Research resource: Aorta- and liver-specific ERα-binding patterns and gene regulation by estrogen

Molecular Endocrinology

Volumn 28, Issue 8, 2014, Pages 1337-1351

  Gordon, Francesca K ^a   Vallaster, Caroline S ^a   Westerling, Thomas ^b   Iyer, Lakshmanan K ^a   Brown, Myles ^b   Schnitzler, Gavin R ^a  

^a TUFTS MEDICAL CENTER   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESTRADIOL; ESTROGEN RECEPTOR ALPHA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AP 1; TRANSCRIPTION FACTOR RUNX1; CHROMATIN; ESTROGEN; PROTEIN BINDING;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; AORTA; ARTICLE; BINDING SITE; BIOINFORMATICS; CHROMATIN; CONTROLLED STUDY; DOWN REGULATION; DRUG MECHANISM; DRUG RECEPTOR BINDING; EX VIVO STUDY; FEMALE; GENE; GENE CONTROL; GENE EXPRESSION; LIVER; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN LOCALIZATION; TISSUE SPECIFICITY; UPREGULATION; ANIMAL; ANTIBODY SPECIFICITY; C57BL MOUSE; CARDIOVASCULAR DISEASE; CONSENSUS SEQUENCE; GENE EXPRESSION REGULATION; METABOLISM; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; SIGNAL TRANSDUCTION;

ANIMALS; AORTA; BASE SEQUENCE; CARDIOVASCULAR DISEASES; CHROMATIN; CONSENSUS SEQUENCE; ESTRADIOL; ESTROGEN RECEPTOR ALPHA; ESTROGENS; FEMALE; GENE EXPRESSION REGULATION; LIVER; MICE, INBRED C57BL; ORGAN SPECIFICITY; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; SIGNAL TRANSDUCTION;

EID: 84905220427     PISSN: 08888809     EISSN: 19449917     Source Type: Journal    
DOI: 10.1210/me.2013-1395     Document Type: Article

References (60)

