Epigenetics in breast cancer: What's new?

Breast Cancer Research

Volumn 13, Issue 6, 2011, Pages

  Huang, Yi ^a,b   Nayak, Shweta ^b,c   Jankowitz, Rachel ^a,c   Davidson, Nancy E ^a,b   Oesterreich, Steffi ^a,b  

^a UNIVERSITY OF PITTSBURGH CANCER INSTITUTE   (United States)

^b UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

8 HYDROXYGUANINE; BENZAMIDE; BISULFITE; DNA GLYCOSYLTRANSFERASE; DNA TOPOISOMERASE (ATP HYDROLYSING); ENTINOSTAT; HISTONE; HISTONE DEACETYLASE; HISTONE METHYLTRANSFERASE; HYDROGEN PEROXIDE; HYDROXAMIC ACID; LYSINE; LYSINE SPECIFIC DEMETHYLASE 1; METHYLTRANSFERASE; PARGYLINE; RESTRICTION ENDONUCLEASE; ROMIDEPSIN; SHORT CHAIN FATTY ACID; TETRAPEPTIDE; TRANSCRIPTION FACTOR EZH2; TRANYLCYPROMINE; UNCLASSIFIED DRUG; VORINOSTAT;

APOPTOSIS; BREAST CANCER; CANCER INHIBITION; CHROMATIN STRUCTURE; CPG ISLAND; DEMETHYLATION; DISORDERS OF DNA SYNTHESIS AND REPAIR; DNA CONFORMATION; DNA METHYLATION; DNA MODIFICATION; DNA SEQUENCE; DRUG MECHANISM; ENZYME INHIBITION; EPIGENETICS; GENE EXPRESSION; GENE OVEREXPRESSION; GENETIC ASSOCIATION; HISTONE ACETYLATION; HISTONE DEMETHYLATION; HISTONE METHYLATION; HISTONE MODIFICATION; HISTONE PHOSPHORYLATION; HISTONE RIBOSYLATION; HISTONE UBIQUITINATION; HUMAN; IMMUNOPRECIPITATION; PROGNOSIS; RESTRICTION MAPPING; REVIEW; SUMOYLATION; TISSUE MICROARRAY; ACETYLATION; ANIMAL; BREAST TUMOR; FEMALE; GENETIC EPIGENESIS; GENETICS; METABOLISM; METHYLATION;

ACETYLATION; ANIMALS; BREAST NEOPLASMS; DNA METHYLATION; EPIGENESIS, GENETIC; EPIGENOMICS; FEMALE; HISTONES; HUMANS; METHYLATION;

EID: 80755173292     PISSN: 14655411     EISSN: 1465542X     Source Type: Journal    
DOI: 10.1186/bcr2925     Document Type: Review

References (82)

