A quantitative atlas of histone modification signatures from human cancer cells

Epigenetics and Chromatin

Volumn 6, Issue 1, 2013, Pages

  Leroy, Gary ^a   Dimaggio, Peter A ^b   Chan, Eric Y ^c   Zee, Barry M ^a   Blanco, M Andres ^a   Bryant, Barbara ^c   Flaniken, Ian Z ^a   Liu, Sherry ^d   Kang, Yibin ^a   Trojer, Patrick ^c   Garcia, Benjamin A ^d  

^a PRINCETON UNIVERSITY   (United States)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c Department of Structural Biology   (United States)

^d UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; HISTONE H4;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; ATLAS; BREAST CELL; CANCER CELL; CHROMATIN; CONTROLLED STUDY; FEMALE; GENE EXPRESSION; HISTONE MODIFICATION; METHYLATION; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; TRANSCRIPTION INITIATION;

ANIMALIA;

EID: 84879818703     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-6-20     Document Type: Article

References (46)

1. Hallmarks of cancer: the next generation. Hanahan D, Weinberg RA, Cell 2011 144 646 674 10.1016/j.cell.2011.02.013 21376230
2. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, et al. Nature 2000 403 503 511 10.1038/35000501 10676951 (Pubitemid 30082188)
3. Translating the histone code. Jenuwein T, Allis CD, Science 2001 293 1074 1080 10.1126/science.1063127 11498575 (Pubitemid 32758077)
4. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, Jones RS, Zhang Y, Science 2002 298 1039 1043 10.1126/science.1076997 12351676 (Pubitemid 35247314)
5. Cancer epigenetics: from mechanism to therapy. Dawson MA, Kouzarides T, Cell 2012 150 12 27 10.1016/j.cell.2012.06.013 22770212
6. Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins. Leroy G, Chepelev I, DiMaggio P, Blanco MA, Zee BM, Zhao K, Garcia BA, Genome Biol 2012 13 68 10.1186/gb-2012-13-8-r68 22897906
7. Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Dawson MA, Prinjha RK, Dittmann A, Giotopoulos G, Bantscheff M, Chan WI, Robson SC, Chung CW, Hopf C, Savitski MM, Huthmacher C, Gudgin E, Lugo D, Beinke S, Chapman TD, Roberts EJ, Soden PE, Auger KR, Mirguet O, Doehner K, Delwel R, Burnett AK, Jeffrey P, Drewes G, Lee K, Huntly BJ, Kouzarides T, Nature 2011 478 529 533 10.1038/nature10509 21964340
8. BRD-NUT oncoproteins: a family of closely related nuclear proteins that block epithelial differentiation and main the growth of carcinoma cells. French CA, Ramirez CL, Kolmakova J, Hickman TT, Cameron MJ, Thyne ME, Kutok JL, Toretsky JA, Tadavarthy AK, Kees UR, Fletcher JA, Aster JC, Oncogene 2008 27 2237 2242 10.1038/sj.onc.1210852 17934517 (Pubitemid 351483375)
9. Selective inhibition of BET bromodomains. Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, Fedorov O, Morse EM, Keates T, Hickman TT, Felletar I, Philpott M, Munro S, McKeown MR, Wang Y, Christie AL, West N, Cameron MJ, Schwartz B, Heightman TD, La Thangue N, French CA, Wiest O, Kung AL, Knapp S, Bradner JE, Nature 2010 468 1067 1073 10.1038/nature09504 20871596
10. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, Paul JE, Boyle M, Woolcock BW, Kuchenbauer F, Yap D, Humphries RK, Griffith OL, Shah S, Zhu H, Kimbara M, Shashkin P, Charlot JF, Tcherpakov M, Corbett R, Tam A, Varhol R, Smailus D, Moksa M, Zhao Y, Delaney A, Qian H, Birol I, Schein J, Moore R, et al. Nat Genet 2010 42 181 185 10.1038/ng.518 20081860
11. Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes. Nikoloski G, Langemeijer SM, Kuiper RP, Knops R, Massop M, Tönnissen ER, van der Heijden A, Scheele TN, Vandenberghe P, de Witte T, van der Reijden BA, Jansen JH, Nat Genet 2010 42 665 667 10.1038/ng.620 20601954
12. Akt-mediated phosphorylation of EZH2 suppresses methylation of lysine 27 in histone H3. Cha TL, Zhou BP, Xia W, Wu Y, Yang CC, Chen CT, Ping B, Otte AP, Hung MC, Science 2005 310 306 310 10.1126/science.1118947 16224021 (Pubitemid 41457195)
13. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Tan M, Luo H, Lee S, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, Zhao Y, Cell 2011 146 1016 1028 10.1016/j.cell.2011.08.008 21925322
14. H3K36 methylation antagonizes PRC2-mediated H3K27 methylation. Yuan W, Xu M, Huang C, Liu N, Chen S, Zhu B, J Biol Chem 2011 286 7983 7989 10.1074/jbc.M110.194027 21239496
15. Total kinetic analysis reveals how combinatorial methylation patterns are established on lysines 27 and 36 of histone H3. Zheng Y, Sweet SM, Popovic R, Martinez-Garcia E, Tipton JD, Thomas PM, Licht JD, Kelleher NL, Proc Natl Acad Sci USA 2012 109 13549 13554 10.1073/pnas.1205707109 22869745
16. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Rea S, Eisenhaber F, O'Carroll D, Strahl BD, Sun ZW, Schmid M, Opravil S, Mechtler K, Ponting CP, Allis CD, Jenuwein T, Nature 2000 406 593 599 10.1038/35020506 10949293 (Pubitemid 30641039)
17. Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies. DiMaggio PA Jr, McAllister SR, Floudas CA, Feng XJ, Rabinowitz JD, Rabitz HA, BMC Bioinformatics 2008 9 458 473 10.1186/1471-2105-9-458 18954459
18. Selective interactions between vertebrate Polycomb homologs and the SUV39H1 histone lysine methyltransferase suggest that histone H3-K9 methylation contributes to chromosomal targeting of Polycomb group proteins. Sewalt RG, Lachner M, Vargas M, Hamer KM, den Blaauwen JL, Hendrix T, Melcher M, Schweizer D, Jenuwein T, Otte AP, Mol Cell Biol 2002 22 5539 5553 10.1128/MCB.22.15.5539- 5553.2002 12101246 (Pubitemid 34755763)
19. Polycomb protein EZH2 regulates tumor invasion via the transcriptional repression of the metastasis suppressor RKIP in breast and prostate cancer. Ren G, Baritaki S, Marathe H, Feng J, Park S, Beach S, Bazeley PS, Beshir AB, Fenteany G, Mehra R, Daignault S, Al-Mulla F, Keller E, Bonavida B, de la Serna I, Yeung KC, Cancer Res 2012 72 3091 3104 10.1158/0008-5472.CAN-11-3546 22505648
20. Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation. Zippo A, Serafini R, Rocchigiani M, Pennacchini S, Krepelova A, Oliviero S, Cell 2009 138 1122 1136 10.1016/j.cell.2009.07.031 19766566
21. Mapping and analysis of chromatin state dynamics in nine human cell types. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE, Nature 2011 473 43 49 10.1038/nature09906 21441907
22. Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. Peach SE, Rudomin EL, Udeshi ND, Carr SA, Jaffe JD, Mol Cell Proteomics 2012 11 128 137 10.1074/mcp.M111.015941 22442256
23. Poly-acetylated chromatin signatures are preferred epitopes for site-specific histone H4 acetyl antibodies. Rothbart SB, Lin S, Britton LM, Krajewski K, Keogh MC, Garcia BA, Strahl BD, Sci Rep 2012 2 489 22761995