1. Mendelsohn ME, Karas RH. HRT and the young at heart. N Engl J Med. 2007;356:2639-2641
2. Mendelsohn ME, Karas RH. Molecular and cellular basis of cardiovascular gender differences. Science. 2005;308:1583-1587
3. Shifren JL, Schiff I. Role of hormone therapy in the management of menopause. Obstet Gynecol. 2010;115:839-855
4. Parker WH, Broder MS, Chang E, et al. Ovarian conservation at the time of hysterectomy and long-term health outcomes in the nurses' health study. Obstet Gynecol. 2009;113:1027-1037
5. Rivera CM, Grossardt BR, Rhodes DJ, et al. Increased cardiovascular mortality after early bilateral oophorectomy. Menopause. 2009;16:15-23
6. Manson JE, Allison MA, Rossouw JE, et al. Estrogen therapy and coronary-artery calcification.NEngl J Med. 2007;356:2591-2602
7. Studd J. Ten reasons to be happy about hormone replacement therapy: a guide for patients. Menopause Int. 2010;16:44-46
8. North American Menopause Society. Estrogen and progestogen use in postmenopausal women: 2010 position statement of The North American Menopause Society. Menopause 2010;17:242-255
9. Pare G, Krust A, Karas RH, Dupont S, Aronovitz M, Chambon P, Mendelsohn ME. Estrogen receptor-α mediates the protective effects of estrogen against vascular injury. Circ Res. 2002;90:1087-1092
10. Brouchet L, Krust A, Dupont S, Chambon P, Bayard F, Arnal JF. Estradiol accelerates reendothelialization in mouse carotid artery through estrogen receptor-α but not estrogen receptor-β. Circulation. 2001;103:423-428
11. -/- mice. J Clin Invest. 2001;107:333-340
12. Zhu Y, Bian Z, Lu P, et al. Abnormal vascular function and hypertension in mice deficient in estrogen receptor β. Science. 2002;295: 505-508
13. Demissie S, Cupples LA, Shearman AM, et al. Estrogen receptor-α variants are associated with lipoprotein size distribution and particle levels in women: the Framingham Heart Study. Atherosclerosis. 2006;185:210-218
14. Peter I, Kelley-Hedgepeth A, Huggins GS, et al. Association between arterial stiffness and variations in oestrogen-related genes. J Hum Hypertens. 2009;23:636-644
15. Marino M, Galluzzo P, Ascenzi P. Estrogen signaling multiple pathways to impact gene transcription. Curr Genomics. 2006;7:497-508
16. Meyer MR, Haas E, Prossnitz ER, Barton M. Non-genomic regulation of vascular cell function and growth by estrogen. Mol Cell Endocrinol. 2009;308:9-16
17. Wu Q, Chambliss K, Umetani M, Mineo C, Shaul PW. Non-nuclear estrogen receptor signaling in the endothelium. J Biol Chem. 2011; 286:14737-14743
18. Björnström L, Sjöberg M. Mechanisms of estrogen receptor signaling: convergence of genomic and nongenomic actions on target genes. Mol Endocrinol. 2005;19:833-842
19. Madak-Erdogan Z, Kieser KJ, Kim SH, Komm B, Katzenellenbogen JA, Katzenellenbogen BS. Nuclear and extranuclear pathway inputs in the regulation of global gene expression by estrogen receptors. Mol Endocrinol. 2008;22:2116-2127
20. Bernelot Moens SJ, Schnitzler GR, Nickerson M, et al. Rapid estrogen receptor signaling is essential for the protective effects of estrogen against vascular injury. Circulation. 2012;126:1993-2004
21. Krum SA, Miranda-Carboni GA, Lupien M, Eeckhoute J, Carroll JS, Brown M. Unique ERα cistromes control cell type-specific gene regulation. Mol Endocrinol. 2008;22:2393-2406
22. Watanabe H, Suzuki A, Goto M, Lubahn DB, Handa H, Iguchi T. Tissue-specific estrogenic and non-estrogenic effects of a xenoestrogen, nonylphenol. J Mol Endocrinol. 2004;33:243-252
23. Ahlbory-Dieker DL, Stride BD, Leder G, et al. DNA binding by estrogen receptor-α is essential for the transcriptional response to estrogen in the liver and the uterus. Mol Endocrinol. 2009;23: 1544-1555
24. Boverhof DR, Fertuck KC, Burgoon LD, Eckel JE, Gennings C, Zacharewski TR. Temporal- and dose-dependent hepatic gene expression changes in immature ovariectomized mice following exposure to ethynyl estradiol. Carcinogenesis. 2004;25:1277-1291
25. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory- efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25
26. Ramskold D, Wang ET, Burge CB, Sandberg R. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol. 2009;5:e1000598
27. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106
28. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139-140
29. Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9:R137
30. Schnoes KK, Jaffe IZ, Iyer L, et al. Rapid recruitment of temporally distinct vascular gene sets by estrogen. Mol Endocrinol. 2008;22: 2544-2556
