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Estrogen Receptor-Mediated Gene Transcription and Cistrome

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Estrogen Receptor and Breast Cancer

Abstract

The discovery of the estrogen receptor 60 years ago radically transformed the field of hormonal signaling and led to the recognition of ER as a prototype nuclear receptor that primarily functions as a transcription factor. In this chapter, we will first describe the conserved domain architecture of ER and its regulation through various modifications by diverse intracellular pathways. We will then discuss the history and most recent advancement in the understanding of ER regulation of target genes at both individual gene and whole genome levels. A number of new concepts emanated from these studies, including ER cistrome, pioneer factors, chromosome looping and enhancer RNA, etc. and their potential impact on the fight against breast cancer therapeutic resistance all will be discussed in detail in this chapter.

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References

  1. Jensen EV (1958) Studies of growth phenomena using tritium-labeled steroids. In: Proc. 4th Int. Congress of Biochem, vol 15. Pergamon Press, Vienna, p 119

    Google Scholar 

  2. Jensen EV, Jacobson H (1962) Basic guides to the mechanism of estrogen action. Recent Prog Horm Res 18:318–414

    Google Scholar 

  3. Jensen EV (2005) The contribution of “alternative approaches” to understanding steroid hormone action. Mol Endocrinol 19:1439–1442. https://doi.org/10.1210/me.2005-0154

    Article  CAS  PubMed  Google Scholar 

  4. Jensen EV (2004) From chemical warfare to breast cancer management. Nat Med 10:1018–1021

    Article  CAS  PubMed  Google Scholar 

  5. O’Malley BW, McGuire WL (1968) Studies on the mechanism of estrogen-mediated tissue differentiation: regulation of nuclear transcription and induction of new RNA species. Proc Natl Acad Sci U S A 60:1527–1534. https://doi.org/10.1073/pnas.60.4.1527

    Article  PubMed  PubMed Central  Google Scholar 

  6. O’Malley BW, McGuire W, Middleton P (1968) Altered gene expression during differentiation: population changes in hybridizable RNA after stimulation of the chick oviduct with oestrogen. Nature 218:1249–1251

    Article  PubMed  Google Scholar 

  7. Greene GL, Gilna P, Waterfield M, Baker A, Hort Y, Shine J (1986) Sequence and expression of human estrogen receptor complementary DNA. Science 231:1150–1154

    Article  CAS  PubMed  Google Scholar 

  8. Green S, Walter P, Kumar V, Krust A, Bornert J-M, Argos P, Chambon P (1986) Human oestrogen receptor cDNA: sequence, expression and homology to v-erb-A. Nature 320:134–139

    Article  CAS  PubMed  Google Scholar 

  9. O’Malley BW, Khan S (2013) Elwood V. Jensen (1920-2012): father of the nuclear receptors. Proc Natl Acad Sci 110:3707–3708. https://doi.org/10.1073/pnas.1301566110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Lavery DN, Mcewan IJ (2005) Structure and function of steroid receptor AF1 transactivation domains: induction of active conformations. Biochem J 391:449–464. https://doi.org/10.1042/BJ20050872

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Yaşar P, Ayaz G, User SD, Güpür G, Muyan M (2017) Molecular mechanism of estrogen–estrogen receptor signaling. Reprod Med Biol 16:4–20. https://doi.org/10.1002/rmb2.12006

    Article  CAS  PubMed  Google Scholar 

  12. Schwabe JW, Chapman L, Finch JT, Rhodes D (1993) The crystal structure of the estrogen-receptor DNA-binding domain bound to DNA - how receptors discriminate between their response elements. Cell 75:567–576. https://doi.org/10.1016/0092-8674(93)90390-C

    Article  CAS  PubMed  Google Scholar 

  13. Mader S, Chambon P, White JH (1993) Defining a minimal estrogen receptor DNA binding domain. Nucleic Acids Res 21:1125–1132. https://doi.org/10.1093/nar/21.5.1125

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Leclercq G, Lacroix M, Laïos I, Laurent G (2006) Estrogen receptor alpha: impact of ligands on intracellular shuttling and turnover rate in breast cancer cells. Curr Cancer Drug Targets 6:39–64. https://doi.org/10.2174/156800906775471716

    Article  CAS  PubMed  Google Scholar 

  15. Zwart W, de Leeuw R, Rondaij M, Neefjes J, Mancini MA, Michalides R (2010) The hinge region of the human estrogen receptor determines functional synergy between AF-1 and AF-2 in the quantitative response to estradiol and tamoxifen. J Cell Sci 123:1253–1261. https://doi.org/10.1242/jcs.061135

    Article  CAS  PubMed  Google Scholar 

  16. Echeverria PC, Picard Didier D (2010) Molecular chaperones, essential partners of steroid hormone receptors for activity and mobility. Biochim Biophys Acta, Mol Cell Res 1803:641–649. https://doi.org/10.1016/j.bbamcr.2009.11.012

