Interrogating the genome to understand oestrogen-receptor-mediated transcription

Expert Reviews in Molecular Medicine

Volumn 10, Issue 10, 2008, Pages

  Dietz, Sara C ^a   Carroll, Jason S ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC HYDROCARBON RECEPTOR; BETA GLOBIN; CATHEPSIN D; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; DNA; ESTROGEN; ESTROGEN RECEPTOR; ESTROGEN RECEPTOR ALPHA; ESTROGEN RECEPTOR BETA; GLUCOCORTICOID RECEPTOR; HEPATOCYTE NUCLEAR FACTOR 3ALPHA; HISTONE ACETYLTRANSFERASE PCAF; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MESSENGER RNA; MICRORNA; MYC PROTEIN; PROGESTERONE RECEPTOR; RECEPTOR INTERACTING PROTEIN 140; RNA POLYMERASE II; TAMOXIFEN; TRANSCRIPTION FACTOR AP 1; TRANSCRIPTION FACTOR SP1; VITELLOGENIN;

ANTINEOPLASTIC ACTIVITY; BINDING SITE; BREAST CANCER; BREAST CARCINOGENESIS; CANCER GROWTH; CANCER HORMONE THERAPY; CANCER RESISTANCE; CHROMATIN IMMUNOPRECIPITATION; ESTROGEN ACTIVITY; ESTROGEN RESPONSIVE ELEMENT; GENE CONTROL; GENE EXPRESSION PROFILING; GENE MUTATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROGNOSIS; PROMOTER REGION; PROTEIN DNA BINDING; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION REGULATION; BREAST TUMOR; DNA RESPONSIVE ELEMENT; FEMALE; GENE EXPRESSION REGULATION; GENETICS; GENOME; METABOLISM; PROTEIN BINDING;

BREAST NEOPLASMS; CHROMATIN IMMUNOPRECIPITATION; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOME, HUMAN; HUMANS; PROTEIN BINDING; RECEPTORS, ESTROGEN; RESPONSE ELEMENTS; TRANSCRIPTION, GENETIC;

EID: 42049108810     PISSN: 14623994     EISSN: 14623994     Source Type: Journal    
DOI: 10.1017/S1462399408000653     Document Type: Review

References (79)

