Chem 282 38 2007 27923 27934
121. S. John, P.J. Sabo, T.K. Canfield, K. Lee, S. Vong, M. Weaver, and et al. Genome-scale mapping of DNase I hypersensitivity Curr Protoc Mol Biol 2013 (Chapter 27, Unit 21.27)
122. D.S. Johnson, A. Mortazavi, R.M. Myers, and B. Wold Genome-wide mapping of in vivo protein-DNA interactions Science 316 5830 2007 1497 1502
123. S. Jones, T.-L. Wang, I.-M. Shih, T.-L. Mao, K. Nakayama, R. Roden, and et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma Science 330 6001 2010 228 231
124. S. Jørgensen, G. Schotta, and C.S. Sørensen Histone H4 lysine 20 methylation: key player in epigenetic regulation of genomic integrity Nucleic Acids Res 41 5 2013 2797 2806
125. Z. Kan, B.S. Jaiswal, J. Stinson, V. Janakiraman, D. Bhatt, H.M. Stern, and et al. Diverse somatic mutation patterns and pathway alterations in human cancers Nature 466 7308 2010 869 873
126. C. Kandoth, M.D. McLellan, F. Vandin, K. Ye, B. Niu, C. Lu, and et al. Mutational landscape and significance across 12 major cancer types Nature 502 7471 2013 333 339
127. A. Kapoor, M.S. Goldberg, L.K. Cumberland, K. Ratnakumar, M.F. Segura, P.O. Emanuel, and et al. The histone variant macroH2A suppresses melanoma progression through regulation of CDK8 Nature 468 7327 2010 1105 1109
128. K.R. Karch, J.E. Denizio, B.E. Black, and B.A. Garcia Identification and interrogation of combinatorial histone modifications Front Genet 4 2013 264
129. M. Kasten, H. Szerlong, H. Erdjument-Bromage, P. Tempst, M. Werner, and B.R. Cairns Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14 EMBO J 23 6 2004 1348 1359
130. J.J. Keats, T. Reiman, A.R. Belch, and L.M. Pilarski Ten years and counting: so what do we know about t(4;14)(p16;q32) multiple myeloma Leuk Lymphoma 47 11 2009 2289 2300
131. J.J. Keats, T. Reiman, C.A. Maxwell, B.J. Taylor, L.M. Larratt, M.J. Mant, and et al. In multiple myeloma, t(4;14)(p16;q32) is an adverse prognostic factor irrespective of FGFR3 expression Blood 101 4 2003 1520 1529
132. S.K. Kia, M.M. Gorski, S. Giannakopoulos, and C.P. Verrijzer SWI/SNF mediates polycomb eviction and epigenetic reprogramming of the INK4b-ARF-INK4a locus Mol Cell Biol 28 10 2008 3457 3464
133. J.-H. Kim, A. Sharma, S.S. Dhar, S.-H. Lee, B. Gu, C.-H. Chan, and et al. UTX and MLL4 coordinately regulate transcriptional programs for cell proliferation and invasiveness in breast cancer cells Cancer Res 74 6 2014 1705 1717
134. J. Kim, S. Sif, B. Jones, A. Jackson, J. Koipally, E. Heller, and et al. Ikaros DNA-binding proteins direct formation of chromatin remodeling complexes in lymphocytes Immunity 10 3 1999 345 355
135. A. Kirmizis, S.M. Bartley, A. Kuzmichev, R. Margueron, D. Reinberg, R. Green, and et al. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27 Genes Dev 18 13 2004 1592 1605
136. S.K. Knutson, S. Kawano, Y. Minoshima, N.M. Warholic, K.-C. Huang, Y. Xiao, and et al. Selective inhibition of EZH2 by EPZ-6438 leads to potent antitumor activity in EZH2-mutant non-Hodgkin lymphoma Mol Cancer Ther 13 4 2014 842 854
137. S.K. Knutson, T.J. Wigle, N.M. Warholic, C.J. Sneeringer, C.J. Allain, C.R. Klaus, and et al. A selective inhibitor of EZH2 blocks H3K27 methylation and kills mutant lymphoma cells Nat Chem Biol 8 11 2012 890 896
138. J. Koipally, A. Renold, J. Kim, and K. Georgopoulos Repression by Ikaros and Aiolos is mediated through histone deacetylase complexes EMBO J 18 11 1999 3090 3100
139. R.D. Kornberg Chromatin structure: a repeating unit of histones and DNA Science 184 4139 1974 868 871
140. M. Kostaki, A.D. Manona, I. Stavraka, P. Korkolopoulou, G. Levidou, E.-A. Trigka, and et al. High-frequency p16(INK) (4A) promoter methylation is associated with histone methyltransferase SETDB1 expression in sporadic cutaneous melanoma Exp Dermatol 23 5 2014 332 338
141. A.V. Krivtsov, and S.A. Armstrong MLL translocations, histone modifications and leukaemia stem-cell development Nat Rev Cancer 7 11 2007 823 833
142. A.V. Krivtsov, Z. Feng, M.E. Lemieux, J. Faber, S. Vempati, A.U. Sinha, and et al. H3K79 methylation profiles define murine and human MLL-AF4 leukemias Cancer Cell 14 5 2008 355 368
143. N.J. Krogan, J. Dover, A. Wood, J. Schneider, J. Heidt, M.A. Boateng, and et al. The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation Mol Cell 11 3 2003 721 729
144. E. Kroon, J. Krosl, U. Thorsteinsdottir, S. Baban, A.M. Buchberg, and G. Sauvageau Hoxa9 transforms primary bone marrow cells through specific collaboration with Meis1a but not Pbx1b EMBO J 17 13 1998 3714 3725
145. M.W.M. Kühn, M.J. Hadler, S.R. Daigle, R.P. Koche, A.V. Krivtsov, E.J. Olhava, and et al. MLL partial tandem duplication leukemia cells are sensitive to small molecule DOT1L inhibition Haematologica 100 5 2015 e190 e193
146. A.J. Kuo, P. Cheung, K. Chen, B.M. Zee, M. Kioi, J. Lauring, and et al. NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming Mol Cell 44 4 2011 609 620
147. N. Kwiatkowski, T. Zhang, P.B. Rahl, B.J. Abraham, J. Reddy, S.B. Ficarro, and et al. Targeting transcription regulation in cancer with a covalent CDK7 inhibitor Nature 511 7511 2014 616 620
148. H. Kwon, A.N. Imbalzano, P.A. Khavari, R.E. Kingston, and M.R. Green Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex Nature 370 6489 1994 477 481