    Article  CAS  PubMed  Google Scholar 

  17. Kumar R, Zakharov MN, Khan SH, Miki R, Jang H, Toraldo G, Singh R, Bhasin S, Jasuja R (2011) The dynamic structure of the estrogen receptor. J Amino Acids 2011:1. https://doi.org/10.4061/2011/812540

    Article  CAS  Google Scholar 

  18. Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, Agard DA, Greene GL (1998) The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 95:927–937. https://doi.org/10.1016/S0092-8674(00)81717-1

    Article  CAS  PubMed  Google Scholar 

  19. Montano MM, Müller V, Trobaugh A, Katzenellenbogen BS (1995) The carboxy-terminal F domain of the human estrogen receptor: role in the transcriptional activity of the receptor and the effectiveness of antiestrogens as estrogen antagonists. Mol Endocrinol 9:814–825

    CAS  PubMed  Google Scholar 

  20. Patel SR, Skafar DF (2015) Modulation of nuclear receptor activity by the F domain. Mol Cell Endocrinol 418:298–305. https://doi.org/10.1016/j.mce.2015.07.009

    Article  CAS  PubMed  Google Scholar 

  21. Ali S, Metzger D, Bornert J, Chambon P (1993) Modulation of transcriptional activation by ligand-dependent phosphorylation of the human oestrogen receptor A/B region. EMBO J 12:1153–1160. https://doi.org/10.1002/j.1460-2075.1993.tb05756.x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Bunone G, Briand PA, Miksicek RJ, Picard D (1996) Activation of the unliganded estrogen receptor by EGF involves the MAP kinase pathway and direct phosphorylation. EMBO J 15:2174–2183. https://doi.org/10.1016/j.jsbmb.2015.07.018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Le Romancer M, Poulard C, Cohen P, Sentis SP, Renoir JM, Corbo L (2011) Cracking the estrogen receptor’s posttranslational code in breast tumors. Endocr Rev 32:597–622. https://doi.org/10.1210/er.2010-0016

    Article  CAS  PubMed  Google Scholar 

  24. Sheeler C, Singleton DW, Khan SA (2003) Mutation of serines 104, 106, and 118 inhibits dimerization of the human estrogen receptor in yeast. Endocr Res 29:237–255

    Article  CAS  PubMed  Google Scholar 

  25. Ward RD, Weigel NL (2009) Steroid receptor phosphorylation: assigning function to site-specific phosphorylation. Biofactors 35:528–536. https://doi.org/10.1002/biof.66

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Chen D, Pace PE, Coombes RC, Ali S (1999) Phosphorylation of human estrogen receptor alpha by protein kinase A regulates dimerization. Mol Cell Biol 19:1002–1015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Shindo S, Sakuma T, Negishi M, Squires J (2012) Phosphorylation of serine 212 confers novel activity to human estrogen receptor α. Steroids 77:448–453. https://doi.org/10.1016/j.steroids.2012.01.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Anbalagan M, Rowan BG (2015) Estrogen receptor alpha phosphorylation and its functional impact in human breast cancer. Mol Cell Endocrinol 418:264–272. https://doi.org/10.1016/j.mce.2015.01.016

    Article  CAS  PubMed  Google Scholar 

  29. Cui Y, Zhang M, Pestell R, Curran EM, Welshons WV, Fuqua SAW (2004) Phosphorylation of estrogen receptor α blocks its acetylation and regulates estrogen sensitivity. Cancer Res 64:9199–9208. https://doi.org/10.1158/0008-5472.CAN-04-2126

    Article  CAS  PubMed  Google Scholar 

  30. Atsriku C, Britton DJ, Held JM, Schilling B, Scott GK, Gibson BW, Benz CC, Baldwin MA (2009) Systematic mapping of posttranslational modifications in human estrogen receptor-alpha with emphasis on novel phosphorylation sites. Mol Cell Proteomics 8:467–480. https://doi.org/10.1074/mcp.M800282-MCP200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Tecalco-Cruz AC, Ramírez-Jarquín JO (2017) Mechanisms that increase stability of estrogen receptor alpha in breast cancer. Clin Breast Cancer 17:1–10. https://doi.org/10.1016/j.clbc.2016.07.015

    Article  CAS  PubMed  Google Scholar 

  32. Nawaz Z, Lonard DM, Dennis AP, Smith CL, O’Malley BW (1999) Proteasome-dependent degradation of the human estrogen receptor. Proc Natl Acad Sci U S A 96:1858–1862. https://doi.org/10.1073/pnas.96.5.1858