1. Jenuwein T, Allis CD. Translating the histone code. Science 2001, 293:1074-1080. 10.1126/science.1063127, 11498575.
2. Jones PA, Baylin SB. The epigenomics of cancer. Cell 2007, 128:683-692. 10.1016/j.cell.2007.01.029, 17320506.
3. Stearns V, Zhou Q, Davidson NE. Epigenetic regulation as a new target for breast cancer therapy. Cancer Invest 2007, 25:659-665. 10.1080/07357900701719234, 18058459.
4. Minucci S, Pelicci PG. Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat Rev Cancer 2006, 6:38-51. 10.1038/nrc1779, 16397526.
5. Dokmanovic M, Marks PA. Prospects: histone deacetylase inhibitors. J Cell Biochem 2005, 96:293-304. 10.1002/jcb.20532, 16088937.
6. Marks PA, Richon VM, Miller T, Kelly WK. Histone deacetylase inhibitors. Adv Cancer Res 2004, 91:137-168.
7. Ficner R. Novel structural insights into class I and II histone deacetylases. Curr Top Med Chem 2009, 9:235-240. 10.2174/156802609788085304, 19355988.
8. Marson CM. Histone deacetylase inhibitors: design, structure-activity relationships and therapeutic implications for cancer. Anticancer Agents Med Chem 2009, 9:661-692.
9. Khan O, La Thangue NB. Drug Insight: histone deacetylase inhibitor-based therapies for cutaneous T-cell lymphomas. Nat Clin Pract Oncol 2008, 5:714-726. 10.1038/ncponc1238, 18839006.
10. Keen JC, Yan L, Mack KM, Pettit C, Smith D, Sharma D, Davidson NE. A novel histone deacetylase inhibitor, scriptaid, enhances expression of functional estrogen receptor alpha (ER) in ER negative human breast cancer cells in combination with 5-aza 2'-deoxycytidine. Breast Cancer Res Treat 2003, 81:177-186. 10.1023/A:1026146524737, 14620913.
11. Zhou Q, Atadja P, Davidson NE. Histone deacetylase inhibitor LBH589 reactivates silenced estrogen receptor alpha (ER) gene expression without loss of DNA hypermethylation. Cancer Biol Ther 2007, 6:64-69. 10.4161/cbt.6.1.3549, 17172825.
12. Yang X, Ferguson AT, Nass SJ, Phillips DL, Butash KA, Wang SM, Herman JG, Davidson NE. Transcriptional activation of estrogen receptor alpha in human breast cancer cells by histone deacetylase inhibition. Cancer Res 2000, 60:6890-6894.
13. Sharma D, Saxena NK, Davidson NE, Vertino PM. Restoration of tamoxifen sensitivity in estrogen receptor-negative breast cancer cells: tamoxifenbound reactivated ER recruits distinctive corepressor complexes. Cancer Res 2006, 66:6370-6378. 10.1158/0008-5472.CAN-06-0402, 2925469, 16778215.
14. Pathiraja TN, Shetty TB, Jelinek J, He R, Hartmaier R, Margossian AL, Hilsenbeck SG, Issa JP, Oesterreich S. Progesterone receptor isoform-specific promoter methylation - Association of PRA methylation with worse outcome in breast cancer patients. Clin Cancer Res 2011, 17:4177-4186. 10.1158/1078-0432.CCR-10-2950, 21459801.
15. Pruitt K, Zinn RL, Ohm JE, McGarvey KM, Kang SH, Watkins DN, Herman JG, Baylin SB. Inhibition of SIRT1 reactivates silenced cancer genes without loss of promoter DNA hypermethylation. PLoS Genet 2006, 2:e40. 10.1371/journal.pgen.0020040, 1420676, 16596166.
16. ClinicalTrials.gov. , http://clinicaltrials.gov
17. Pathiraja TN, Stearns V, Oesterreich S. Epigenetic regulation in estrogen receptor positive breast cancer - role in treatment response. J Mammary Gland Biol Neoplasia 2010, 15:35-47. 10.1007/s10911-010-9166-0, 2874203, 20101445.
18. Cameron EE, Bachman KE, Myohanen S, Herman JG, Baylin SB. Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nat Genet 1999, 21:103-107. 10.1038/5047, 9916800.
19. Belinsky SA, Klinge DM, Stidley CA, Issa JP, Herman JG, March TH, Baylin SB. Inhibition of DNA methylation and histone deacetylation prevents murine lung cancer. Cancer Res 2003, 63:7089-7093.