149. F.H. Lam, D.J. Steger, and E.K. O'Shea Chromatin decouples promoter threshold from dynamic range Nature 453 7192 2008 246 250
150. D.A. Landau, K. Clement, M.J. Ziller, P. Boyle, J. Fan, H. Gu, and et al. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia Cancer Cell 26 6 2014 813 825
151. A. Laugesen, and K. Helin Chromatin repressive complexes in stem cells, development, and cancer Cell Stem Cell 14 6 2014 735 751
152. J. Lauring, A.M. Abukhdeir, H. Konishi, J.P. Garay, J.P. Gustin, Q. Wang, and et al. The multiple myeloma associated MMSET gene contributes to cellular adhesion, clonogenic growth, and tumorigenicity Blood 111 2 2008 856 864
153. M.S. Lawrence, P. Stojanov, C.H. Mermel, J.T. Robinson, L.A. Garraway, T.R. Golub, and et al. Discovery and saturation analysis of cancer genes across 21 tumour types Nature 505 7484 2014 495 501
154. J. Lee, D.-H. Kim, S. Lee, Q.-H. Yang, D.K. Lee, S.-K. Lee, and et al. A tumor suppressive coactivator complex of p53 containing ASC-2 and histone H3-lysine-4 methyltransferase MLL3 or its paralogue MLL4 Proc Natl Acad Sci U S A 106 21 2009 8513 8518
155. S.T. Lee, Z. Li, Z. Wu, M. Aau, P. Guan, R.K.M. Karuturi, and et al. Context-specific regulation of NF-κB target gene expression by EZH2 in breast cancers Mol Cell 43 5 2011 798 810
156. T.L. Lenstra, J.J. Benschop, T. Kim, J.M. Schulze, N.A.C. Brabers, H. Margaritis, and et al. The specificity and topology of chromatin interaction pathways in yeast Mol Cell 42 4 2011 536 549
157. G. Leroy, P.A. Dimaggio, E.Y. Chan, B.M. Zee, M.A. Blanco, B. Bryant, and et al. A quantitative atlas of histone modification signatures from human cancer cells Epigenetics Chromatin 6 1 2013 20
158. J. Lessard, J.I. Wu, J.A. Ranish, M. Wan, M.M. Winslow, B.T. Staahl, and et al. An essential switch in subunit composition of a chromatin remodeling complex during neural development Neuron 55 2 2007 201 215
159. M. Levine, C. Cattoglio, and R. Tjian Looping back to leap forward: transcription enters a new era Cell 157 1 2014 13 25
160. G. Li, M. Levitus, C. Bustamante, and J. Widom Rapid spontaneous accessibility of nucleosomal DNA Nat Struct Mol Biol 12 1 2005 46 53
161. W.-D. Li, Q.-R. Li, S.-N. Xu, F.-J. Wei, Z.-J. Ye, J.-K. Cheng, and et al. Exome sequencing identifies an MLL3 gene germ line mutation in a pedigree of colorectal cancer and acute myeloid leukemia Blood 121 8 2013 1478 1479
162. F. Li, G. Mao, D. Tong, J. Huang, L. Gu, W. Yang, and et al. The histone mark H3K36me3 regulates human DNA mismatch repair through its interaction with MutSα Cell 153 3 2013 590 600
163. Z. Li, and W.-G. Zhu Targeting histone deacetylases for cancer therapy: from molecular mechanisms to clinical implications Int J Biol Sci 10 7 2014 757 770
164. J.D. Licht, C. Chomienne, A. Goy, A. Chen, A.A. Scott, D.R. Head, and et al. Clinical and molecular characterization of a rare syndrome of acute promyelocytic leukemia associated with translocation (11;17) Blood 85 4 1995 1083 1094
165. J. Lindberg, I.G. Mills, D. Klevebring, W. Liu, M. Neiman, J. Xu, and et al. The mitochondrial and autosomal mutation landscapes of prostate cancer Eur Urol 63 4 2013 702 708
166. C. Linghu, H. Zheng, L. Zhang, and J. Zhang Discovering common combinatorial histone modification patterns in the human genome Gene 518 1 2013 171 178
167. W. Liu, L. Deng, Y. Song, and M. Redell DOT1L inhibition sensitizes MLL-rearranged AML to chemotherapy PLoS One 9 5 2014 e98270
168. L. Liu, S. Kimball, H. Liu, A. Holowatyj, and Z.-Q. Yang Genetic alterations of histone lysine methyltransferases and their significance in breast cancer Oncotarget 6 4 2015 2466 2482
169. J.G. Lohr, P. Stojanov, M.S. Lawrence, D. Auclair, B. Chapuy, C. Sougnez, and et al. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing Proc Natl Acad Sci U S A 109 10 2012 3879 3884
170. J. Lovén, H.A. Hoke, C.Y. Lin, A. Lau, D.A. Orlando, C.R. Vakoc, and et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers Cell 153 2 2013 320 334
171. C. Lu, P.S. Ward, G.S. Kapoor, D. Rohle, S. Turcan, O. Abdel-Wahab, and et al. IDH mutation impairs histone demethylation and results in a block to cell differentiation Nature 483 7390 2012 474 478
172. K. Luger, A.W. Mäder, R.K. Richmond, D.F. Sargent, and T.J. Richmond Crystal structure of the nucleosome core particle at 2.8 A resolution Nature 389 6648 1997 251 260
173. M. Lupien, J. Eeckhoute, C.A. Meyer, Q. Wang, Y. Zhang, W. Li, and et al. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription Cell 132 6 2008 958 970
174. F.A. Mallette, F. Mattiroli, G. Cui, L.C. Young, M.J. Hendzel, G. Mer, and et al. RNF8- and RNF168-dependent degradation of KDM4A/JMJD2A triggers 53BP1 recruitment to DNA damage sites EMBO J 31 8 2012 1865 1878
175. M. Mann Functional and quantitative proteomics using SILAC Nat Rev Mol Cell Biol 7 12 2006 952 958
176. M. Mann, N.A. Kulak, N. Nagaraj, and J. Cox The coming age of complete, accurate, and ubiquitous proteomes Mol Cell 49 4 2013 583 590
177. M.R. Mansour, B.J. Abraham, L. Anders, A. Berezovskaya, A. Gutierrez, A.D. Durbin, and et al. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element Science 346 6215 2014 1373 1377