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Lonard DM, Nawaz Z, Smith CL, O’Malley BW (2000) The 26S proteasome is required for estrogen receptor-alpha and coactivator turnover and for efficient estrogen receptor-alpha transactivation. Mol Cell 5:939–948. https://doi.org/10.1016/S1097-2765(00)80259-2

    Article  CAS  PubMed  Google Scholar 

  34. Métivier R, Penot G, Hübner MR, Reid G, Brand H, Koš M, Gannon F (2003) Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115:751–763. https://doi.org/10.1016/S0092-8674(03)00934-6

    Article  PubMed  Google Scholar 

  35. Shang Y, Hu X, DiRenzo J, Lazar MA, Brown M (2000) Cofactor dynamics and sufficiency in estrogen receptor–regulated transcription. Cell 103:843–852. https://doi.org/10.1016/S0092-8674(00)00188-4

    Article  CAS  PubMed  Google Scholar 

  36. Reid G, Hübner MR, Métivier R, Brand H, Denger S, Manu D, Beaudouin J, Ellenberg J, Gannon F (2003) Cyclic, proteasome-mediated turnover of unliganded and liganded ERα on responsive promoters is an integral feature of estrogen signaling. Mol Cell 11:695–707. https://doi.org/10.1016/S1097-2765(03)00090-X

    Article  CAS  PubMed  Google Scholar 

  37. Berry NB, Fan M, Nephew KP (2008) Estrogen receptor-α hinge-region lysines 302 and 303 regulate receptor degradation by the proteasome. Mol Endocrinol 22:1535–1551. https://doi.org/10.1210/me.2007-0449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Duong V, Boulle N, Daujat S, Chauvet J, Bonnet S, Neel H, Cavaillès V (2007) Differential regulation of estrogen receptor α turnover and transactivation by Mdm2 and stress-inducing agents. Cancer Res 67:5513–5521. https://doi.org/10.1158/0008-5472.CAN-07-0967

    Article  CAS  PubMed  Google Scholar 

  39. Li L, Li Z, Howley PM, Sacks DB (2006) E6AP and calmodulin reciprocally regulate estrogen receptor stability. J Biol Chem 281:1978–1985. https://doi.org/10.1074/jbc.M508545200

    Article  CAS  PubMed  Google Scholar 

  40. Zhou W, Srinivasan S, Nawaz Z, Slingerland JM (2014) ERα, SKP2 and E2F-1 form a feed forward loop driving late ERα targets and G1 cell cycle progression. Oncogene 33:2341–2353. https://doi.org/10.1038/onc.2013.197

    Article  CAS  PubMed  Google Scholar 

  41. Bhatt S, Xiao Z, Meng Z, Katzenellenbogen BS (2012) Phosphorylation by p38 mitogen-activated protein kinase promotes estrogen receptor α turnover and functional activity via the SCF(Skp2) proteasomal complex. Mol Cell Biol 32:1928–1943. https://doi.org/10.1128/MCB.06561-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Shao W, Keeton EK, McDonnell DP, Brown M (2004) Coactivator AIB1 links estrogen receptor transcriptional activity and stability. Proc Natl Acad Sci U S A 101:11599–11604. https://doi.org/10.1073/pnas.0402997101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Zhang H, Sun L, Liang J, Yu W, Zhang Y, Wang Y, Chen Y, Li R, Sun X, Shang Y (2006) The catalytic subunit of the proteasome is engaged in the entire process of estrogen receptor-regulated transcription. EMBO J 25:4223–4233. https://doi.org/10.1038/sj.emboj.7601306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Stanišić V, Malovannaya A, Qin J, Lonard DM, O’Malley BW (2009) OTU domain-containing ubiquitin aldehyde-binding protein 1 (OTUB1) deubiquitinates estrogen receptor (ER)α and affects ERα transcriptional activity. J Biol Chem 284:16135–16145. https://doi.org/10.1074/jbc.M109.007484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Wang C, Fu M, Angeletti RH, Siconolfi-Baez L, Reutens AT, Albanese C, Lisanti MP, Katzenellenbogen BS, Kato S, Hopp T, Fuqua SAW, Lopez GN, Kushner PJ, Pestell RG (2001) Direct acetylation of the estrogen receptor α hinge region by p300 regulates transactivation and hormone sensitivity. J Biol Chem 276:18375–18383. https://doi.org/10.1074/jbc.M100800200

    Article  CAS  PubMed  Google Scholar 

  46. Kim MY, Woo EM, Chong YTE, Homenko DR, Kraus WL (2006) Acetylation of estrogen receptor α by p300 at lysines 266 and 268 enhances the deoxyribonucleic acid binding and transactivation activities of the receptor. Mol Endocrinol 20:1479–1493. https://doi.org/10.1210/me.2005-0531

