A co-ordinated interaction between CTCF and ER in breast cancer cells

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Ross Innes, Caryn S ^a,b   Brown, Gordon D ^a   Carroll, Jason S ^a,b  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ESTROGEN; ESTROGEN RECEPTOR; HEPATOCYTE NUCLEAR FACTOR 3ALPHA; TAMOXIFEN; TRANSCRIPTION FACTOR CTCF; CCCTC-BINDING FACTOR; FOXA1 PROTEIN, HUMAN; REPRESSOR PROTEIN;

ARTICLE; BREAST CANCER; CANCER CELL; CELL STRAIN MCF 7; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; ESTROGEN BINDING; ESTROGEN RESPONSIVE ELEMENT; GENE EXPRESSION REGULATION; GENE LOCUS; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; PROTEIN LOCALIZATION; TRANSCRIPTION REGULATION; BREAST TUMOR; FEMALE; GENETICS; METABOLISM; PROTEIN BINDING; TUMOR CELL LINE;

BREAST NEOPLASMS; CELL LINE, TUMOR; ESTROGENS; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HEPATOCYTE NUCLEAR FACTOR 3-ALPHA; HUMANS; PROTEIN BINDING; RECEPTORS, ESTROGEN; REPRESSOR PROTEINS; TAMOXIFEN;

EID: 82655189429     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-593     Document Type: Article

References (41)

1. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS, Brown M. Genome-wide analysis of estrogen receptor binding sites. Nat Genet 2006, 38(11):1289-1297. 10.1038/ng1901, 17013392.
2. Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, Bourque G, Wei CL, Liu ET. Whole-Genome Cartography of Estrogen Receptor alpha Binding Sites. PLoS Genet 2007, 3(6):e87. 10.1371/journal.pgen.0030087, 1885282, 17542648.
3. Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA, Brown M. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 2005, 122(1):33-43. 10.1016/j.cell.2005.05.008, 16009131.
4. Laganiere J, Deblois G, Lefebvre C, Bataille AR, Robert F, Giguere V. Location analysis of estrogen receptor alpha target promoters reveals that FOXA1 defines a domain of the estrogen response. Proc Natl Acad Sci USA 2005, 102(33):11651-11656. 10.1073/pnas.0505575102, 1183449, 16087863.
5. Hurtado A, Holmes KA, Ross-Innes CS, Schmidt D, Carroll JS. FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nat Genet 2011, 43(1):27-33. 10.1038/ng.730, 3024537, 21151129.
6. Barnett DH, Sheng S, Charn TH, Waheed A, Sly WS, Lin CY, Liu ET, Katzenellenbogen BS. Estrogen receptor regulation of carbonic anhydrase XII through a distal enhancer in breast cancer. Cancer Res 2008, 68(9):3505-3515. 10.1158/0008-5472.CAN-07-6151, 18451179.
7. Pan YF, Wansa KD, Liu MH, Zhao B, Hong SZ, Tan PY, Lim KS, Bourque G, Liu ET, Cheung E. Regulation of estrogen receptor-mediated long range transcription via evolutionarily conserved distal response elements. J Biol Chem 2008, 283(47):32977-32988. 10.1074/jbc.M802024200, 18728018.
8. Filippova GN, Fagerlie S, Klenova EM, Myers C, Dehner Y, Goodwin G, Neiman PE, Collins SJ, Lobanenkov VV. An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes. Mol Cell Biol 1996, 16(6):2802-2813. 231272, 8649389.
9. Klenova EM, Nicolas RH, Paterson HF, Carne AF, Heath CM, Goodwin GH, Neiman PE, Lobanenkov VV. CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms. Mol Cell Biol 1993, 13(12):7612-7624. 364833, 8246978.
10. Lobanenkov VV, Nicolas RH, Adler VV, Paterson H, Klenova EM, Polotskaja AV, Goodwin GH. A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5'-flanking sequence of the chicken c-myc gene. Oncogene 1990, 5(12):1743-1753.
11. Vostrov AA, Quitschke WW. The zinc finger protein CTCF binds to the APBbeta domain of the amyloid beta-protein precursor promoter. Evidence for a role in transcriptional activation. J Biol Chem 1997, 272(52):33353-33359. 10.1074/jbc.272.52.33353, 9407128.
12. Awad TA, Bigler J, Ulmer JE, Hu YJ, Moore JM, Lutz M, Neiman PE, Collins SJ, Renkawitz R, Lobanenkov VV, Filippova GN. Negative transcriptional regulation mediated by thyroid hormone response element 144 requires binding of the multivalent factor CTCF to a novel target DNA sequence. J Biol Chem 1999, 274(38):27092-27098. 10.1074/jbc.274.38.27092, 10480923.
13. Burcin M, Arnold R, Lutz M, Kaiser B, Runge D, Lottspeich F, Filippova GN, Lobanenkov VV, Renkawitz R. Negative protein 1, which is required for function of the chicken lysozyme gene silencer in conjunction with hormone receptors, is identical to the multivalent zinc finger repressor CTCF. Mol Cell Biol 1997, 17(3):1281-1288. 231853, 9032255.
14. Bell AC, West AG, Felsenfeld G. The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell 1999, 98(3):387-396. 10.1016/S0092-8674(00)81967-4, 10458613.
15. Kanduri C, Pant V, Loukinov D, Pugacheva E, Qi CF, Wolffe A, Ohlsson R, Lobanenkov VV. Functional association of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive. Curr Biol 2000, 10(14):853-856. 10.1016/S0960-9822(00)00597-2, 10899010.
16. Filippova GN, Cheng MK, Moore JM, Truong JP, Hu YJ, Nguyen DK, Tsuchiya KD, Disteche CM. Boundaries between chromosomal domains of X inactivation and escape bind CTCF and lack CpG methylation during early development. Dev Cell 2005, 8(1):31-42. 10.1016/j.devcel.2004.10.018, 15669143.
17. Botta M, Haider S, Leung IX, Lio P, Mozziconacci J. Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide. Mol Syst Biol 2010, 6:426. 3010120, 21045820.
18. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129(4):823-837. 10.1016/j.cell.2007.05.009, 17512414.
19. Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007, 128(6):1231-1245. 10.1016/j.cell.2006.12.048, 2572726, 17382889.
20. Schmidt D, Schwalie PC, Ross-Innes CS, Hurtado A, Brown GD, Carroll JS, Flicek P, Odom DT. A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res 2010, 20(5):578-588. 10.1101/gr.100479.109, 2860160, 20219941.
21. Ross-Innes CS, Stark R, Holmes KA, Schmidt D, Spyrou C, Russell R, Massie CE, Vowler SL, Eldridge M, Carroll JS. Cooperative interaction between retinoic acid receptor-alpha and estrogen receptor in breast cancer. Genes Dev 2010, 24(2):171-182. 10.1101/gad.552910, 2807352, 20080953.
22. Welboren WJ, van Driel MA, Janssen-Megens EM, van Heeringen SJ, Sweep FC, Span PN, Stunnenberg HG. ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands. Embo J 2009, 28(10):1418-1428. 10.1038/emboj.2009.88, 2688537, 19339991.
23. Chan CS, Song JS. CCCTC-binding factor confines the distal action of estrogen receptor. Cancer Res 2008, 68(21):9041-9049. 10.1158/0008-5472.CAN-08-2632, 18974150.
24. Zhang Y, Liang J, Li Y, Xuan C, Wang F, Wang D, Shi L, Zhang D, Shang Y. CCCTC-binding factor acts upstream of FOXA1 and demarcates the genomic response to estrogen. J Biol Chem 2010, 285(37):28604-28613. 10.1074/jbc.M110.149658, 2937886, 20610384.
25. Bell AC, Felsenfeld G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 2000, 405(6785):482-485. 10.1038/35013100, 10839546.
26. Deschenes J, Bourdeau V, White JH, Mader S. Regulation of GREB1 transcription by estrogen receptor alpha through a multipartite enhancer spread over 20 kb of upstream flanking sequences. J Biol Chem 2007, 282(24):17335-17339. 10.1074/jbc.C700030200, 17463000.
27. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based Analysis of ChIP-Seq (MACS). Genome Biol 2008, 9(9):R137. 10.1186/gb-2008-9-9-r137, 2592715, 18798982.
28. Hua S, Kittler R, White KP. Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell 2009, 137(7):1259-1271. 10.1016/j.cell.2009.04.043, 19563758.
29. Bickel PJ, Boley N, Brown JB, Huang H, Zhang NR. Subsampling methods for genomic inference. Annals of applied statistics 2010, 4(6):1660-1697.
30. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447(7146):799-816. 10.1038/nature05874, 2212820, 17571346.
31. Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 2009, 462(7269):58-64. 10.1038/nature08497, 2774924, 19890323.
32. Soule HD, Maloney TM, Wolman SR, Peterson WD, Brenz R, McGrath CM, Russo J, Pauley RJ, Jones RF, Brooks SC. Isolation and characterization of a spontaneously immortalized human breast epithelial cell line, MCF-10. Cancer Res 1990, 50(18):6075-6086.
33. Lutz M, Baniahmad A, Renkawitz R. Modulation of thyroid hormone receptor silencing function by co-repressors and a synergizing transcription factor. Biochem Soc Trans 2000, 28(4):386-389. 10.1042/0300-5127:0280386, 10961925.
34. Kanduri M, Kanduri C, Mariano P, Vostrov AA, Quitschke W, Lobanenkov V, Ohlsson R. Multiple nucleosome positioning sites regulate the CTCF-mediated insulator function of the H19 imprinting control region. Mol Cell Biol 2002, 22(10):3339-3344. 10.1128/MCB.22.10.3339-3344.2002, 133793, 11971967.
35. Davey C, Fraser R, Smolle M, Simmen MW, Allan J. Nucleosome positioning signals in the DNA sequence of the human and mouse H19 imprinting control regions. J Mol Biol 2003, 325(5):873-887. 10.1016/S0022-2836(02)01340-2, 12527297.
36. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 2009, 48(3):240-248. 10.1016/j.ymeth.2009.03.001, 19275939.
37. Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11(8):R86. 10.1186/gb-2010-11-8-r86, 2945788, 20738864.
38. Saldanha AJ. Java Treeview--extensible visualization of microarray data. Bioinformatics 2004, 20(17):3246-3248. 10.1093/bioinformatics/bth349, 15180930.
39. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:Article3.
40. Benjamini Y, Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Royal Stat Soc B 1995, 57:289-300.
41. Fisher RA. On the Interpretation of χ2 from Contingency Tables, and the Calculation of P. Journal of the Royal Statistical Society 1922, 85(1):87-94.