Whole-genome cartography of estrogen receptor α binding sites

PLoS Genetics

Volumn 3, Issue 6, 2007, Pages 0867-0885

  Lin, Chin Yo ^a,d   Vega, Vinsensius B ^a   Thomsen, Jane S ^a   Zhang, Tao ^a   Say, Li Kong ^a   Xie, Min ^a   Kuo, Ping Chiu ^a   Lipovich, Leonard ^a   Barnett, Daniel H ^b   Stossi, Fabio ^b   Yeo, Ailing ^c   George, Joshy ^a   Kuznetsov, Vladimir A ^a   Yew, Kok Lee ^a   Tze, Howe Charn ^a   Palanisamy, Nallasivam ^a   Miller, Lance D ^a   Cheung, Edwin ^a,c   Katzenellenbogen, Benita S ^b   Ruan, Yijun ^a   Bourque, Guillaume ^a   Wei, Chia Lin ^a   Liu, Edison T ^a   more..

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^d BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESTRADIOL; ESTROGEN RECEPTOR ALPHA; DNA;

ARTICLE; BINDING SITE; CELL STRAIN MCF 7; CONTROLLED STUDY; ESTROGEN RESPONSIVE ELEMENT; GENE EXPRESSION; GENE MAPPING; GENE REPRESSION; GENOME ANALYSIS; HUMAN; HUMAN CELL; PROMOTER REGION; TRANSCRIPTION REGULATION; ANIMAL; FEMALE; GENE EXPRESSION REGULATION; GENETICS; GENOME; METABOLISM; PHYSIOLOGY; TUMOR CELL LINE; VALIDATION STUDY;

VERTEBRATA;

ANIMALS; BINDING SITES; CELL LINE, TUMOR; DNA; ESTROGEN RECEPTOR ALPHA; FEMALE; GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS;

EID: 34347345081     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0030087     Document Type: Article

References (48)