24. Differential expression of histone post-translational modifications in acute myeloid and chronic lymphocytic leukemia determined by high-pressure liquid chromatography and mass spectrometry. Zhang L, Freitas MA, Wickham J, Parthun MR, Klisovic MI, Marcucci G, Byrd JC, J Am Soc Mass Spectrom 2004 15 77 86 10.1016/j.jasms.2003.10.001 14698558 (Pubitemid 38091670)
25. Histone proteins determined in a human colon cancer by high-performance liquid chromatography and mass spectrometry. Naldi M, Andrisano V, Fiori J, Calonghi N, Pagnotta E, Parolin C, Pieraccini G, Masotti L, J Chromatogr A 2006 1129 73 81 10.1016/j.chroma.2006.06.100 16887128 (Pubitemid 44331864)
26. Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Fraga MF, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta G, Bonaldi T, Haydon C, Ropero S, Petrie K, Iyer NG, Pérez-Rosado A, Calvo E, Lopez JA, Cano A, Calasanz MJ, Colomer D, Piris MA, Ahn N, Imhof A, Caldas C, Jenuwein T, Esteller M, Nat Genet 2005 37 391 400 10.1038/ng1531 15765097
27. Global histone modification pattern associated with recurrence and disease-free survival in non-small cell lung cancer patients. Song JS, Kim YS, Kim DK, Park SI, Jang SJ, Pathol Int 2012 62 182 190 10.1111/j.1440-1827.2011. 02776.x 22360506
28. Global histone modifications in breast cancer correlate with tumor phenotypes, prognostic factors, and patient outcome. Elsheikh SE, Green AR, Rakha EA, Powe DG, Ahmed RA, Collins HM, Soria D, Garibaldi JM, Paish CE, Ammar AA, Grainge MJ, Ball GR, Abdelghany MK, Martinez-Pomares L, Heery DM, Ellis IO, Cancer Res 2009 69 3802 3809 10.1158/0008-5472.CAN-08-3907 19366799
29. Prognostic significance of global histone modifications in resected squamous cell carcinoma of the esophagus. Tzao C, Tung HJ, Jin JS, Sun GH, Hsu HS, Chen BH, Yu CP, Lee SC, Mod Pathol 2009 22 252 260 10.1038/modpathol.2008. 172 18953329
30. Global levels of specific histone modifications and an epigenetic gene signature predict prostate cancer progression and development. Biano-Miotto T, Chiam K, Buchanan G, Jindal S, Day TK, Thomas M, Pickering MA, O'Loughlin MA, Ryan NK, Raymond WA, Horvath LG, Kench JG, Stricker PD, Marshall VR, Sutherland RL, Henshall SM, Gerald WL, Scher HI, Risbridger GP, Clements JA, Butler LM, Tilley WD, Horsfall DJ, Ricciardelli C, Australian Prostate Cancer BioResource, Cancer Epidemiol Biomarkers Prev 2010 19 2611 2622 10.1158/1055-9965.EPI-10-0555 20841388
31. SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells. Hamamoto R, Furukawa Y, Morita M, Iimura Y, Silva FP, Li M, Yagyu R, Nakamura Y, Nat Cell Biol 2004 6 731 740 10.1038/ncb1151 15235609 (Pubitemid 39144478)
32. Profiling of histone H3 lysine 9 trimethylation levels predicts transcription factor activity and survival in acute myeloid leukemia. Müller-Tidow C, Klein HU, Hascher A, Isken F, Tickenbrock L, Thoennissen N, Agrawal-Singh S, Tschanter P, Disselhoff C, Wang Y, Becker A, Thiede C, Ehninger G, zur Stadt U, Koschmieder S, Seidl M, Müller FU, Schmitz W, Schlenke P, McClelland M, Berdel WE, Dugas M, Serve H, Study Alliance Leukemia, Blood 2010 116 3564 3571 10.1182/blood-2009-09-240978 20498303
33. Relevance of histone marks H3K9me3 and H4K20me3 in cancer. Leszinski G, Gezer U, Siegele B, Stoetzer O, Holdenrieder S, Anticancer Res 2012 32 2199 2205 22593510
