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
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
Jensen EV, Jacobson H (1962) Basic guides to the mechanism of estrogen action. Recent Prog Horm Res 18:318–414
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
Jensen EV (2004) From chemical warfare to breast cancer management. Nat Med 10:1018–1021
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Simonis M, Kooren J, de Laat W (2007) An evaluation of 3C-based methods to capture DNA interactions. Nat Methods 4:895–901
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
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
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
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
Yuen KC, Gerton JL (2018) Taking cohesin and condensin in context. PLoS Genet 14:1–14. https://doi.org/10.1371/journal.pgen.1007118
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
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
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
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
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
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
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
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
Shiekhattar R (2013) Opening the chromatin by eRNAs. Mol Cell 51:557–558. https://doi.org/10.1016/j.molcel.2013.08.033
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
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
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
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
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
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
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
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
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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