178. B.G. Mar, L. Bullinger, E. Basu, K. Schlis, L.B. Silverman, K. Döhner, and et al. Sequencing histone-modifying enzymes identifies UTX mutations in acute lymphoblastic leukemia Leukemia 26 8 2012 1881 1883
179. B.G. Mar, L.B. Bullinger, K.M. McLean, P.V. Grauman, M.H. Harris, K. Stevenson, and et al. Mutations in epigenetic regulators including SETD2 are gained during relapse in paediatric acute lymphoblastic leukaemia Nat Commun 5 2014 3469
180. R. Margueron, G. Li, K. Sarma, A. Blais, J. Zavadil, C.L. Woodcock, and et al. Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms Mol Cell 32 4 2008 503 518
181. R. Margueron, and D. Reinberg The Polycomb complex PRC2 and its mark in life Nature 469 7330 2011 343 349
182. E. Martinez-Garcia, R. Popovic, D.-J. Min, S.M.M. Sweet, P.M. Thomas, L. Zamdborg, and et al. The MMSET histone methyl transferase switches global histone methylation and alters gene expression in t(4;14) multiple myeloma cells Blood 117 1 2011 211 220
183. C.E. Massie, and I.G. Mills Transcriptional regulation A. Vancura, Methods in molecular biology Methods Mol Biol Vol. 809 2012 Springer New York New York, NY
184. A.G.W. Matthews, A.J. Kuo, S. Ramón-Maiques, S. Han, K.S. Champagne, D. Ivanov, and et al. RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination Nature 450 7172 2007 1106 1110
185. M.T. McCabe, A.P. Graves, G. Ganji, E. Diaz, W.S. Halsey, Y. Jiang, and et al. Mutation of A677 in histone methyltransferase EZH2 in human B-cell lymphoma promotes hypertrimethylation of histone H3 on lysine 27 (H3K27) Proc Natl Acad Sci U S A 109 8 2012 2989 2994
186. M.T. McCabe, H.M. Ott, G. Ganji, S. Korenchuk, C. Thompson, G.S. Van Aller, and et al. EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations Nature 492 7427 2012 108 112
187. J. McGrath, and P. Trojer Targeting histone lysine methylation in cancer Pharmacol Ther 150 2015 1 22
188. R.W. McKenna, R.A. Kyle, W.M. Kuehl, T.M. Grogan, N.L. Harris, and R.W. Couplan Plasma cell neoplasms S.H. Swedlow, E. Campo, N.L. Harris, E.S. Jaffe, S.A. Pileri, H. Stein, WHO Classif tumours Haematop lymphoid tissues 2008 International Agency for Research on Cancer Lyon
189. K.J. McManus, V.L. Biron, R. Heit, D.A. Underhill, and M.J. Hendzel Dynamic changes in histone H3 lysine 9 methylations: identification of a mitosis-specific function for dynamic methylation in chromosome congression and segregation J Biol Chem 281 13 2006 8888 8897
190. J.A. Mertz, A.R. Conery, B.M. Bryant, P. Sandy, S. Balasubramanian, D.A. Mele, and et al. Targeting MYC dependence in cancer by inhibiting BET bromodomains Proc Natl Acad Sci U S A 108 40 2011 16669 16674
191. E. Metzger, A. Imhof, D. Patel, P. Kahl, K. Hoffmeyer, N. Friedrichs, and et al. Phosphorylation of histone H3T6 by PKCbeta(I) controls demethylation at histone H3K4 Nature 464 7289 2010 792 796
192. E. Metzger, N. Yin, M. Wissmann, N. Kunowska, K. Fischer, N. Friedrichs, and et al. Phosphorylation of histone H3 at threonine 11 establishes a novel chromatin mark for transcriptional regulation Nat Cell Biol 10 1 2008 53 60
193. C.A. Meyer, and X.S. Liu Identifying and mitigating bias in next-generation sequencing methods for chromatin biology Nat Rev Genet 15 11 2014 709 721
194. N. Meyer, and L.Z. Penn Reflecting on 25 years with MYC Nat Rev Cancer 8 12 2008 976 990
195. T.S. Mikkelsen, M. Ku, D.B. Jaffe, B. Issac, E. Lieberman, G. Giannoukos, and et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells Nature 448 7153 2007 553 560
196. T.A. Milne, S.D. Briggs, H.W. Brock, M.E. Martin, D. Gibbs, C.D. Allis, and et al. MLL targets SET domain methyltransferase activity to Hox gene promoters Mol Cell 10 5 2002 1107 1117
197. T.A. Milne, M.E. Martin, H.W. Brock, R.K. Slany, and J.L. Hess Leukemogenic MLL fusion proteins bind across a broad region of the Hox a9 locus, promoting transcription and multiple histone modifications Cancer Res 65 24 2005 11367 11374
198. C.S. Mitsiades, N.S. Mitsiades, C.J. McMullan, V. Poulaki, R. Shringarpure, T. Hideshima, and et al. Transcriptional signature of histone deacetylase inhibition in multiple myeloma: biological and clinical implications Proc Natl Acad Sci U S A 101 2 2004 540 545
199. S. Miura, C. Maesawa, M. Shibazaki, S. Yasuhira, S. Kasai, K. Tsunoda, and et al. Immunohistochemistry for histone h3 lysine 9 methyltransferase and demethylase proteins in human melanomas Am J Dermatopathol 36 3 2014 211 216
200. R.D. Morin, M. Mendez-Lago, A.J. Mungall, R. Goya, K.L. Mungall, R.D. Corbett, and et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma Nature 476 7360 2011 298 303
201. J. Morinière, S. Rousseaux, U. Steuerwald, M. Soler-López, S. Curtet, A.-L. Vitte, and et al. Cooperative binding of two acetylation marks on a histone tail by a single bromodomain Nature 461 7264 2009 664 668
202. K. Mousavi, H. Zare, A.H. Wang, and V. Sartorelli Polycomb protein Ezh1 promotes RNA polymerase II elongation Mol Cell 45 2 2012 255 262
203. D. Mueller, C. Bach, D. Zeisig, S. Monroe, A. Sreekumar, R. Zhou, and et al. A role for the MLL fusion partner ENL in transcriptional elongation and chromatin modification Blood 110 13 2007 4445 4454