20. Belinsky SA, Grimes MJ, Picchi MA, Mitchell HD, Stidley CA, Tesfaigzi Y, Channell MM, Liu Y, Casero RA, Baylin SB, Reed MD, Tellez CS, March TH. Combination therapy with vidaza and entinostat suppresses tumor growth and reprograms the epigenome in an orthotopic lung cancer model. Cancer Res 2011, 71:454-462. 10.1158/0008-5472.CAN-10-3184, 21224363.
21. Fan J, Yin WJ, Lu JS, Wang L, Wu J, Wu FY, Di GH, Shen ZZ, Shao ZM. ER alpha negative breast cancer cells restore response to endocrine therapy by combination treatment with both HDAC inhibitor and DNMT inhibitor. J Cancer Res Clin Oncol 2008, 134:883-890. 10.1007/s00432-008-0354-x, 18264725.
22. Gore SD. Six (or more) drugs in search of a mechanism: DNA methyltransferase and histone deacetylase inhibitors in the treatment of myelodysplastic syndromes. J Natl Compr Canc Netw 2006, 4:83-90.
23. Juergens RA, Vendetti F, Coleman B, Sebree RS, Rudek MA, Belinsky SA, Brock MV, Herman JG, Baylin SB, Rudin CM. Phase I trial of 5-azacitidine (5AC) and SNDX-275 in advanced lung cancer (NSCLC). J Clin Oncol 2008, 26(May 20 suppl):abstract 19036.
24. Martin C, Zhang Y. The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 2005, 6:838-849. 10.1038/nrm1761, 16261189.
25. Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G. Genome regulation by polycomb and trithorax proteins. Cell 2007, 128:735-745. 10.1016/j.cell.2007.02.009, 17320510.
26. Baylin S, Ohm J. Epigenetic gene silencing in cancer - a mechanism for early oncogenic pathway addiction?. Nat Rev Cancer 2006, 6:107-116. 10.1038/nrc1799, 16491070.
27. Kuzmichev A, Margueron R, Vaquero A, Preissner TS, Scher M, Kirmizis A, Ouyang X, Brockdorff N, Abate-Shen C, Farnham P, Reinberg D. Composition and histone substrates of polycomb repressive group complexes change during cellular differentiation. Proc Natl Acad Sci USA 2005, 102:1859-1864. 10.1073/pnas.0409875102, 548563, 15684044.
28. van der Vlag J, Otte AP. Transcriptional repression mediated by the human polycomb-group protein EED involves histone deacetylation. Nat Genet 1999, 23:474-478. 10.1038/70602, 10581039.
29. Kleer CG, Cao Q, Varambally S, Shen R, Ota I, Tomlins SA, Ghosh D, Sewalt RG, Otte AP, Hayes DF, Sabel MS, Livant D, Weiss SJ, Rubin MA, Chinnaiyan AM. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Sci USA 2003, 100:11606-11611. 10.1073/pnas.1933744100, 208805, 14500907.
30. Collett K, Eide GE, Arnes J, Stefansson IM, Eide J, Braaten A, Aas T, Otte AP, Akslen LA. Expression of enhancer of zeste homologue 2 is significantly associated with increased tumor cell proliferation and is a marker of aggressive breast cancer. Clin Cancer Res 2006, 12:1168-1174. 10.1158/1078-0432.CCR-05-1533, 16489070.
31. Bachmann IM, Halvorsen OJ, Collett K, Stefansson IM, Straume O, Haukaas SA, Salvesen HB, Otte AP, Akslen LA. EZH2 expression is associated with high proliferation rate and aggressive tumor subgroups in cutaneous melanoma and cancers of the endometrium, prostate, and breast. J Clin Oncol 2006, 24:268-273.
32. Chang CJ, Yang JY, Xia W, Chen CT, Xie X, Chao CH, Woodward WA, Hsu JM, Hortobagyi GN, Hung MC. EZH2 promotes expansion of breast tumor initiating cells through activation of RAF1-beta-catenin signaling. Cancer Cell 2011, 19:86-100. 10.1016/j.ccr.2010.10.035, 21215703.
33. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 2004, 119:941-953. 10.1016/j.cell.2004.12.012, 15620353.
34. Lee MG, Wynder C, Cooch N, Shiekhattar R. An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature 2005, 437:432-435.