31. O'Lone R, Knorr K, Jaffe IZ, et al. Estrogen receptors α and β mediate distinct pathways of vascular gene expression, including genes involved in mitochondrial electron transport and generation of reactive oxygen species. Mol Endocrinol. 2007;21:1281-1296
32. Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 2004;32:D91-D94
33. Schones DE, Smith AD, Zhang MQ. Statistical significance of cisregulatory modules. BMC Bioinformatics. 2007;8:19
34. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B. 1995;57:289-300
35. Mahony S, Auron PE, Benos PV. DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput Biol. 2007;3:e61
36. Barlovic DP, Soro-Paavonen A, Jandeleit-Dahm KA. RAGE biology, atherosclerosis and diabetes. Clin Sci (Lond). 2011;121: 43-55
37. Karakas M, Koenig W. CRP in cardiovascular disease. Herz. 2009; 34:607-613
38. da Costa Martins P, García-Vallejo JJ, van Thienen JV, et al. P-selectin glycoprotein ligand-1 is expressed on endothelial cells and mediates monocyte adhesion to activated endothelium. Arterioscler Thromb Vasc Biol. 2007;27:1023-1029
39. Guo F, Zarella C, Wagner WD. STAT4 and the proliferation of artery smooth muscle cells in atherosclerosis. Exp Mol Pathol. 2006;81:15-22
40. Aoki S, Hayakawa M, Ozaki H, et al. ST2 gene expression is proliferation- dependent and its ligand, IL-33, induces inflammatory reaction in endothelial cells. Mol Cell Biochem. 2010;335:75-81
41. Carroll JS, Meyer CA, Song J, et al. Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 2006;38:1289-1297
42. Shin H, Liu T, Manrai AK, Liu XS. CEAS: cis-regulatory element annotation system. Bioinformatics. 2009;25:2605-2606
43. Ji X, Li W, Song J, Wei L, Liu XS. CEAS: cis-regulatory element annotation system. Nucleic Acids Res. 2006;34:W551-W554
44. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004;14:1188-1190
45. Hewitt SC, Li L, Grimm SA, et al. Research resource: Whole-genome estrogen receptor α binding in mouse uterine tissue revealed by ChIP-seq. Mol Endocrinol. 2012;26:887-898
46. Gao H, Fält S, Sandelin A, Gustafsson JA, Dahlman-Wright K. Genome-wide identification of estrogen receptor α-binding sites in mouse liver. Mol Endocrinol. 2008;22:10-22
47. Joshi SR, Ghattamaneni RB, Scovell WM. Expanding the paradigm for estrogen receptor binding and transcriptional activation. Mol Endocrinol. 2011;25:980-994
48. Grober OM, Mutarelli M, Giurato G, et al. A global analysis of estrogen receptor β binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor α for target gene regulation. BMC Genomics. 2011;12:36
49. Lin CY, Vega VB, Thomsen JS, et al. Whole-genome cartography of estrogen receptor α binding sites. PLoS Genet. 2007;3:e87
50. Stender JD, Kim K, Charn TH, et al. Genome-wide analysis of estrogen receptor α DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation. Mol Cell Biol. 2010;30:3943-3955
51. Welboren WJ, van Driel MA, Janssen-Megens EM, et al. ChIP-Seq of ERα andRNApolymerase II defines genes differentially responding to ligands. EMBO J. 2009;28:1418-1428
52. Carroll JS, Liu XS, Brodsky AS, et al. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell. 2005;122:33-43
53. Derrien T, Johnson R, Bussotti G, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012;22:1775-1789
54. Djebali S, Davis CA, Merkel A, et al. Landscape of transcription in human cells. Nature. 2012;489:101-108
55. Cunningham M, Gilkeson G. Estrogen receptors in immunity and autoimmunity. Clin Rev Allergy Immunol. 2011;40:66-73
56. Newton K, Dixit VM. Signaling in innate immunity and inflammation. Cold Spring Harb Perspect Biol. 2012;4:a006049
57. Nakagawa M, Shimabe M, Watanabe-Okochi N, et al. AML1/ RUNX1 functions as a cytoplasmic attenuator of NF-kappaB signaling in the repression of myeloid tumors. Blood. 2011;118:6626-6637
58. Müller M, Morotti A, Ponzetto C. Activation of NF-kappaB is essential for hepatocyte growth factor-mediated proliferation and tubulogenesis. Mol Cell Biol. 2002;22:1060-1072
59. Vanden Berghe W, Plaisance S, Boone E, et al. p38 and extracellular signal-regulated kinase mitogen-activated protein kinase pathways are required for nuclear factor-kappaB p65 transactivation mediated by tumor necrosis factor. J Biol Chem. 1998;273:3285-3290
60. Romashkova JA, Makarov SS. NF-kappaB is a target of AKT in anti-apoptotic PDGF signalling. Nature. 1999;401:86-90.