204. C.G. Mullighan, J. Zhang, L.H. Kasper, S. Lerach, D. Payne-Turner, L.A. Phillips, and et al. CREBBP mutations in relapsed acute lymphoblastic leukaemia Nature 471 7337 2011 235 239
205. M. Muraoka, M. Konishi, R. Kikuchi-Yanoshita, K. Tanaka, N. Shitara, J.M. Chong, and et al. p300 gene alterations in colorectal and gastric carcinomas Oncogene 12 7 1996 1565 1569
206. C.A. Musselman, M.-E. Lalonde, J. Côté, and T.G. Kutateladze Perceiving the epigenetic landscape through histone readers Nat Struct Mol Biol 19 12 2012 1218 1227
207. T. Nakamura, T. Mori, S. Tada, W. Krajewski, T. Rozovskaia, R. Wassell, and et al. ALL-1 Is a histone methyltransferase that assembles a supercomplex of proteins involved in transcriptional regulation Mol Cell 10 5 2002 1119 1128
208. A. Nebbioso, N. Clarke, E. Voltz, E. Germain, C. Ambrosino, P. Bontempo, and et al. Tumor-selective action of HDAC inhibitors involves TRAIL induction in acute myeloid leukemia cells Nat Med 11 1 2005 77 84
209. T. Neff, A.U. Sinha, M.J. Kluk, N. Zhu, M.H. Khattab, L. Stein, and et al. Polycomb repressive complex 2 is required for MLL-AF9 leukemia Proc Natl Acad Sci U S A 109 13 2012 5028 5033
210. H.H. Ng, D.N. Ciccone, K.B. Morshead, M.A. Oettinger, and K. Struhl Lysine-79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: a potential mechanism for position-effect variegation Proc Natl Acad Sci U S A 100 4 2003 1820 1825
211. H.H. Ng, Q. Feng, H. Wang, H. Erdjument-Bromage, P. Tempst, Y. Zhang, and et al. Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association Genes Dev 16 12 2002 1518 1527
212. M.L. Nickerson, G.M. Dancik, K.M. Im, M.G. Edwards, S. Turan, J. Brown, and et al. Concurrent alterations in TERT, KDM6A, and the BRCA pathway in bladder cancer Clin Cancer Res 20 18 2014 4935 4948
213. E. Nicodeme, K.L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C.-W. Chung, and et al. Suppression of inflammation by a synthetic histone mimic Nature 468 7327 2010 1119 1123
214. G. Nikoloski, S.M.C. Langemeijer, R.P. Kuiper, R. Knops, M. Massop, E.R.L. Tönnissen, and et al. Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes Nat Genet 42 8 2010 665 667
215. P. Ntziachristos, A. Tsirigos, P. Van Vlierberghe, J. Nedjic, T. Trimarchi, M.S. Flaherty, and et al. Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia Nat Med 18 2 2012 298 301
216. P. Ntziachristos, A. Tsirigos, G.G. Welstead, T. Trimarchi, S. Bakogianni, L. Xu, and et al. Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia Nature 514 7523 2014 513 517
217. V.V. Ogryzko, R.L. Schiltz, V. Russanova, B.H. Howard, and Y. Nakatani The transcriptional coactivators p300 and CBP are histone acetyltransferases Cell 87 5 1996 953 959
218. Y. Okada, Q. Feng, Y. Lin, Q. Jiang, Y. Li, V.M. Coffield, and et al. hDOT1L links histone methylation to leukemogenesis Cell 121 2 2005 167 178
219. J.V. Olsen, and M. Mann Status of large-scale analysis of post-translational modifications by mass spectrometry Mol Cell Proteomics 12 12 2013 3444 3452
220. T.T. Onder, N. Kara, A. Cherry, A.U. Sinha, N. Zhu, K.M. Bernt, and et al. Chromatin-modifying enzymes as modulators of reprogramming Nature 483 7391 2012 598 602
221. C.K. Ong, C. Subimerb, C. Pairojkul, S. Wongkham, I. Cutcutache, W. Yu, and et al. Exome sequencing of liver fluke-associated cholangiocarcinoma Nat Genet 44 6 2012 690 693
222. L. Ooi, N.D. Belyaev, K. Miyake, I.C. Wood, and N.J. Buckley BRG1 chromatin remodeling activity is required for efficient chromatin binding by repressor element 1-silencing transcription factor (REST) and facilitates REST-mediated repression J Biol Chem 281 51 2006 38974 38980
223. D.J. Owen, P. Ornaghi, J.C. Yang, N. Lowe, P.R. Evans, P. Ballario, and et al. The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p EMBO J 19 22 2000 6141 6149
224. J.A. Oyer, X. Huang, Y. Zheng, J. Shim, T. Ezponda, Z. Carpenter, and et al. Point mutation E1099K in MMSET/NSD2 enhances its methyltranferase activity and leads to altered global chromatin methylation in lymphoid malignancies Leukemia 28 1 2014 198 201
225. R. Pacaud, M. Cheray, A. Nadaradjane, F.M. Vallette, and P.-F. Cartron Histone H3 phosphorylation in GBM: a new rational to guide the use of kinase inhibitors in anti-GBM therapy Theranostics 5 1 2015 12 22
226. J.C. Pajuelo-Gámez, J. Cervera, Z. García-Casado, A.V. Mena-Durán, A. Valencia, E. Barragán, and et al. MLL amplification in acute myeloid leukemia Cancer Genet Cytogenet 174 2 2007 127 131
227. M. Papamichos-Chronakis, and C.L. Peterson Chromatin and the genome integrity network Nat Rev Genet 14 1 2013 62 75
228. P.J. Park ChIP-seq: advantages and challenges of a maturing technology Nat Rev Genet 10 10 2009 669 680
229. S.C.J. Parker, M.L. Stitzel, D.L. Taylor, J.M. Orozco, M.R. Erdos, J.A. Akiyama, and et al. Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants Proc Natl Acad Sci U S A 110 44 2013 17921 17926
230. D.W. Parsons, M. Li, X. Zhang, S. Jones, R.J. Leary, J.C.-H. Lin, and et al. The genetic landscape of the childhood cancer medulloblastoma Science 331 6016 2011 435 439
231. L. Pasqualucci, D. Dominguez-Sola, A. Chiarenza, G. Fabbri, A. Grunn, V. Trifonov, and et al. Inactivating mutations of acetyltransferase genes in B-cell lymphoma Nature 471 7337 2011 189 195