    Article  CAS  PubMed  Google Scholar 

  47. Zhang X, Tanaka K, Yan J, Li J, Peng D, Jiang Y, Yang Z, Barton MC, Wen H, Shi X (2013) Regulation of estrogen receptor α by histone methyltransferase SMYD2-mediated protein methylation. Proc Natl Acad Sci 110:17284–17289. https://doi.org/10.1073/pnas.1307959110

    Article  PubMed  PubMed Central  Google Scholar 

  48. Subramanian K, Jia D, Kapoor-Vazirani P, Powell DR, Collins RE, Sharma D, Peng J, Cheng X, Vertino PM (2008) Regulation of estrogen receptor α by the SET7 lysine methyltransferase. Mol Cell 30:336–347. https://doi.org/10.1016/j.molcel.2008.03.022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. O’Lone R, Frith MC, Karlsson EK, Hansen U (2004) Genomic targets of nuclear estrogen receptors. Mol Endocrinol 18:1859–1875. https://doi.org/10.1210/me.2003-0044

    Article  CAS  PubMed  Google Scholar 

  50. Klinge CM (2001) Estrogen receptor interaction with estrogen response elements. Nucleic Acids Res 29:2905–2919. https://doi.org/10.1093/nar/29.14.2905

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Gruber CJ, Gruber DM, Gruber IML, Wieser F, Huber JC (2004) Anatomy of the estrogen response element. Trends Endocrinol Metab 15:73–78. https://doi.org/10.1016/j.tem.2004.01.008

    Article  CAS  PubMed  Google Scholar 

  52. Björnström L, Sjöberg M (2005) Mechanisms of estrogen receptor signaling: convergence of genomic and nongenomic actions on target genes. Mol Endocrinol 19:833–842. https://doi.org/10.1210/me.2004-0486

    Article  CAS  PubMed  Google Scholar 

  53. Lu T, Achari Y, Sciore P, Hart DA (2006) Estrogen receptor alpha regulates matrix metalloproteinase-13 promoter activity primarily through the AP-1 transcriptional regulatory site. Biochim Biophys Acta Mol basis Dis 1762:719–731. https://doi.org/10.1016/j.bbadis.2006.06.007

    Article  CAS  Google Scholar 

  54. Jeffy BD, Hockings JK, Kemp MQ, Morgan SS, Hager JA, Beliakoff J, Whitesell LJ, Bowden GT, Romagnolo DF (2005) An estrogen receptor-α/p300 complex activates the BRCA-1 promoter at an AP-1 site that binds Jun/Fos transcription factors: repressive effects of p53 on BRCA-1 transcription. Neoplasia 7:873–882. https://doi.org/10.1593/neo.05256

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Teyssier C, Belguise K, Galtier F, Chalbos D (2001) Characterization of the physical interaction between estrogen receptor α and JUN proteins. J Biol Chem 276:36361–36369. https://doi.org/10.1074/jbc.M101806200

    Article  CAS  PubMed  Google Scholar 

  56. Kushner PJ, Agard DA, Greene GL, Scanlan TS, Shiau AK, Uht RM, Webb P (2000) Estrogen receptor pathways to AP-1. J Steroid Biochem Mol Biol 74:311–317. https://doi.org/10.1016/S0960-0760(00)00108-4

    Article  CAS  PubMed  Google Scholar 

  57. Wang C, Mayer JA, Mazumdar A, Fertuck K, Kim H, Brown M, Brown PH (2011) Estrogen induces c-myc gene expression via an upstream enhancer activated by the estrogen receptor and the AP-1 transcription factor. Mol Endocrinol 25:1527–1538. https://doi.org/10.1210/me.2011-1037

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Petz LN, Nardulli AM (2000) Sp1 binding sites and an estrogen response element half-site are involved in regulation of the human progesterone receptor A promoter. Mol Endocrinol 14:972–985. https://doi.org/10.1210/mend.14.7.0493

    Article  CAS  PubMed  Google Scholar 

  59. Rishi AK, Shao ZM, Baumann RG, Li XS, Sheikh MS, Kimura S, Bashirelahi N, Fontana JA (1995) Estradiol regulation of the human retinoic acid receptor α gene in human breast carcinoma cells is mediated via an imperfect half-palindromic estrogen response element and sp1 motifs. Cancer Res 55:4999–5006

    CAS  PubMed  Google Scholar 

  60. Roeder RG (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci 21:327–335. https://doi.org/10.1016/0968-0004(96)10050-5

    Article  CAS  PubMed  Google Scholar 

  61. Roeder RG (1998) Role of general and gene-specific cofactors in the regulation of eukaryotic transcription. Cold Spring Harb Symp Quant Biol 63:201–218

    Article  CAS  PubMed  Google Scholar 

  62. Glass CK, Rosenfeld MG (2000) The coregulator exchange in transcriptional functions of nuclear receptors. Genes Dev 14:121–141. https://doi.org/10.1101/gad.14.2.121