1. Osborne, C.K. (1998) Tamoxifen in the treatment of breast cancer. N Engl J Med 339, 1609-1618
2. MacGregor, J.I. and Jordan, V.C. (1998) Basic guide to the mechanisms of antiestrogen action. Pharmacol Rev 50, 151-196
3. Jordan, V.C. (2003) Tamoxifen: A most unlikely pioneering medicine. Nat Rev Drug Discov 2, 205-213
4. Anzick, S.L. et al. (1997) AIB1, a steroid receptor coactivator amplified in breast and ovarian cancer. Science 277, 965-968
5. Lavinsky, R.M. et al. (1998) Diverse signaling pathways modulate nuclear receptor recruitment of N-CoR and SMRTcomplexes. Proc Natl Acad Sci U S A 95, 2920-2925
6. Shang, Y. and Brown, M. (2002) Molecular determinants for the tissue specificity of SERMs. Science 295, 2465-2468
7. Torres-Arzayus, M.I. et al. (2004) High tumor incidence and activation of the PI3K/AKT pathway in transgenic mice define AIB1 as an oncogene. Cancer Cell 6, 263-274
8. Klinge, C.M. (2001) Estrogen receptor interaction with estrogen response elements. Nucleic Acids Res 29, 2905-2919
9. Klein-Hitpass, L. et al. (1986)An estrogen-responsive element derived from the 5′ flanking region of the Xenopus vitellogenin A2 gene functions in transfected human cells. Cell 46, 1053-1061
10. Berry, M., Nunez, A.M. and Chambon, P. (1989) Estrogen-responsive element of the human pS2 gene is an imperfectly palindromic sequence. Proc Natl Acad Sci U S A 86, 1218-1222
11. Brown, A.M. et al. (1984) Activation of pS2 gene transcription is a primary response to estrogen in the human breast cancer cell line MCF-7. Proc Natl Acad Sci U S A 81, 6344-6348
12. Ikeda, K. et al. (2000) Promoter analysis and chromosomal mapping of human EBAG9 gene. Biochem Biophys Res Commun 273, 654-660
13. Cavailles, V., Augereau, P. and Rochefort, H. (1993) Cathepsin D gene is controlled by a mixed promoter, and estrogens stimulate only TATA-dependent transcription in breast cancer cells. Proc Natl Acad Sci U S A 90, 203-207
14. Krishnan, V., Wang, X. and Safe, S. (1994) Estrogen receptor-Sp1 complexes mediate estrogen-induced cathepsin D gene expression in MCF-7 human breast cancer cells. J Biol Chem 269, 15912-15917
15. Wang, F. et al. (1997) Identification of a functional imperfect estrogen-responsive element in the 5′-promoter region of the human cathepsin D gene. Biochemistry 36, 7793-7801
16. Prall, O.W. et al. (1998) c-Myc or cyclin D1 mimics estrogen effects on cyclin E-Cdk2 activation and cell cycle reentry. Mol Cell Biol 18, 4499-4508
17. Cheung, E., Schwabish, M.A. and Kraus, W.L. (2003) Chromatin exposes intrinsic differences in the transcriptional activities of estrogen receptors alpha and beta. EMBO J 22, 600-611
18. Shang, Y. et al. (2000) Cofactor dynamics and sufficiency in estrogen receptor-regulated transcription. Cell 103, 843-852
19. Metivier, R. et al. (2003) Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115, 751-763
20. Stenoien, D.L. et al. (2001) Ligand-mediated assembly and real-time cellular dynamics of estrogen receptor alpha-coactivator complexes in living cells. Mol Cell Biol 21, 4404-4412
21. Becker, M. et al. (2002) Dynamic behavior of transcription factors on a natural promoter in living cells. EMBO Rep 3, 1188-1194
22. Bajic, V.B. et al. (2003) Dragon ERE Finder version 2: A tool for accurate detection and analysis of estrogen response elements in vertebrate genomes. Nucleic Acids Res 31, 3605-3607
23. Lin, C.Y. et al. (2004) Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells. Genome Biol 5, R66
24. Kamalakaran, S.,Radhakrishnan, S.K. and Beck,W.T. (2005) Identification of estrogen-responsive genes using a genome-wide analysis of promoter elements for transcription factor binding sites. J Biol Chem 280, 21491-21497
25. Cavailles, V. et al. (1995) Nuclear factor RIP140 modulates transcriptional activation by the estrogen receptor. EMBO J 14, 3741-3751
26. Wei, L.N. et al. (2000) Receptor-interacting protein 140 directly recruits histone deacetylases for gene silencing. J Biol Chem 275, 40782-40787
27. Forrester,W.C. et al. (1990) A deletion of the human beta-globin locus activation region causes a major alteration in chromatin structure and replication across the entire beta-globin locus. Genes Dev 4, 1637-1649
28. Kim, C.G. et al. (1992) Inactivation of the human beta-globin gene by targeted insertion into the beta-globin locus control region. Genes Dev 6, 928-938
29. Aladjem, M.I. et al. (1995) Participation of the human beta-globin locus control region in initiation of DNA replication. Science 270, 815-819
30. Sawado, T. et al. (2003) The beta -globin locus control region (LCR) functions primarily by enhancing the transition from transcription initiation to elongation. Genes Dev 17, 1009-1018
31. Bourdeau, V. et al. (2004) Genome-wide identification of high-affinity estrogen response elements in human and mouse. Mol Endocrinol 18, 1411-1427
32. Vega, V.B. et al. (2006) Multi-platform genome-wide identification and modeling of functional human estrogen receptor binding sites. Genome Biol 7, R82
33. Davis, D.L. and Burch, J.B. (1996) The chicken vitellogenin II gene is flanked by a GATA factordependent estrogen response unit. Mol Endocrinol 10, 937-944
34. Dellovade, T.L. et al. (1996) Thyroid hormone and estrogen interact to regulate behavior. Proc Natl Acad Sci U S A 93, 12581-12586
35. Batistuzzo de Medeiros, S.R. et al. (1997) Functional interactions between the estrogen receptor and the transcription activator Sp1 regulate the estrogen-dependent transcriptional activity of the vitellogenin A1 io promoter. J Biol Chem 272, 18250-18260
36. Wang, F., Samudio, I. and Safe, S. (2001) Transcriptional activation of rat creatine kinase B by 17beta-estradiol in MCF-7 cells involves an estrogen responsive element and GC-rich sites. J Cell Biochem 84, 156-172