35. Lim S, Janzer A, Becker A, Zimmer A, Schule R, Buettner R, Kirfel J. Lysine-specific demethylase 1 (LSD1) is highly expressed in ER-negative breast cancers and a biomarker predicting aggressive biology. Carcinogenesis 2010, 31:512-520. 10.1093/carcin/bgp324, 20042638.
36. Garcia-Bassets I, Kwon YS, Telese F, Prefontaine GG, Hutt KR, Cheng CS, Ju BG, Ohgi KA, Wang J, Escoubet-Lozach L, Rose DW, Glass CK, Fu XD, Rosenfeld MG. Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell 2007, 128:505-518. 10.1016/j.cell.2006.12.038, 1994663, 17289570.
37. Perillo B, Ombra MN, Bertoni A, Cuozzo C, Sacchetti S, Sasso A, Chiariotti L, Malorni A, Abbondanza C, Avvedimento EV. DNA oxidation as triggered by H3K9me2 demethylation drives estrogen-induced gene expression. Science 2008, 319:202-206. 10.1126/science.1147674, 18187655.
38. Huang Y, Vasilatos SN, Boric L, Shaw PG, Davidson NE. Inhibitors of histone demethylation and histone deacetylation cooperate in regulating gene expression and inhibiting growth in human breast cancer cells. Breast Cancer Res Treat 2011, [Epub ahead of print].
39. Huang J, Sengupta R, Espejo AB, Lee MG, Dorsey JA, Richter M, Opravil S, Shiekhattar R, Bedford MT, Jenuwein T, Berger SL. p53 is regulated by the lysine demethylase LSD1. Nature 2007, 449:105-108. 10.1038/nature06092, 17805299.
40. Wang J, Hevi S, Kurash JK, Lei H, Gay F, Bajko J, Su H, Sun W, Chang H, Xu G, Gaudet F, Li E, Chen T. The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation. Nat Genet 2009, 41:125-129. 10.1038/ng.268, 19098913.
41. Schulte JH, Lim S, Schramm A, Friedrichs N, Koster J, Versteeg R, Ora I, Pajtler K, Klein-Hitpass L, Kuhfittig-Kulle S, Metzger E, Schule R, Eggert A, Buettner R, Kirfel J. Lysine-specific demethylase 1 is strongly expressed in poorly differentiated neuroblastoma: implications for therapy. Cancer Res 2009, 69:2065-2071.
42. Klose RJ, Yamane K, Bae Y, Zhang D, Erdjument-Bromage H, Tempst P, Wong J, Zhang Y. The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 2006, 442:312-316. 10.1038/nature04853, 16732292.
43. Yamane K, Toumazou C, Tsukada Y, Erdjument-Bromage H, Tempst P, Wong J, Zhang Y. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 2006, 125:483-495. 10.1016/j.cell.2006.03.027, 16603237.
44. Chen Z, Zang J, Whetstine J, Hong X, Davrazou F, Kutateladze TG, Simpson M, Mao Q, Pan CH, Dai S, Hagman J, Hansen K, Shi Y, Zhang G. Structural insights into histone demethylation by JMJD2 family members. Cell 2006, 125:691-702. 10.1016/j.cell.2006.04.024, 16677698.
45. Yamane K, Tateishi K, RKlose RJ, Fang J, Fabrizio LA, Erdjument-Bromage H, Taylor-Papadimitriou J, Tempst P, Zhang Y. PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. Mol Cell 2007, 25:801-812. 10.1016/j.molcel.2007.03.001, 17363312.
46. Sharma SV, Lee DY, Li B, Quinlan MP, Takahashi F, Maheswaran S, McDermott U, Azizian N, Zou L, Fischbach MA, Wong KK, Brandstetter K, Wittner B, Ramaswamy S, Classon M, Settleman J. A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell 2010, 141:69-80. 10.1016/j.cell.2010.02.027, 2851638, 20371346.
47. Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, Zeng T, Senz J, McConechy MK, Anglesio MS, Kalloger SE, Yang W, Heravi-Moussavi A, Giuliany R, Chow C, Fee J, Zayed A, Prentice L, Melnyk N, Turashvili G, Delaney AD, Madore J, Yip S, McPherson AW, Ha G, Bell L, Fereday S, Tam A, Galletta L, Tonin PN, Provencher D, Miller D, Jones SJ, Moore RA, Morin GB, Oloumi A, Boyd N, Aparicio SA, Shih Ie M, Mes-Masson AM, Bowtell DD, Hirst M, Gilks B, Marra MA, Huntsman DG. ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med 2010, 363:1532-1543. 10.1056/NEJMoa1008433, 2976679, 20942669.