    Article  CAS  PubMed  Google Scholar 

  63. McKenna NJ, O’Malley BW (2002) Combinatorial control of gene expression by nuclear receptors and coregulators. Cell 108:465–474. https://doi.org/10.1016/S0092-8674(02)00641-4

    Article  CAS  PubMed  Google Scholar 

  64. Lonard DM, O’Malley BW (2007) Nuclear receptor coregulators: judges, juries, and executioners of cellular regulation. Mol Cell 27:691–700. https://doi.org/10.1016/j.molcel.2007.08.012

    Article  CAS  PubMed  Google Scholar 

  65. Nilsson S, Mäkelä S, Treuter E, Tujague M, Thomsen J, Andersson G, Enmark E, Pettersson K, Warner M, Gustafsson J-Å (2001) Mechanisms of estrogen action. Physiol Rev 81:1535–1565. https://doi.org/10.1152/physrev.2001.81.4.1535

    Article  CAS  PubMed  Google Scholar 

  66. Malik S, Baek HJ, Wu W, Roeder RG (2005) Structural and functional characterization of PC2 and RNA polymerase II-associated subpopulations of metazoan mediator. Mol Cell Biol 25:2117–2129. https://doi.org/10.1128/MCB.25.6.2117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Conaway RC, Sato S, Tomomori-Sato C, Yao T, Conaway JW (2005) The mammalian mediator complex and its role in transcriptional regulation. Trends Biochem Sci 30:250–255. https://doi.org/10.1016/j.tibs.2005.03.002

    Article  CAS  PubMed  Google Scholar 

  68. Kornberg RD (2005) Mediator and the mechanism of transcriptional activation. Trends Biochem Sci 30:235–239. https://doi.org/10.1016/j.tibs.2005.03.011

    Article  CAS  PubMed  Google Scholar 

  69. Zhang X, Krutchinsky A, Fukuda A, Chen W, Yamamura S, Chait BT, Roeder RG (2005) MED1/TRAP220 exists predominantly in a TRAP/mediator subpopulation enriched in RNA polymerase II and is required for ER-mediated transcription. Mol Cell 19:89–100. https://doi.org/10.1016/j.molcel.2005.05.015

    Article  CAS  PubMed  Google Scholar 

  70. Jiang P, Hu Q, Ito M, Meyer S, Waltz S, Khan S, Roeder RG, Zhang X (2010) Key roles for MED1 LxxLL motifs in pubertal mammary gland development and luminal-cell differentiation. Proc Natl Acad Sci U S A 107:6765–6770. https://doi.org/10.1073/pnas.1001814107

    Article  PubMed  PubMed Central  Google Scholar 

  71. Yang Y, Leonard M, Zhang Y, Zhao D, Charif M, Khan S, Wang J, Lower E, Zhang X (2018) HER2-driven breast tumorigenesis relies upon interactions of the estrogen receptor with coactivator MED1. 78:422–435

    Google Scholar 

  72. Wärnmark A, Almlöf T, Leers J, Gustafsson JÅ, Treuter E (2001) Differential recruitment of the mammalian mediator subunit TRAP220 by estrogen receptors ERalpha and ERbeta. J Biol Chem 276:23397–23404. https://doi.org/10.1074/jbc.M011651200

    Article  PubMed  Google Scholar 

  73. Kang YK, Guermah M, Yuan C-X, Roeder RG (2002) The TRAP/mediator coactivator complex interacts directly with estrogen receptors and through the TRAP220 subunit and directly enhances estrogen receptor function in vitro. Proc Natl Acad Sci 99:2642–2647. https://doi.org/10.1073/pnas.261715899

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Fondell JD, Ge H, Roeder RG (1996) Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex. Proc Natl Acad Sci U S A 93:8329–8333. https://doi.org/10.1073/pnas.93.16.8329

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Mcnally JG, Walker D, Wolford R, Hager GL (2000) The glucocorticoid receptor: rapid exchange with regulatory sites in living cells. Science 287:1262–1266. https://doi.org/10.1126/science.287.5456.1262

    Article  CAS  PubMed  Google Scholar 

  76. Yi P, Wang Z, Feng Q, Chou CK, Pintilie GD, Shen H, Foulds CE, Fan G, Serysheva I, Ludtke SJ, Schmid MF, Hung MC, Chiu W, O’Malley BW (2017) Structural and functional impacts of ER coactivator sequential recruitment. Mol Cell 67:733–743.e4. https://doi.org/10.1016/j.molcel.2017.07.026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Voss TC, Schiltz RL, Sung MH, Yen PM, Stamatoyannopoulos JA, Biddie SC, Johnson TA, Miranda TB, John S, Hager GL (2011) Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism. Cell 146:544–554. https://doi.org/10.1016/j.cell.2011.07.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Watanabe T, Inoue S, Hiroi H, Orimo A, Kawashima H, Muramatsu M (1998) Isolation of estrogen-responsive genes with a CpG island library. Mol Cell Biol 18:442–449. https://doi.org/10.1128/MCB.18.1.442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Dubik D, Dembinski TC, Shiu RP (1987) Stimulation of c-myc oncogene expression associated with estrogen-induced proliferation of human breast cancer cells. Cancer Res 47:6517–6521

