Research resource: Genome-wide profiling of progesterone receptor binding in the mouse uterus

Molecular Endocrinology

Volumn 26, Issue 8, 2012, Pages 1428-1442

  Rubel, Cory A ^a   Lanz, Rainer B ^a   Kommagani, Ramakrishna ^a   Franco, Heather L ^a   Lydon, John P ^a   Demayo, Francesco J ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROGESTERONE; PROGESTERONE RECEPTOR; TRANSCRIPTION FACTOR SOX17;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; CIRCADIAN RHYTHM; CONTROLLED STUDY; ENDOMETRIAL DISEASE; FEMALE; GENE EXPRESSION; GENE SEQUENCE; GENE TARGETING; GENETIC ASSOCIATION; HORMONE RESPONSIVE ELEMENT; HUMAN; HUMAN CELL; METHODOLOGY; MOUSE; NONHUMAN; OVARIECTOMY; PRIORITY JOURNAL; PROTEIN MICROARRAY; RECEPTOR BINDING; SEQUENCE ANALYSIS; UTERUS;

ANIMALS; BASE SEQUENCE; BINDING SITES; CELLS, CULTURED; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CONSENSUS SEQUENCE; FEMALE; GENOME; HMGB PROTEINS; HUMANS; MICE; MICE, INBRED C57BL; MOLECULAR SEQUENCE ANNOTATION; PROGESTERONE; PROTEIN BINDING; REAL-TIME POLYMERASE CHAIN REACTION; RECEPTORS, PROGESTERONE; RESPONSE ELEMENTS; SEQUENCE ANALYSIS, DNA; SIGNAL TRANSDUCTION; SOXF TRANSCRIPTION FACTORS; TRANSCRIPTOME; UTERUS;

MURINAE; MUS;

EID: 84864489010     PISSN: 08888809     EISSN: None     Source Type: Journal    
DOI: 10.1210/me.2011-1355     Document Type: Article

References (57)