232. L. Pasqualucci, V. Trifonov, G. Fabbri, J. Ma, D. Rossi, A. Chiarenza, and et al. Analysis of the coding genome of diffuse large B-cell lymphoma Nat Genet 43 9 2011 830 837
233. C. Pastori, M. Daniel, C. Penas, C.-H. Volmar, A.L. Johnstone, S.P. Brothers, and et al. BET bromodomain proteins are required for glioblastoma cell proliferation Epigenetics 9 4 2014 611 620
234. S.E. Peach, E.L. Rudomin, N.D. Udeshi, S.A. Carr, and J.D. Jaffe Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules Mol Cell Proteomics 11 5 2012 128 137
235. M.J. Peart, G.K. Smyth, R.K. van Laar, D.D. Bowtell, V.M. Richon, P.A. Marks, and et al. Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors Proc Natl Acad Sci U S A 102 10 2005 3697 3702
236. M. Peifer, L. Fernández-Cuesta, M.L. Sos, J. George, D. Seidel, L.H. Kasper, and et al. Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer Nat Genet 44 10 2012 1104 1110
237. S.X. Pfister, S. Ahrabi, L.-P. Zalmas, S. Sarkar, F. Aymard, C.Z. Bachrati, and et al. SETD2-dependent histone H3K36 trimethylation is required for homologous recombination repair and genome stability Cell Rep 7 6 2014 2006 2018
238. R. Popovic, E. Martinez-Garcia, E.G. Giannopoulou, Q. Zhang, Q. Zhang, T. Ezponda, and et al. Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation PLoS Genet 10 9 2014 e1004566
239. S. Pott, and J.D. Lieb What are super-enhancers? Nat Genet 47 1 2014 8 12
240. H.M. Prince, and M. Dickinson Romidepsin for cutaneous T-cell lymphoma Clin Cancer Res 18 13 2012 3509 3515
241. B.F. Pugh, and R. Tjian Mechanism of transcriptional activation by Sp1: evidence for coactivators Cell 61 7 1990 1187 1197
242. T.J. Pugh, S.D. Weeraratne, T.C. Archer, D.A. Pomeranz Krummel, D. Auclair, J. Bochicchio, and et al. Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations Nature 488 7409 2012 106 110
243. A. Rada-Iglesias, R. Bajpai, T. Swigut, S.A. Brugmann, R.A. Flynn, and J. Wysocka A unique chromatin signature uncovers early developmental enhancers in humans Nature 470 7333 2011 279 283
244. P.B. Rahl, C.Y. Lin, A.C. Seila, R.A. Flynn, S. McCuine, C.B. Burge, and et al. c-Myc regulates transcriptional pause release Cell 141 3 2010 432 445
245. S. Ramón-Maiques, A.J. Kuo, D. Carney, A.G.W. Matthews, M.A. Oettinger, O. Gozani, and et al. The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2 Proc Natl Acad Sci U S A 104 48 2007 18993 18998
246. O.J. Rando Global patterns of histone modifications Curr Opin Genet Dev 17 2 2007 94 99
247. D.N. Reisman, J. Sciarrotta, W. Wang, W.K. Funkhouser, and B.E. Weissman Loss of BRG1/BRM in human lung cancer cell lines and primary lung cancers: correlation with poor prognosis Cancer Res 63 3 2003 560 566
248. T.J. Richmond, and C.A. Davey The structure of DNA in the nucleosome core Nature 423 6936 2003 145 150
249. V.M. Richon, T.W. Sandhoff, R.A. Rifkind, and P.A. Marks Histone deacetylase inhibitor selectively induces p21WAF1 expression and gene-associated histone acetylation Proc Natl Acad Sci U S A 97 18 2000 10014 10019
250. J.M. Rizzo, J.E. Bard, and M.J. Buck Standardized collection of MNase-seq experiments enables unbiased dataset comparisons BMC Mol Biol 13 1 2012 15
251. G. Robertson, M. Hirst, M. Bainbridge, M. Bilenky, Y. Zhao, T. Zeng, and et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing Nat Methods 4 8 2007 651 657
252. G. Robinson, M. Parker, T.A. Kranenburg, C. Lu, X. Chen, L. Ding, and et al. Novel mutations target distinct subgroups of medulloblastoma Nature 488 7409 2012 43 48
253. M. Rodriguez-Paredes, A. Martinez de Paz, L. Simó-Riudalbas, S. Sayols, C. Moutinho, S. Moran, and et al. Gene amplification of the histone methyltransferase SETDB1 contributes to human lung tumorigenesis Oncogene 33 21 2014 2807 2813
254. S. Ropero, and M. Esteller The role of histone deacetylases (HDACs) in human cancer Mol Oncol 1 1 2007 19 25
255. R. Rosati, R. La Starza, A. Veronese, A. Aventin, C. Schwienbacher, T. Vallespi, and et al. NUP98 is fused to the NSD3 gene in acute myeloid leukemia associated with t(8;11)(p11.2;p15) Blood 99 10 2002 3857 3860
256. S.B. Rothbart, and B.D. Strahl Interpreting the language of histone and DNA modifications Biochim Biophys Acta 1839 8 2014 627 643
257. J.D. Rowley The der(11) chromosome contains the critical breakpoint junction in the 4;11, 9;11, and 11;19 translocations in acute leukemia Genes Chromosom Cancer 5 3 1992 264 266
258. T. Rozovskaia, E. Feinstein, O. Mor, R. Foa, J. Blechman, T. Nakamura, and et al. Upregulation of Meis1 and HoxA9 in acute lymphocytic leukemias with the t(4: 11) abnormality Oncogene 20 7 2001 874 878
259. A.J. Ruthenburg, H. Li, T.A. Milne, S. Dewell, R.K. McGinty, M. Yuen, and et al. Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions Cell 145 5 2011 692 706
260. S. Salmoiraghi, M.L.G. Montalvo, E. D'Agostini, G. Amicarelli, G. Minnucci, O. Spinelli, and et al. Mutations and chromosomal rearrangements of JAK2: not only a myeloid issue Expert Rev Hematol 6 4 2013 429 439
261. M.A. Santos, R.B. Faryabi, A.V. Ergen, A.M. Day, A. Malhowski, A. Canela, and et al. DNA-damage-induced differentiation of leukaemic cells as an anti-cancer barrier Nature 514 7520 2014 107 111