    CAS  PubMed  Google Scholar 

  80. Sabbah M, Courilleau D, Mester J, Redeuilh G (1999) Estrogen induction of the cyclin D1 promoter: involvement of a cAMP response-like element. Proc Natl Acad Sci 96:11217–11222. https://doi.org/10.1073/pnas.96.20.11217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Bourdeau V, Deschênes J, Métivier R, Nagai Y, Nguyen D, Bretschneider N, Gannon F, White JH, Mader S (2004) Genome-wide identification of high-affinity estrogen response elements in human and mouse. Mol Endocrinol 18:1411–1427. https://doi.org/10.1210/me.2003-0441

    Article  CAS  PubMed  Google Scholar 

  82. Vega VB, Lin C-Y, Lai KS, Kong SL, Xie M, Su X, Teh HF, Thomsen JS, Yeo AL, Sung WK, Bourque G, Liu ET (2006) Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites. Genome Biol 7:R82. https://doi.org/10.1186/gb-2006-7-9-r82

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. 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 (2005) Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122:33–43. https://doi.org/10.1016/j.cell.2005.05.008

    Article  CAS  PubMed  Google Scholar 

  84. 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 (2006) Genome-wide analysis of estrogen receptor binding sites. Nat Genet 38:1289–1297. https://doi.org/10.1038/ng1901

    Article  CAS  PubMed  Google Scholar 

  85. Kwon Y-S, Garcia-Bassets I, Hutt KR, Cheng CS, Jin M, Liu D, Benner C, Wang D, Ye Z, Bibikova M, Fan J-B, Duan L, Glass CK, Rosenfeld MG, Fu X-D (2007) Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc Natl Acad Sci U S A 104:4852–4857. https://doi.org/10.1073/pnas.0700715104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. 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 (2007) Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet 3:e87. https://doi.org/10.1371/journal.pgen.0030087

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Hua S, Kallen CB, Dhar R, Baquero MT, Mason CE, Russell BA, Shah PK, Liu J, Khramtsov A, Tretiakova MS, Krausz TN, Olopade OI, Rimm DL, White KP (2008) Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression. Mol Syst Biol 4. https://doi.org/10.1038/msb.2008.25

  88. Hurtado A, Holmes KA, Geistlinger TR, Hutcheson IR, Nicholson RI, Brown M, Jiang J, Howat WJ, Ali S, Carroll JS (2008) Regulation of ERBB2 by oestrogen receptor-PAX2 determines response to tamoxifen. Nature 456:663–666. https://doi.org/10.1038/nature07483

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Kininis M, Chen BS, Diehl AG, Isaacs GD, Zhang T, Siepel AC, Clark AG, Kraus WL (2007) Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol 27:5090–5104. https://doi.org/10.1128/MCB.00083-07

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Welboren W-J, van Driel MA, Janssen-Megens EM, van Heeringen SJ, Sweep FC, Span PN, Stunnenberg HG (2009) ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands. EMBO J 28:1418–1428. https://doi.org/10.1038/emboj.2009.88

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL (2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 145:622–634. https://doi.org/10.1016/j.cell.2011.03.042

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Joseph R, Orlov YL, Huss M, Sun W, Li Kong S, Ukil L, Pan YF, Li G, Lim M, Thomsen JS, Ruan Y, Clarke ND, Prabhakar S, Cheung E, Liu ET (2010) Integrative model of genomic factors for determining binding site selection by estrogen receptor-α. Mol Syst Biol 6. https://doi.org/10.1038/msb.2010.109

  93. Lin C-Y, Ström A, Vega VB, Kong SL, Yeo AL, Thomsen JS, Chan WC, Doray B, Bangarusamy DK, Ramasamy A, Vergara LA, Tang S, Chong A, Bajic VB, Miller LD, Gustafsson J-Å, Liu ET (2004) Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells. Genome Biol 5:R66. https://doi.org/10.1186/gb-2004-5-9-r66

    Article  PubMed  PubMed Central  Google Scholar 

  94. Cheung E, Kraus WL (2010) Genomic analyses of hormone signaling and gene regulation. Annu Rev Physiol 72:191–218. https://doi.org/10.1146/annurev-physiol-021909-135840