34. Global levels of histone modifications predict prognosis in different cancers. Seligson DB, Horvath S, McBrian MA, Mah V, Yu H, Tze S, Wang Q, Chia D, Goodglick L, Kurdistani S, Am J Pathol 2009 174 1619 1628 10.2353/ajpath.2009. 080874 19349354
35. The knock-down of overexpressed EZH2 and BMI-1 does not prevent osteosarcoma growth. Sasaki H, Setoguchi T, Matsunoshita Y, Gao H, Hirotsu M, Komiya S, Oncol Rep 2010 23 677 684 20127006
36. NUP98-NSD1 links H3K36 methylation to Hox-A gene activation and leukaemogenesis. Wang GG, Pasillas MPCL, Kamps MP, Nat Cell Biol 2007 9 804 812 10.1038/ncb1608 17589499 (Pubitemid 47019467)
37. Alterations of global histone H4K20 methylation during prostate carcinogenesis. Behbahani TE, Kahl P, von der Gathen J, Heukamp LC, Baumann C, Gütgemann I, Walter B, Hofstädter F, Bastian PJ, von Ruecker A, Müller SC, Rogenhofer S, Ellinger J, BMC Urol 2012 12 5 10.1186/1471-2490-12-5 22413846
38. Loss of histone H4K20 trimethylation occurs in preneoplasia and influences prognosis of non-small cell lung cancer. Van Den Broeck A, Brambilla E, Moro-Sibilot D, Lantuejoul S, Brambilla C, Eymin B, Khochbin S, Gazzeri S, Clin Cancer Res 2008 14 7237 7245 10.1158/1078-0432.CCR-08-0869 18974389
39. Global H3K27 trimethylation and EZH2 abundance in breast tumor subtypes. Holm K, Grabau D, Lövgren K, Aradottir S, Gruvberger-Saal S, Howlin J, Saal LH, Ethier SP, Bendahl PO, Stål O, Malmström P, Fernö M, Rydén L, Hegardt C, Borg Å Ringnér M, Mol Oncol 2012 6 494 506 10.1016/j.molonc.2012.06.002 22766277
40. TRIM24 links a non-canonical histone signature to breast cancer. Tsai WW, Wang Z, Yiu TT, Akdemir KC, Xia W, Winter S, Tsai CY, Shi X, Schwarzer D, Plunkett W, Aronow B, Gozani O, Fischle W, Hung MC, Patel DJ, Barton MC, Nature 2010 468 927 932 10.1038/nature09542 21164480
41. Lysine succinylation and lysine malonylation in histones. Xie Z, Dai J, Dai L, Tan M, Cheng Z, Wu Y, Boeke JD, Zhao Y, Mol Cell Proteomics 2012 11 100 107 10.1074/mcp.M111.015875 22389435
42. Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Prat A, Parker JS, Karginova O, Fan C, Livasy C, Herschkowitz JI, He X, Perou CM, Breast Cancer Res 2010 12 68 10.1186/bcr2635 20813035
43. Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer. Varambally S, Cao Q, Mani RS, Shankar S, Wang X, Ateeq B, Laxman B, Cao X, Jing X, Ramnarayanan K, Brenner JC, Yu J, Kim JH, Han B, Tan P, Kumar-Sinha C, Lonigro RJ, Palanisamy N, Maher CA, Chinnaiyan AM, Science 2008 322 1695 1699 10.1126/science.1165395 19008416
44. Decreased microRNA-214 levels in breast cancer cells coincides with increased cell proliferation, invasion and accumulation of the Polycomb Ezh2 methyltransferase. Derfoul A, Juan AH, Difilippantonio MJ, Palanisamy N, Ried T, Sartorelli V, Carcinogenesis 2011 32 1607 1614 10.1093/carcin/bgr184 21828058
45. Origins and formation of histone methylation across the human cell cycle. Zee BM, Britton LM, Wolle D, Haberman DM, Garcia BA, Mol Cell Biol 2012 32 2503 2514 10.1128/MCB.06673-11 22547680
46. Novel phosphorylation sites in the S. cerevisiae Cdc13 protein reveal sew targets for telomere length regulation. Wu Y, Dimaggio PA Jr, Perlman DH, Zakian VA, Garcia BA, J Proteome Res 2013 12 316 327 10.1021/pr300408v 23181431