262. H. Santos-Rosa, R. Schneider, A.J. Bannister, J. Sherriff, B.E. Bernstein, N.C.T. Emre, and et al. Active genes are tri-methylated at K4 of histone H3 Nature 419 6905 2002 407 411
263. M. Santra, F. Zhan, E. Tian, B. Barlogie, and J. Shaughnessy A subset of multiple myeloma harboring the t(4;14)(p16;q32) translocation lacks FGFR3 expression but maintains an IGH/MMSET fusion transcript Blood 101 6 2003 2374 2376
264. S.A. Sarraf, and I. Stancheva Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly Mol Cell 15 4 2004 595 605
265. D. Schübeler, D.M. MacAlpine, D. Scalzo, C. Wirbelauer, C. Kooperberg, F. van Leeuwen, and et al. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote Genes Dev 18 11 2004 1263 1271
266. D.B. Seligson, S. Horvath, T. Shi, H. Yu, S. Tze, M. Grunstein, and et al. Global histone modification patterns predict risk of prostate cancer recurrence Nature 435 7046 2005 1262 1266
267. A.A. Sérandour, S. Avner, F. Percevault, F. Demay, M. Bizot, C. Lucchetti-Miganeh, and et al. Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers Genome Res 21 4 2011 555 565
268. M.A. Shah, E.L. Denton, C.H. Arrowsmith, M. Lupien, and M. Schapira A global assessment of cancer genomic alterations in epigenetic mechanisms Epigenetics Chromatin 7 1 2014 29
269. Z. Shao, F. Raible, R. Mollaaghababa, J.R. Guyon, C.T. Wu, W. Bender, and et al. Stabilization of chromatin structure by PRC1, a Polycomb complex Cell 98 1 1999 37 46
270. A.K. Sharma, S. Bhattacharya, S.A. Khan, B. Khade, and S. Gupta Dynamic alteration in H3 serine 10 phosphorylation is G1-phase specific during ionization radiation induced DNA damage response in human cells Mutat Res Mol Mech Mutagen 773 2015 83 91
271. C. Shen, S.Y. Jo, C. Liao, J.L. Hess, and Z. Nikolovska-Coleska Targeting recruitment of disruptor of telomeric silencing 1-like (DOT1L): characterizing the interactions between DOT1L and mixed lineage leukemia (MLL) fusion proteins J Biol Chem 288 42 2013 30585 30596
272. X. Shen, Y. Liu, Y.-J. Hsu, Y. Fujiwara, J. Kim, X. Mao, and et al. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency Mol Cell 32 4 2008 491 502
273. H. Shen, N. Powers, N. Saini, C.E.S. Comstock, A. Sharma, K. Weaver, and et al. The SWI/SNF ATPase Brm is a gatekeeper of proliferative control in prostate cancer Cancer Res 68 24 2008 10154 10162
274. B. Shi, J. Liang, X. Yang, Y. Wang, Y. Zhao, H. Wu, and et al. Integration of estrogen and Wnt signaling circuits by the polycomb group protein EZH2 in breast cancer cells Mol Cell Biol 27 14 2007 5105 5119
275. W. Shu, H. Chen, X. Bo, and S. Wang Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains Nucleic Acids Res 39 17 2011 7428 7443
276. R. Siersbæk, A. Rabiee, R. Nielsen, S. Sidoli, S. Traynor, A. Loft, and et al. Transcription factor cooperativity in early adipogenic hotspots and super-enhancers Cell Rep 7 5 2014 1443 1455
277. C. Simon, J. Chagraoui, J. Krosl, P. Gendron, B. Wilhelm, S. Lemieux, and et al. A key role for EZH2 and associated genes in mouse and human adult T-cell acute leukemia Genes Dev 26 7 2012 651 656
278. E. Smith, and A. Shilatifard The chromatin signaling pathway: diverse mechanisms of recruitment of histone-modifying enzymes and varied biological outcomes Mol Cell 40 5 2010 689 701
279. L. Song, and G.E. Crawford DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells Cold Spring Harb Protoc 2010 2 2010 (pdb.prot5384)
280. A. Soufi, G. Donahue, and K.S. Zaret Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome Cell 151 5 2012 994 1004
281. T.E. Spencer, G. Jenster, M.M. Burcin, C.D. Allis, J. Zhou, C.A. Mizzen, and et al. Steroid receptor coactivator-1 is a histone acetyltransferase Nature 389 6647 1997 194 198
282. A. Spyropoulou, A. Gargalionis, G. Dalagiorgou, C. Adamopoulos, K.A. Papavassiliou, R.W. Lea, and et al. Role of histone lysine methyltransferases SUV39H1 and SETDB1 in gliomagenesis: modulation of cell proliferation, migration, and colony formation Neuromolecular Med 16 1 2014 70 82
283. D.J. Steger, M.I. Lefterova, L. Ying, A.J. Stonestrom, M. Schupp, D. Zhuo, and et al. DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells Mol Cell Biol 28 8 2008 2825 2839
284. L. Stojic, Z. Jasencakova, C. Prezioso, A. Stützer, B. Bodega, D. Pasini, and et al. Chromatin regulated interchange between polycomb repressive complex 2 (PRC2)-Ezh2 and PRC2-Ezh1 complexes controls myogenin activation in skeletal muscle cells Epigenetics Chromatin 4 2011 16
285. B.D. Strahl, and C.D. Allis The language of covalent histone modifications Nature 403 January 2000 41 45
286. N. Stransky, A.M. Egloff, A.D. Tward, A.D. Kostic, K. Cibulskis, A. Sivachenko, and et al. The mutational landscape of head and neck squamous cell carcinoma Science 333 6046 2011 1157 1160
287. Q.-Y. Sun, L.-W. Ding, J.-F. Xiao, W. Chien, S.-L. Lim, N. Hattori, and et al. SETDB1 accelerates tumourigenesis by regulating the WNT signalling pathway J Pathol 235 4 2015 559 570
288. Y. Sun, M. Wei, S.C. Ren, R. Chen, W.D. Xu, F.B. Wang, and et al. Histone methyltransferase SETDB1 is required for prostate cancer cell proliferation, migration and invasion Asian J Androl 16 2 2014 319 324