    Article  CAS  PubMed  Google Scholar 

  95. Cirillo LA, Lin FR, Cuesta I, Friedman D, Jarnik M, Zaret KS (2002) Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol Cell 9:279–289. https://doi.org/10.1016/S1097-2765(02)00459-8

    Article  CAS  PubMed  Google Scholar 

  96. Hurtado A, Holmes KA, Ross-Innes CS, Schmidt D, Carroll JS (2011) FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nat Genet 43:27–33. https://doi.org/10.1038/ng.730

    Article  CAS  PubMed  Google Scholar 

  97. Holmes KA, Hurtado A, Brown GD, Launchbury R, Ross-Innes CS, Hadfield J, Odom DT, Carroll JS (2012) Transducin-like enhancer protein 1 mediates estrogen receptor binding and transcriptional activity in breast cancer cells. Proc Natl Acad Sci U S A 109:2748–2753. https://doi.org/10.1073/pnas.1018863108

    Article  CAS  PubMed  Google Scholar 

  98. Tan SK, Lin ZH, Chang CW, Varang V, Chng KR, Pan YF, Yong EL, Sung WK, Sung WK, Cheung E (2011) AP-2γ regulates oestrogen receptor-mediated long-range chromatin interaction and gene transcription. EMBO J 30:2569–2581. https://doi.org/10.1038/emboj.2011.151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Magnani L, Ballantyne EB, Zhang X, Lupien M (2011) PBX1 genomic pioneer function drives ERα signaling underlying progression in breast cancer. PLoS Genet 7:1–15. https://doi.org/10.1371/journal.pgen.1002368

    Article  CAS  Google Scholar 

  100. Magnani L, Patten DK, Nguyen VTM, Hong S-P, Steel JH, Patel N, Lombardo Y, Faronato M, Gomes AR, Woodley L, Page K, Guttery D, Primrose L, Fernandez Garcia D, Shaw J, Viola P, Green A, Nolan C, Ellis IO, Rakha EA, Shousha S, Lam EW-F, Gyorffy B, Lupien M, Coombes RC (2015) The pioneer factor PBX1 is a novel driver of metastatic progression in ERalpha-positive breast cancer. Oncotarget 6:21878–21891. https://doi.org/10.18632/oncotarget.4243

    Article  PubMed  PubMed Central  Google Scholar 

  101. Hagège H, Klous P, Braem C, Splinter E, Dekker J, Cathala G, de Laat W, Forné T (2007) Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc 2:1722–1733. https://doi.org/10.1038/nprot.2007.243

    Article  CAS  PubMed  Google Scholar 

  102. Simonis M, Kooren J, de Laat W (2007) An evaluation of 3C-based methods to capture DNA interactions. Nat Methods 4:895–901

    Article  CAS  PubMed  Google Scholar 

  103. Davies JOJ, Oudelaar AM, Higgs DR, Hughes JR (2017) How best to identify chromosomal interactions: a comparison of approaches. Nat Methods 14:125–134. https://doi.org/10.1038/nmeth.4146

    Article  CAS  PubMed  Google Scholar 

  104. Li W, Hu Y, Oh S, Ma Q, Merkurjev D, Song X, Zhou X, Liu Z, Tanasa B, He X, Chen A, Ohgi K, Zhang J, Liu W, Rosenfeld MG (2015) Condensin I and II complexes license full estrogen receptor α-dependent enhancer activation. Mol Cell 59:188–202. https://doi.org/10.1016/j.molcel.2015.06.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EGY, Huang PYH, Welboren W-J, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KDSA, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RKM, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung W-K, Liu ET, Wei C-L, Cheung E, Ruan Y (2009) An oestrogen-receptor-α-bound human chromatin interactome. Nature 462:58–64. https://doi.org/10.1038/nature08497

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Wood AJ, Severson AF, Meyer BJ (2010) Condensin and cohesin complexity: the expanding repertoire of functions. Nat Rev Genet 11:391–404. https://doi.org/10.1038/nrg2794

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Yuen KC, Gerton JL (2018) Taking cohesin and condensin in context. PLoS Genet 14:1–14. https://doi.org/10.1371/journal.pgen.1007118

    Article  CAS  Google Scholar 

  108. Schmidt D, Schwalie PC, Ross-Innes CS, Hurtado A, Brown GD, Carroll JS, Flicek P, Odom DT (2010) A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res 20:578–588. https://doi.org/10.1101/gr.100479.109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Antony J, Dasgupta T, Rhodes JM, McEwan MV, Print CG, O’Sullivan JM, Horsfield JA (2015) Cohesin modulates transcription of estrogen-responsive genes. Biochim Biophys Acta 1849:257–269. https://doi.org/10.1016/j.bbagrm.2014.12.011