1. Charpentier AH, Bednarek AK, Daniel RL, Hawkins KA, Laflin KJ, et al. (2000) Effects of estrogen on global gene expression: Identification of novel targets of estrogen action. Cancer Res 60: 5977-5983.
2. Finlin BS, Gau CL, Murphy GA, Shao H, Kimel T, et al. (2001) RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer. J Biol Chem 276: 42259-42267.
3. Frasor J, Danes JM, Komm B, Chang KC, Lyttle CR, 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.
4. Gruvberger S, Ringner M, Chen Y, Panavally S, Saal LH, et al. (2001) Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res 61: 5979-5984.
5. Inoue A, Yoshida N, Omoto Y, Oguchi S, Yamori T, et al. (2002) Development of cDNA microarray for expression profiling of estrogen-responsive genes. J Mol Endocrinol 29: 175-192.
6. Lin CY, Strom A, Vega VB, Li Kong S, Li Yeo A, et al. (2004) Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells. Genome Biol 5: R66.
7. Soulez M, Parker MG (2001) Identification of novel oestrogen receptor target genes in human ZR75-1 breast cancer cells by expression profiling. J Mol Endocrinol 27: 259-274.
8. Ali S, Coombes RC (2000) Estrogen receptor alpha in human breast cancer: Occurrence and significance. J Mammary Gland Biol Neoplasia 5: 271-281.
9. Kushner PJ, Agard DA, Greene GL, Scanlan TS, Shiau AK, et al. (2000) Estrogen receptor pathways to AP-1. J Steroid Biochem Mol Biol 74: 311-317.
10. Porter W, Saville B, Hoivik D, Safe S (1997) Functional synergy between the transcription factor Sp1 and the estrogen receptor. Mol Endocrinol 11: 1569-1580.
11. Klinge CM (2001) Estrogen receptor interaction with estrogen response elements. Nucleic Acids Res 29: 2905-2919.
12. Shang Y, Hu X, DiRenzo J, Lazar MA, Brown M (2000) Cofactor dynamics and sufficiency in estrogen receptor-regulated transcription. Cell 103: 843-852.
13. Metivier R, Penot G, Hubner MR, Reid G, Brand H, et al. (2003) Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115: 751-763.
14. Orlando V, Strutt H, Paro R (1997) Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11: 205-214.
15. Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, et al. (2005) Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122: 33-43.
16. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, et al. (2006) Genome-ide analysis of estrogen receptor binding sites. Nat Genet 38: 1289-1297.
17. Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, et al. (2005) Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods 2: 105-111.
18. Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, et al. (2006) A global map of p53 transcription-factor binding sites in the human genome. Cell 124: 207-219.
19. Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, et al. (2006) The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 38: 431-440.
20. Kuznetsov VA (2005) Mathematical analysis and modeling of SAGE. In: Wang SM, editor. SAGE: Current technologies and applications. Norwich, United Kingdom: Horizon BioScience. pp. 139-180.
21. Stack G, Kumar V, Green S, Ponglikitmongkol M, Berry M, et al. (1988) Structure and function of the pS2 gene and estrogen receptor in human breast cancer cells. Cancer Treat Res 40: 185-206.
22. Bourdeau V, Deschenes J, Metivier R, Nagai Y, Nguyen D, et al. (2004) Genome-wide identification of high-affinity estrogen response elements in human and mouse. Mol Endocrinol 18: 1411-1427.
23. Miller LD, Smeds J, George J, Vega VB, Vergara L, et al. (2005) An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci U S A 102: 13550-13555.
24. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
25. Pollard DA, Moses AM, Iyer VN, Eisen MB (2006) Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. BMC Bioinformatics 7: 376.
26. Kel AE, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, et al. (2003) MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 31: 3576-3579.
27. Duan R, Porter W, Safe S (1998) Estrogen-induced c-fos protooncogene expression in MCF-7 human breast cancer cells: Role of estrogen receptor Sp1 complex formation. Endocrinology 139: 1981-1990.
28. Dong L, Wang W, Wang F, Stoner M, Reed JC, et al. (1999) Mechanisms of transcriptional activation of bcl-2 gene expression by 17beta-estradiol in breast cancer cells. J Biol Chem 274: 32099-32107.
29. Petz LN, Ziegler YS, Schultz JR, Kim H, Kemper JK, et al. (2004) Differential regulation of the human progesterone receptor gene through an estrogen response element half site and Sp1 sites. J Steroid Biochem Mol Biol 88: 113-122.
30. Schultz JR, Petz LN, Nardulli AM (2003) Estrogen receptor alpha and Sp1 regulate progesterone receptor gene expression. Mol Cell Endocrinol 201: 165-175.
31. Teferedegne B, Green MR, Guo Z, Boss JM (2006) Mechanism of action of a distal NF-kappaB-dependent enhancer. Mol Cell Biol 26: 5759-5770.
32. Frasor J, Stossi F, Danes JM, Komm B, Lyttle CR, et al. (2004) Selective estrogen receptor modulators: Discrimination of agonistic versus antagonistic activities by gene expression profiling in breast cancer cells. Cancer Res 64: 1522-1533.
33. Stossi F, Barnett DH, Frasor J, Komm B, Lyttle CR, et al. (2004) Transcriptional profiling of estrogen-regulated gene expression via estrogen receptor (ER) alpha or ERbeta in human osteosarcoma cells: Distinct and common target genes for these receptors. Endocrinology 145: 3473-3486.
34. van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415: 530-536.
35. Vega VB, Lin CY, Lai KS, Kong SL, Xie M, et al. (2006) Multi-platform genome-wide identification and modeling of functional human estrogen receptor binding sites. Genome Biol 7: R82.
36. Yamamoto T, Kyo M, Kamiya T, Tanaka T, Engel JD, et al. (2006) Predictive base substitution rules that determine the binding and transcriptional specificity of Maf recognition elements. Genes Cells 11: 575-591.
37. Petz LN, Ziegler YS, Loven MA, Nardulli AM (2002) Estrogen receptor alpha and activating protein-1 mediate estrogen responsiveness of the progesterone receptor gene in MCF-7 breast cancer cells. Endocrinology 143: 4583-4591.
38. Vanacker JM, Pettersson K, Gustafsson JA, Laudet V (1999) Transcriptional targets shared by estrogen receptor- related receptors (ERRs) and estrogen receptor (ER) alpha, but not by ERbeta. Embo J 18: 4270-4279.
39. Jeyasuria P, Ikeda Y, Jamin SP, Zhao L, De Rooij DG, et al. (2004) Cell-pecific knockout of steroidogenic factor 1 reveals its essential roles in gonadal function. Mol Endocrinol 18: 1610-1619.
40. Stossi F, Likhite VS, Katzenellenbogen JA, Katzenellenbogen BS (2006) Estrogen-occupied estrogen receptor represses cyclin G2 gene expression and recruits a repressor complex at the cyclin G2 promoter. J Biol Chem 281: 16272-16278.
41. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
42. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.
43. Chiu KP, Wong CH, Chen Q, Ariyaratne P, Ooi HS, et al. (2006) PET-Tool: A software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data. BMC Bioinformatics 7: 390.
44. Oerter KE, Munson PJ, McBride WO, Rodbard D (1990) Computerized estimation of size of nucleic acid fragments using the four-parameter logistic model. Anal Biochem 189: 235-243.
45. Naylor TL, Greshock J, Wang Y, Colligon T, Yu QC, et al. (2005) High resolution genomic analysis of sporadic breast cancer using array-based comparative genomic hybridization. Breast Cancer Res 7: R1186-R1198.
46. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14: 708-715.
47. Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, et al. (2006) The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 34: D590-D598.
48. Cavener DR (1987) Comparison of the consensus sequence flanking translational start sites in Drosophila and vertebrates. Nucleic Acids Res 15: 1353-1361.