289. M.-H. Sung, M.J. Guertin, S. Baek, and G.L. Hager DNase footprint signatures Are dictated by factor dynamics and DNA sequence Mol Cell 56 2 2014 275 285
290. K. Takahashi, and S. Yamanaka Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors Cell 126 4 2006 663 676
291. M. Tan, H. Luo, S. Lee, F. Jin, J.S. Yang, E. Montellier, and et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification Cell 146 6 2011 1016 1028
292. Y. Tang, W. Zhao, Y. Chen, Y. Zhao, and W. Gu Acetylation is indispensable for p53 activation Cell 133 4 2008 612 626
293. K. Tatton-Brown, A. Murray, S. Hanks, J. Douglas, R. Armstrong, S. Banka, and et al. Weaver syndrome and EZH2 mutations: Clarifying the clinical phenotype Am J Med Genet A 161A 12 2013 2972 2980
294. J.H. Taube, K. Allton, S.A. Duncan, L. Shen, and M.C. Barton Foxa1 functions as a pioneer transcription factor at transposable elements to activate Afp during differentiation of embryonic stem cells J Biol Chem 285 21 2010 16135 16144
295. J. Taunton, C.A. Hassig, and S.L. Schreiber A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p Science 272 5260 1996 408 411
296. S.D. Taverna, S. Ilin, R.S. Rogers, J.C. Tanny, H. Lavender, H. Li, and et al. Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs Mol Cell 24 5 2006 785 796
297. J.-M. Terme, L. Millán-Ariño, R. Mayor, N. Luque, A. Izquierdo-Bouldstridge, A. Bustillos, and et al. Dynamics and dispensability of variant-specific histone H1 Lys-26/Ser-27 and Thr-165 post-translational modifications FEBS Lett 588 14 2014 2353 2362
298. H.S. Tims, K. Gurunathan, M. Levitus, and J. Widom Dynamics of nucleosome invasion by DNA binding proteins J Mol Biol 411 2 2011 430 448
299. G. Tonon, K.-K. Wong, G. Maulik, C. Brennan, B. Feng, Y. Zhang, and et al. High-resolution genomic profiles of human lung cancer Proc Natl Acad Sci U S A 102 27 2005 9625 9630
300. W.-W. Tsai, Z. Wang, T.T. Yiu, K.C. Akdemir, W. Xia, S. Winter, and et al. TRIM24 links a non-canonical histone signature to breast cancer Nature 468 7326 2010 927 932
301. M. Tsompana, and M.J. Buck Chromatin accessibility: a window into the genome Epigenetics Chromatin 7 1 2014 33
302. B.M. Turner Defining an epigenetic code Nat Cell Biol 9 1 2007 2 6
303. B.M. Turner Nucleosome signalling; An evolving concept Biochim Biophys Acta 1839 8 2014 623 626
304. J. Van der Meulen, V. Sanghvi, K. Mavrakis, K. Durinck, F. Fang, F. Matthijssens, and et al. The H3K27me3 demethylase UTX is a gender-specific tumor suppressor in T-cell acute lymphoblastic leukemia Blood 125 1 2015 13 21
305. J. Van der Meulen, F. Speleman, and P. Van Vlierberghe The H3K27me3 demethylase UTX in normal development and disease Epigenetics 9 5 2014 658 668
306. G. Van Haaften, G.L. Dalgliesh, H. Davies, L. Chen, G. Bignell, C. Greenman, and et al. Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer Nat Genet 41 5 2009 521 523
307. F. Van Leeuwen, P.R. Gafken, and D.E. Gottschling Dot1p modulates silencing in yeast by methylation of the nucleosome core Cell 109 6 2002 745 756
308. I. Varela, P. Tarpey, K. Raine, D. Huang, C.K. Ong, P. Stephens, and et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma Nature 469 7331 2011 539 542
309. M. Vermeulen, K.W. Mulder, S. Denissov, W.W.M.P. Pijnappel, F.M.A. van Schaik, R.A. Varier, and et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4 Cell 131 1 2007 58 69
310. I. Versteege, N. Sévenet, J. Lange, M.F. Rousseau-Merck, P. Ambros, R. Handgretinger, and et al. Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer Nature 394 6689 1998 203 206
311. T. Vierbuchen, A. Ostermeier, Z.P. Pang, Y. Kokubu, T.C. Südhof, and M. Wernig Direct conversion of fibroblasts to functional neurons by defined factors Nature 463 7284 2010 1035 1041
312. P. Voigt, G. LeRoy, W.J. Drury, B.M. Zee, J. Son, D.B. Beck, and et al. Asymmetrically modified nucleosomes Cell 151 1 2012 181 193
313. P.A. Wade, D. Pruss, and A.P. Wolffe Histone acetylation: chromatin in action Trends Biochem Sci 22 4 1997 128 132
314. G.G. Wang, C.D. Allis, and P. Chi Chromatin remodeling and cancer, Part II: ATP-dependent chromatin remodeling Trends Mol Med 13 9 2007 373 380
315. G.G. Wang, L. Cai, M.P. Pasillas, and M.P. Kamps NUP98-NSD1 links H3K36 methylation to Hox-A gene activation and leukaemogenesis Nat Cell Biol 9 7 2007 804 812
316. L. Wang, A. Gural, X.-J. Sun, X. Zhao, F. Perna, G. Huang, and et al. The leukemogenicity of AML1-ETO is dependent on site-specific lysine acetylation Science 333 6043 2011 765 769
317. J. Wang, V.V. Lunyak, and I.K. Jordan BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets Bioinformatics 29 4 2013 492 493
318. G.G. Wang, J. Song, Z. Wang, H.L. Dormann, F. Casadio, H. Li, and et al. Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger Nature 459 7248 2009 847 851
319. L. Wang, G.-B. Zhou, P. Liu, J.-H. Song, Y. Liang, X.-J. Yan, and et al. Dissection of mechanisms of Chinese medicinal formula Realgar-Indigo naturalis as an effective treatment for promyelocytic leukemia Proc Natl Acad Sci U S A 105 12 2008 4826 4831
320. O.L. Wapinski, T. Vierbuchen, K. Qu, Q.Y. Lee, S. Chanda, D.R. Fuentes, and et al. Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons Cell 155 3 2013 621 635