48. Greiner D, Bonaldi T, Eskeland R, Roemer E, Imhof A. Identification of a specific inhibitor of the histone methyltransferase SU(VAR)3-9. Nat Chem Biol 2005, 1:143-145.
49. Tan J, Yang X, Zhuang L, Jiang X, Chen W, Lee PL, Karuturi RK, Tan PB, Liu ET, Yu Q. Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. Genes Dev 2007, 21:1050-1063. 10.1101/gad.1524107, 1855231, 17437993.
50. Hamamoto R, Silva FP, Tsuge M, Nishidate T, Katagiri T, Nakamura Y, Furukawa Y. Enhanced SMYD3 expression is essential for the growth of breast cancer cells. Cancer Sci 2006, 97:113-118. 10.1111/j.1349-7006.2006.00146.x, 16441421.
51. Luo XG, Zou JN, Wang SZ, Zhang TC, Xi T. Novobiocin decreases SMYD3 expression and inhibits the migration of MDA-MB-231 human breast cancer cells. IUBMB Life 2010, 62:194-199.
52. Lee M, Wynder C, Schmidt D, McCafferty D, Shiekhattar R. Histone H3 lysine 4 demethylation is a target of nonselective antidepressive medications. Chem Biol 2006, 13:563-567. 10.1016/j.chembiol.2006.05.004, 16793513.
53. Metzger E, Wissmann M, Yin N, Muller J, Schneider R, Peters A, Gunther T, Buettner R, Schule R. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature 2005, 437:436-439.
54. Huang Y, Greene E, Stewart TM, Goodwin AC, Baylin SB, Woster PM, Casero RA. Inhibition of lysine-specific demethylase 1 by polyamine analogues results in reexpression of aberrantly silenced genes. Proc Natl Acad Sci USA 2007, 104:8023-8028. 10.1073/pnas.0700720104, 1857229, 17463086.
55. Huang Y, Stewart TM, Wu Y, Baylin SB, Marton LJ, Perkins B, ones RJ, Woster PM Casero JRA. Novel oligoamine analogues inhibit lysine-specific demethylase 1 and induce reexpression of epigenetically silenced genes. Clin Cancer Res 2009, 15:7217-7228. 10.1158/1078-0432.CCR-09-1293, 2927136, 19934284.
56. Zhu Q, Huang Y, Marton LJ, Woster PM, Davidson NE, Casero RA. Polyamine analogs modulate gene expression by inhibiting lysine-specific demethylase 1 (LSD1) and altering chromatin structure in human breast cancer cells. Amino Acids 2011, [Epub ahead of print].
57. Chen Z, Zang J, Kappler J, Hong X, Crawford F, Wang Q, Lan F, Jiang C, Whetstine J, Dai S, Hansen K, Shi Y, Zhang G. Structural basis of the recognition of a methylated histone tail by JMJD2A. Proc Natl Acad Sci USA 2007, 104:10818-10823. 10.1073/pnas.0704525104, 1891149, 17567753.
58. Holm K, Hegardt C, Staaf J, Vallon-Christersson J, Jonsson G, Olsson H, Borg A, Ringner M. Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast Cancer Res 2010, 12:R36. 10.1186/bcr2590, 2917031, 20565864.
59. Pathiraja TN, Stearns V, Oesterreich S. Epigenetic regulation in estrogen receptor positive breast cancer - role in treatment response. J Mammary Gland Biol Neoplasia 2010, 15:35-47. 10.1007/s10911-010-9166-0, 2874203, 20101445.
60. Catteau A, Morris JR. BRCA1 methylation: a significant role in tumour development?. Semin Cancer Biol 2002, 12:359-371. 10.1016/S1044-579X(02)00056-1, 12191635.
61. Esteller M, Silva JM, Dominguez G, Bonilla F, Matias-Guiu X, Lerma E, Bussaglia E, Prat J, Harkes IC, Repasky EA, Gabrielson E, Schutte M, Baylin SB, Herman JG. Promoter hypermethylation and BRCA1 inactivation in sporadic breast and ovarian tumors. J Natl Cancer Inst 2000, 92:564-569. 10.1093/jnci/92.7.564, 10749912.
62. Ordway JM, Budiman MA, Korshunova Y, Maloney RK, Bedell JA, Citek RW, Bacher B, Peterson S, Rohlfing T, Hall J, Brown R, Lakey N, Doerge RW, Martienssen RA, Leon J, McPherson JD, Jeddeloh JA. Identification of novel high-frequency DNA methylation changes in breast cancer. PLoS One 2007, 2:e1314. 10.1371/journal.pone.0001314, 2117343, 18091988.