37. Wang, F. et al. (1998) Functional and physical interactions between the estrogen receptor Sp1 and nuclear aryl hydrocarbon receptor complexes. Nucleic Acids Res 26, 3044-3052
38. Garcia-Arencibia, M. et al. (2005) Identification of two functional estrogen response elements complexed with AP-1-like sites in the human insulin receptor gene promoter. J Steroid Biochem Mol Biol 94, 1-14
39. Blanchette, M. et al. (2006) Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res 16, 656-668
40. Laganiere, J., Deblois, G. and Giguere, V. (2005) Functional genomics identifies a mechanism for estrogen activation of the retinoic acid receptor alpha1 gene in breast cancer cells. Mol Endocrinol 19, 1584-1592
41. Impey, S. et al. (2004) Defining the CREB regulon: A genome-wide analysis of transcription factor regulatory regions. Cell 119, 1041-1054
42. Wei, C.L. et al. (2006) A global map of p53 transcription-factor binding sites in the human genome. Cell 124, 207-219
43. Lin, C.Y. et al. (2007) Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet 3, e87
44. Ng, P. et al. (2006) Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res 34, e84
45. Carroll, J.S. et al. (2005) Chromosome-wide mapping of estrogen receptor binding reveals longrange regulation requiring the forkhead protein FoxA1. Cell 122, 33-43
46. Laganiere, J. et al. (2005) Location analysis of estrogen receptor alpha target promoters reveals that FOXA1 defines a domain of the estrogen response. Proc Natl Acad Sci U S A 102, 11651-11656
47. Cheng, A.S. et al. (2006) Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters. Mol Cell 21, 393-404
48. Kwon, Y.S. et al. (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
49. Carroll, J.S. et al. (2006) Genome-wide analysis of estrogen receptor binding sites. Nat Genet 38, 1289-1297
50. Frasor, J. et al. (2003) Profiling of estrogen up- and down-regulated gene expression in human breast cancer cells: Insights into gene networks and pathways underlying estrogenic control of proliferation and cell phenotype. Endocrinology 144, 4562-4574
51. Teyssier, C. et al. (2003) Receptor-interacting protein 140 binds c-Jun and inhibits estradiol-induced activator protein-1 activity by reversing glucocorticoid receptor-interacting protein 1 effect. Mol Endocrinol 17, 287-299
52. Kim, T.H. et al. (2005) A high-resolution map of active promoters in the human genome. Nature 436, 876-880
53. Yang, A. et al. (2006) Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell 24, 593-602
54. Kim, T.H. et al. (2007) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128, 1231-1245
55. Mikkelsen, T.S. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560
56. Johnson, D.S. et al. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502
57. Odom, D.T. et al. (2007) Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet 39, 730-732
58. Gao, H. et al. (2008) Genome-wide identification of estrogen receptor {alpha}-binding sites in mouse liver. Mol Endocrinol 22, 10-22
59. Ballestar, E. et al. (2003) Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. EMBO J 22, 6335-6345
60. Miao, F. and Natarajan, R. (2005) Mapping global histone methylation patterns in the coding regions of human genes. Mol Cell Biol 25, 4650-4661
61. Bernstein, B.E. et al. (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169-181
62. Huebert, D.J. et al. (2006) Genome-wide analysis of histone modifications by ChIP-on-chip. Methods 40, 365-369
63. Lupien, M. et al. FoxA1 translates epigenetic signatures into enhancer driven lineage-specific transcription. Cell (in press)
64. Bender, M.A. et al. (2000) Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region. Mol Cell 5, 387-393
65. Schubeler, D., Groudine, M. and Bender, M.A. (2001) The murine beta-globin locus control region regulates the rate of transcription but not the hyperacetylation of histones at the active genes. Proc Natl Acad Sci U S A 98, 11432-11437
66. Cohen, A. et al. (2007) Alterations in microRNA expression profiles reveal a novel pathway for estrogen regulation. Endocrinology Dec 20; [Epub ahead of print]
67. Iorio, M.V. et al. (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65, 7065-7070
68. Ma, L., Teruya-Feldstein, J. and Weinberg, R.A. (2007) Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature 449, 682-688
69. Wang, Q., Carroll, J.S. and Brown, M. (2005) Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking. Mol Cell 19, 631-642
70. Dekker, J. et al. (2002) Capturing chromosome conformation. Science 295, 1306-1311
71. Dostie, J. et al. (2006) Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Res 16, 1299-1309
72. Zhao, Z. et al. (2006) Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 38, 1341-1347
73. Simonis, M. et al. (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38, 1348-1354
74. O'Neill, L.P., VerMilyea, M.D. and Turner, B.M. (2006) Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nat Genet 38, 835-841
75. Easton, D.F. et al. (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447, 1087-1093
76. Badve, S. et al. (2007) FOXA1 expression in breast cancer-correlation with luminal subtype A and survival. Clin Cancer Res 13, 4415-4421
77. Howell, A. et al. (1996) Pharmacokinetics, pharmacological and anti-tumour effects of the specific anti-oestrogen ICI 182780 in women with advanced breast cancer. Br J Cancer 74, 300-308
78. Johnston, S.R. (1997) Acquired tamoxifen resistance in human breast cancer-potential mechanisms and clinical implications. Anticancer Drugs 8, 911-930
79. Johnston, S.R. et al. (1995) Changes in estrogen receptor, progesterone receptor, and pS2 expression in tamoxifen-resistant human breast cancer. Cancer Res 55, 3331-3338