    Article  CAS  PubMed  Google Scholar 

  110. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, Young RA (2010) Mediator and cohesin connect gene expression and chromatin architecture. Nature 467:430–435. https://doi.org/10.1038/nature09380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Ebmeier CC, Taatjes DJ (2010) Activator-mediator binding regulates mediator-cofactor interactions. Proc Natl Acad Sci 107:11283–11288. https://doi.org/10.1073/pnas.0914215107

    Article  PubMed  PubMed Central  Google Scholar 

  112. Chen Z, Zhang C, Wu D, Chen H, Rorick A, Zhang X, Wang Q (2011) Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth. EMBO J 30:2405–2419. https://doi.org/10.1038/emboj.2011.154

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Saramäki A, Diermeler S, Kellner R, Laitinen H, Väisänen S, Cariberg C (2009) Cyclical chromatin looping and transcription factor association on the regulatory regions of the p21 (CDKN1A) gene in response to 1α,25-dihydroxyvitamin D3. J Biol Chem 284:8073–8082. https://doi.org/10.1074/jbc.M808090200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Plank JL, Dean A (2014) Enhancer function: mechanistic and genome-wide insights come together. Mol Cell 55:5–14. https://doi.org/10.1016/j.molcel.2014.06.015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Kim TK, Hemberg M, Gray JM (2015) Enhancer RNAs: a class of long noncoding RNAs synthesized at enhancers. Cold Spring Harb Perspect Biol 7:2015–2018. https://doi.org/10.1101/cshperspect.a018622

    Article  CAS  Google Scholar 

  116. Shiekhattar R (2013) Opening the chromatin by eRNAs. Mol Cell 51:557–558. https://doi.org/10.1016/j.molcel.2013.08.033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Li W, Notani D, Rosenfeld MG (2016) Enhancers as non-coding RNA transcription units: recent insights and future perspectives. Nat Rev Genet 17:207–223. https://doi.org/10.1038/nrg.2016.4

    Article  CAS  PubMed  Google Scholar 

  118. Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X, Oh S, Kim H-S, Glass CK, Rosenfeld MG (2013) Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498:516–520. https://doi.org/10.1038/nature12210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Liu Z, Merkurjev D, Yang F, Li W, Oh S, Friedman MJ, Song X, Zhang F, Ma Q, Ohgi KA, Krones A, Rosenfeld MG (2014) Enhancer activation requires trans-recruitment of a mega transcription factor complex. Cell 159:356–373. https://doi.org/10.1016/j.cell.2014.08.027

    Article  CAS  Google Scholar 

  120. Hah N, Murakami S, Nagari A, Danko CG, Kraus WL (2013) Enhancer transcripts mark active estrogen receptor binding sites. Genome Res 23:1210–1223. https://doi.org/10.1101/gr.152306.112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Bhat-Nakshatri P, Wang G, Appaiah H, Luktuke N, Carroll JS, Geistlinger TR, Brown M, Badve S, Liu Y, Nakshatri H (2008) AKT alters genome-wide estrogen receptor binding and impacts estrogen signaling in breast cancer. Mol Cell Biol 28:7487–7503. https://doi.org/10.1128/MCB.00799-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Michalides R, Griekspoor A, Balkenende A, Verwoerd D, Janssen L, Jalink K, Floore A, Velds A, Van’t Veer L, Neefjes J (2004) Tamoxifen resistance by a conformational arrest of the estrogen receptor after PKA activation in breast cancer. Cancer Cell 5:597–605. https://doi.org/10.1016/j.ccr.2004.05.016

    Article  CAS  PubMed  Google Scholar 

  123. De Leeuw R, Flach K, Toaldo CB, Alexi X, Canisius S, Neefjes J, Michalides R, Zwart W (2013) PKA phosphorylation redirects ERα to promoters of a unique gene set to induce tamoxifen resistance. Oncogene 32:3543–3551. https://doi.org/10.1038/onc.2012.361

    Article  CAS  PubMed  Google Scholar 

  124. Lupien M, Meyer CA, Bailey ST, Eeckhoute J, Cook J, Westerling T, Zhang X, Carroll JS, Rhodes DR, Liu XS, Brown M (2010) Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance. Genes Dev 24:2219–2227. https://doi.org/10.1101/gad.1944810

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

We thank Zhang lab members for helpful discussion and Mr. Glenn Doerman for figure illustrations. This study was supported by NCI R01 CA197865, University of Cincinnati Cancer Center Startup and College of Medicine Innovation Seed Grant (to X.Z). G.B was supported by NCI training grant T32CA117846.

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Bick, G., Zhao, D., Zhang, X. (2019). Estrogen Receptor-Mediated Gene Transcription and Cistrome. In: Zhang, X. (eds) Estrogen Receptor and Breast Cancer. Cancer Drug Discovery and Development. Humana Press, Cham. https://doi.org/10.1007/978-3-319-99350-8_3

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