1. DeMayo FJ, Zhao B, Takamoto N, Tsai SY 2002 Mechanisms of action of estrogen and progesterone. Ann NY Acad Sci 955:48-59; discussion 86-88, 396-406
2. Jemal A, Siegel R, Xu J, Ward E 2010 Cancer statistics, 2010. CA Cancer J Clin 60:277-300
3. Rubel CA, Jeong JW, Tsai SY, Lydon JP, Demayo FJ 2010 Epithelial-stromal interaction and progesterone receptors in the mouse uterus. Semin Reprod Med 28:27-35
4. Conneely OM, Maxwell BL, Toft DO, Schrader WT, O'Malley BW 1987 The A and B forms of the chicken progesterone receptor arise by alternate initiation of translation of a unique mRNA. Biochem Biophys Res Commun 149:493-501
5. Tsai MJ, O'Malley BW 1994 Molecular mechanisms of action of steroid/thyroid receptor superfamily members. Annu Rev Biochem 63:451-486
6. Ribeiro RC, Kushner PJ, Baxter JD 1995 The nuclear hormone receptor gene superfamily. Annu Rev Med 46:443-453
7. Li X, O'Malley BW 2003 Unfolding the action of progesterone receptors. J Biol Chem 278:39261-39264
8. Umesono K, Evans RM 1989 Determinants of target gene specificity for steroid/thyroid hormone receptors. Cell 57:1139-1146
9. Owen GI, Richer JK, Tung L, Takimoto G, Horwitz KB 1998 Progesterone regulates transcription of the p21(WAF1) cyclindependent kinase inhibitor gene through Sp1 and CBP/p300. J Biol Chem 273:10696-10701
10. Gao J, Mazella J, Seppala M, Tseng L 2001 Ligand activated hPR modulates the glycodelin promoter activity through the Sp1 sites in human endometrial adenocarcinoma cells. Mol Cell Endocrinol 176:97-102
11. Gizard F, Robillard R, Gervois P, Faucompré A, Révillion F, Peyrat JP, Hum WD, Staels B 2005 Progesterone inhibits human breast cancer cell growth through transcriptional upregulation of the cyclin-dependent kinase inhibitor p27Kip1 gene. FEBS Lett 579: 5535-5541
12. Cheon YP, Li Q, Xu X, DeMayo FJ, Bagchi IC, Bagchi MK 2002 A genomic approach to identify novel progesterone receptor regulated pathways in the uterus during implantation. Mol Endocrinol 16:2853-2871
13. Pan H, Zhu L, Deng Y, Pollard JW 2006 Microarray analysis of uterine epithelial gene expression during the implantation window in the mouse. Endocrinology 147:4904-4916
14. Jeong JW, Lee KY, Kwak I, White LD, Hilsenbeck SG, Lydon JP, DeMayo FJ 2005 Identification of murine uterine genes regulated in a ligand-dependent manner by the progesterone receptor. Endocrinology 146:3490-3505
15. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS 2008 Modelbased analysis of ChIP-Seq (MACS). Genome Biol 9:R137
16. Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XS 2011 Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol 12:R83
17. Huang da W, Sherman BT, Lempicki RA 2009 Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44-57
18. 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
19. 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 β binding sites. PLoS Genet 3:e87
20. Lanz RB, Bulynko Y, Malovannaya A, Labhart P, Wang L, Li W, Qin J, Harper M, O'Malley BW 2010 Global characterization of transcriptional impact of the SRC-3 coregulator. Mol Endocrinol 24:859-872
21. Wyce A, Bai Y, Nagpal S, Thompson CC 2010 Research Resource: the androgen receptor modulates expression of genes with critical roles in muscle development and function. Mol Endocrinol 24: 1665-1674
22. 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
23. Shin H, Liu T, Manrai AK, Liu XS 2009 CEAS: cis-regulatory element annotation system. Bioinformatics 25:2605-2606
24. Huang da W, Sherman BT, Lempicki RA 2009 Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37:1-13
25. Boden MJ, Kennaway DJ 2006 Circadian rhythms and reproduction. Reproduction 132:379-392
26. Lydon JP, DeMayo FJ, Funk CR, Mani SK, Hughes AR, Montgomery Jr CA, Shyamala G, Conneely OM, O'Malley BW 1995 Mice lacking progesterone receptor exhibit pleiotropic reproductive abnormalities. Genes Dev 9:2266-2278
27. Rubel CA, Franco HL, Jeong JW, Lydon JP, Demayo FJ 2012 GATA2 is expressed at critical times in the mouse uterus during pregnancy. Gene Expr Patterns 12:196-203
28. Garcia C, Calvo E, Nieto A 2007 The transcription factor SOX17 is involved in the transcriptional control of the uteroglobin gene in rabbit endometrium. J Cell Biochem 102:665-679
29. Mulac-Jericevic B, Mullinax RA, DeMayo FJ, Lydon JP, Conneely OM 2000 Subgroup of reproductive functions of progesterone mediated by progesterone receptor-B isoform. Science 289:1751-1754
30. Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X, Schones DE, Zhao K, Omenn GS, Hood L 2009 Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS One 4:e6589
31. Welboren WJ, van Driel MA, Janssen-Megens EM, van Heeringen SJ, Sweep FC, Span PN, Stunnenberg HG 2009 ChIP-Seq of ERβ and RNA polymerase II defines genes differentially responding to ligands. EMBO J 28:1418-1428