321. C.M. Weber, and S. Henikoff Histone variants: dynamic punctuation in transcription Genes Dev 28 7 2014 672 682
322. C.M. Weber, S. Ramachandran, and S. Henikoff Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase Mol Cell 53 5 2014 819 830
323. Y. Wei, L. Yu, J. Bowen, M.A. Gorovsky, and C.D. Allis Phosphorylation of histone H3 is required for proper chromosome condensation and segregation Cell 97 1 1999 99 109
324. W.A. Whyte, D.A. Orlando, D. Hnisz, B.J. Abraham, C.Y. Lin, M.H. Kagey, and et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes Cell 153 2 2013 307 319
325. B.G. Wilson, X. Wang, X. Shen, E.S. McKenna, M.E. Lemieux, Y.-J. Cho, and et al. Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation Cancer Cell 18 4 2010 316 328
326. G.A. Wray, M.W. Hahn, E. Abouheif, J.P. Balhoff, M. Pizer, M.V. Rockman, and et al. The evolution of transcriptional regulation in eukaryotes Mol Biol Evol 20 9 2003 1377 1419
327. J.I. Wu, J. Lessard, and G.R. Crabtree Understanding the words of chromatin regulation Cell 136 2 2009 200 206
328. P.-C. Wu, J.-W. Lu, J.-Y. Yang, I.-H. Lin, D.-L. Ou, Y.-H. Lin, and et al. H3K9 histone methyltransferase, KMT1E/SETDB1, cooperates with the SMAD2/3 pathway to suppress lung cancer metastasis Cancer Res 74 24 2014 7333 7343
329. X.-S. Xiao, M.-Y. Cai, J.-W. Chen, X.-Y. Guan, H.-F. Kung, Y.-X. Zeng, and et al. High expression of p300 in human breast cancer correlates with tumor recurrence and predicts adverse prognosis Chin J Cancer Res 23 3 2011 201 207
330. J. Xu, Z. Shao, D. Li, H. Xie, W. Kim, J. Huang, and et al. Developmental control of polycomb subunit composition by GATA factors mediates a switch to Non-canonical functions Mol Cell 57 2 2015 304 316
331. K. Xu, Z.J. Wu, A.C. Groner, H.H. He, C. Cai, R.T. Lis, and et al. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent Science 338 6113 2012 1465 1469
332. Z.-Q. Yang, G. Liu, A. Bollig-Fischer, C.N. Giroux, and S.P. Ethier Transforming properties of 8p11-12 amplified genes in human breast cancer Cancer Res 70 21 2010 8487 8497
333. E.-J. Yeoh, M.E. Ross, S.A. Shurtleff, W.K. Williams, D. Patel, R. Mahfouz, and et al. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling Cancer Cell 1 2 2002 133 143
334. A. Yokoyama, Z. Wang, J. Wysocka, M. Sanyal, D.J. Aufiero, I. Kitabayashi, and et al. Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression Mol Cell Biol 24 13 2004 5639 5649
335. W. Yu, E.J. Chory, A.K. Wernimont, W. Tempel, A. Scopton, A. Federation, and et al. Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors Nat Commun 3 2012 1288
336. B.D. Yu, R.D. Hanson, J.L. Hess, S.E. Horning, and S.J. Korsmeyer MLL, a mammalian trithorax-group gene, functions as a transcriptional maintenance factor in morphogenesis Proc Natl Acad Sci U S A 95 18 1998 10632 10636
337. B.D. Yu, J.L. Hess, S.E. Horning, G.A. Brown, and S.J. Korsmeyer Altered Hox expression and segmental identity in Mll-mutant mice Nature 378 6556 1995 505 508
338. W. Yu, D. Smil, F. Li, W. Tempel, O. Fedorov, K.T. Nguyen, and et al. Bromo-deaza-SAH: a potent and selective DOT1L inhibitor Bioorg Med Chem 21 7 2013 1787 1794
339. Z.J. Zang, I. Cutcutache, S.L. Poon, S.L. Zhang, J.R. McPherson, J. Tao, and et al. Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes Nat Genet 44 5 2012 570 574
340. K.S. Zaret, and J.S. Carroll Pioneer transcription factors: establishing competence for gene expression Genes Dev 25 21 2011 2227 2241
341. G.E. Zentner, and S. Henikoff Surveying the epigenomic landscape, one base at a time Genome Biol 13 10 2012 250
342. J. Zhang, L. Ding, L. Holmfeldt, G. Wu, S.L. Heatley, D. Payne-Turner, and et al. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia Nature 481 7380 2012 157 163
343. K. Zhang, L. Li, M. Zhu, G. Wang, J. Xie, Y. Zhao, and et al. Comparative analysis of histone H3 and H4 post-translational modifications of esophageal squamous cell carcinoma with different invasive capabilities J Proteomics 112 2015 180 189
344. Z. Zhang, and B.F. Pugh High-resolution genome-wide mapping of the primary structure of chromatin Cell 144 2 2011 175 186
345. W. Zhang, X. Xia, M.R. Reisenauer, C.S. Hemenway, and B.C. Kone Dot1a-AF9 complex mediates histone H3 Lys-79 hypermethylation and repression of ENaCalpha in an aldosterone-sensitive manner J Biol Chem 281 26 2006 18059 18068
346. Y. Zhao, J. Tan, L. Zhuang, X. Jiang, E.T. Liu, and Q. Yu Inhibitors of histone deacetylases target the Rb-E2F1 pathway for apoptosis induction through activation of proapoptotic protein Bim Proc Natl Acad Sci U S A 102 44 2005 16090 16095
347. S. Zhao, W. Xu, W. Jiang, W. Yu, Y. Lin, T. Zhang, and et al. Regulation of cellular metabolism by protein lysine acetylation Science 327 5968 2010 1000 1004
348. Z. Zhou, R. Thomsen, S. Kahns, and A.L. Nielsen The NSD3L histone methyltransferase regulates cell cycle and cell invasion in breast cancer cells Biochem Biophys Res Commun 398 3 2010 565 570
349. J. Zuber, J. Shi, E. Wang, A.R. Rappaport, H. Herrmann, E.A. Sison, and et al. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia Nature 478 7370 2011 524 528