63. Korshunova Y, Maloney RK, Lakey N, Citek RW, Bacher B, Budiman A, Ordway JM, McCombie WR, Leon J, Jeddeloh JA, McPherson JD. Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA. Genome Res 2008, 18:19-29. 2134785, 18032725.
64. Ruike Y, Imanaka Y, Sato F, Shimizu K, Tsujimoto G. Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. BMC Genomics 2010, 11:137. 10.1186/1471-2164-11-137, 2838848, 20181289.
65. Fang F, Turcan S, Rimner A, Kaufman A, Giri D, Morris LG, Shen R, Seshan V, Mo Q, Heguy A, Baylin SB, Ahuja N, Viale A, Massague J, Norton L, Vahdat LT, Moynahan ME, Chan TA. Breast cancer methylomes establish an epigenomic foundation for metastasis. Sci Transl Med 2011, 3:75ra25. 10.1126/scitranslmed.3001875, 3146366, 21430268.
66. Sproul D, Nestor C, Culley J, Dickson JH, Dixon JM, Harrison DJ, Meehan RR, Sims AH, Ramsahoye BH. Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer. Proc Natl Acad Sci USA 2011, 108:4364-4369. 10.1073/pnas.1013224108, 3060255, 21368160.
67. International Human Epigenome Consortium. , http://www.ihec-epigenomes.org
68. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462:315-322. 10.1038/nature08514, 2857523, 19829295.
69. Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods 2010, 7:47-49. 10.1038/nmeth.1404, 2862482, 19946276.
70. Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 2010, 28:817-825. 10.1038/nbt.1662, 2919626, 20657582.
71. Bock C, Tomazou EM, Brinkman AB, Muller F, Simmer F, Gu H, Jager N, Gnirke A, Stunnenberg HG, Meissner A. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 2010, 28:1106-1114. 10.1038/nbt.1681, 3066564, 20852634.
72. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 2010, 28:1097-1105. 10.1038/nbt.1682, 2955169, 20852635.
73. Dickinson LA, Dickinson CD, Kohwi-Shigematsu T. An atypical homeodomain in SATB1 promotes specific recognition of the key structural element in a matrix attachment region. J Biol Chem 1997, 272:11463-11470. 10.1074/jbc.272.17.11463, 9111059.
74. de Belle I, Cai S, Kohwi-Shigematsu T. The genomic sequences bound to special AT-rich sequence-binding protein 1 (SATB1) in vivo in Jurkat T cells are tightly associated with the nuclear matrix at the bases of the chromatin loops. J Cell Biol 1998, 141:335-348. 10.1083/jcb.141.2.335, 2148460, 9548713.
75. Alvarez JD, Yasui DH, Niida H, Joh T, Loh DY, ohwi-Shigematsu T. The MAR-binding protein SATB1 orchestrates temporal and spatial expression of multiple genes during T-cell development. Genes Dev 2000, 14:521-535. 316425, 10716941.
76. Han HJ, Russo J, Kohwi Y, Kohwi-Shigematsu T. SATB1 reprogrammes gene expression to promote breast tumour growth and metastasis. Nature 2008, 452:187-193. 10.1038/nature06781, 18337816.
77. Iorns E, Hnatyszyn HJ, Seo P, Clarke J, Ward T, Lippman M. The role of SATB1 in breast cancer pathogenesis. J Natl Cancer Inst 2010, 102:1284-1296. 10.1093/jnci/djq243, 20595686.
78. Cai S, Lee CC, Kohwi-Shigematsu T. SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes. Nat Genet 2006, 38:1278-1288. 10.1038/ng1913, 17057718.
79. Elsasser SJ, Allis CD, Lewis PW. Cancer. New epigenetic drivers of cancers. Science 2011, 331:1145-1146. 10.1126/science.1203280, 21385704.
80. Roadmap Epigenomics Project. , http://www.roadmapepigenomics.org/data
81. Milosavljevic A. Putting epigenome comparison into practice. Nat Biotechnol 2010, 28:1053-1056. 10.1038/nbt1010-1053, 20944597.
82. The Cancer Genome Atlas Data Portal. , http://tcga-data.nci.nih.gov/tcga/