32. Wang Q, Li W, Liu XS, Carroll JS, Janne OA, Keeton EK, Chinnaiyan AM, Pienta KJ, Brown M 2007 A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell 27:380-392
33. Bulger M, Groudine M 2011 Functional and mechanistic diversity of distal transcription enhancers. Cell 144:327-339
34. Maywood ES, O'Brien JA, Hastings MH 2003 Expression of mCLOCK and other circadian clock-relevant proteins in the mouse suprachiasmatic nuclei. J Neuroendocrinol 15:329-334
35. Reick M, Garcia JA, Dudley C, McKnight SL 2001 NPAS2: an analog of clock operative in the mammalian forebrain. Science 293: 506-509
36. Yamamoto T, Nakahata Y, Soma H, Akashi M, Mamine T, Takumi T 2004 Transcriptional oscillation of canonical clock genes in mouse peripheral tissues. BMC Mol Biol 5:18
37. Liu S, Cai Y, Sothern RB, Guan Y, Chan P 2007 Chronobiological analysis of circadian patterns in transcription of seven key clock genes in six peripheral tissues in mice. Chronobiol Int 24:793-820
38. Johnson MH, Lim A, Fernando D, Day ML 2002 Circadian clockwork genes are expressed in the reproductive tract and conceptus of the early pregnant mouse. Reprod Biomed Online 4:140-145
39. Nakamura TJ, Sellix MT, Menaker M, Block GD 2008 Estrogen directly modulates circadian rhythms of PER2 expression in the uterus. Am J Physiol Endocrinol Metab 295:E1025-E1031
40. Horard B, Rayet B, Triqueneaux G, Laudet V, Delaunay F, Vanacker JM 2004 Expression of the orphan nuclear receptor ERRalpha is under circadian regulation in estrogen-responsive tissues. J Mol Endocrinol 33:87-97
41. He PJ, Hirata M, Yamauchi N, Hattori MA 2007 Up-regulation of Per1 expression by estradiol and progesterone in the rat uterus. J Endocrinol 194:511-519
42. Nakamura TJ, Moriya T, Inoue S, Shimazoe T, Watanabe S, Ebihara S, Shinohara K 2005 Estrogen differentially regulates expression of Per1 and Per2 genes between central and peripheral clocks and between reproductive and nonreproductive tissues in female rats. J Neurosci Res 82:622-630
43. Nakamura TJ, Sellix MT, Kudo T, Nakao N, Yoshimura T, Ebihara S, Colwell CS, Block GD 2010 Influence of the estrous cycle on clock gene expression in reproductive tissues: effects of fluctuating ovarian steroid hormone levels. Steroids 75:203-212
44. Kennaway DJ, Boden MJ, Voultsios A 2004 Reproductive performance in female Clock 19 mutant mice. Reprod Fertil Dev 16: 801-810
45. Alvarez JD, Hansen A, Ord T, Bebas P, Chappell PE, Giebultowicz JM, Williams C, Moss S, Sehgal A 2008 The circadian clock protein BMAL1 is necessary for fertility and proper testosterone production in mice. J Biol Rhythms 23:26-36
46. Pilorz V, Steinlechner S 2008 Low reproductive success in Per1 and Per2 mutant mouse females due to accelerated ageing? Reproduction 135:559-568
47. Bowles J, Schepers G, Koopman P 2000 Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. Dev Biol 227:239-255
48. Wegner M 1999 From head to toes: the multiple facets of Sox proteins. Nucleic Acids Res 27:1409-1420
49. Hudson C, Clements D, Friday RV, Stott D, Woodland HR 1997 Xsox17β and mediate endoderm formation in Xenopus. Cell 91:397-405
50. Liu Y, Asakura M, Inoue H, Nakamura T, Sano M, Niu Z, Chen M, Schwartz RJ, Schneider MD 2007 Sox17 is essential for the specification of cardiac mesoderm in embryonic stem cells. Proc Natl Acad Sci USA 104:3859-3864
51. Sakamoto Y, Hara K, Kanai-Azuma M, Matsui T, Miura Y, Tsunekawa N, Kurohmaru M, Saijoh Y, Koopman P, Kanai Y 2007 Redundant roles of Sox17 and Sox18 in early cardiovascular development of mouse embryos. Biochem Biophys Res Commun 360: 539-544
52. Jang YY, Sharkis SJ 2007 Fetal to adult stem cell transition: knocking Sox17 off. Cell 130:403-404
53. Kanai Y, Kanai-Azuma M, Noce T, Saido TC, Shiroishi T, Hayashi Y, Yazaki K 1996 Identification of two Sox17 messenger RNA isoforms, with and without the high mobility group box region, and their differential expression in mouse spermatogenesis. J Cell Biol 133:667-681
54. Van Vaerenbergh I, Van Lommel L, Ghislain V, In'T Veld P, Schuit F, Fatemi HM, Devroey P, Bourgain C 2009 In GnRH antagonist/ rec-FSH stimulated cycles, advanced endometrial maturation on the day of oocyte retrieval correlates with altered gene expression. Hum Reprod 24:1085-1091
55. Giangrande PH, McDonnell DP 1999 The A and B isoforms of the human progesterone receptor: two functionally different transcription factors encoded by a single gene. Recent Prog Horm Res 54: 291-313; discussion 313-314
56. Nakshatri H, Badve S 2009 FOXA1 in breast cancer. Expert Rev Mol Med 11:e8
57. Chou J, Provot S, Werb Z 2010 GATA3 in development and cancer differentiation: cells GATA have it! J Cell Physiol 222:42-49