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Volumn 22, Issue 9, 2008, Pages 1999-2011

Nuclear receptor location analyses in mammalian genomes: From gene regulation to regulatory networks

Author keywords

[No Author keywords available]

Indexed keywords

ANDROGEN RECEPTOR; BRCA1 ASSOCIATED RING DOMAIN PROTEIN 1; CCAAT ENHANCER BINDING PROTEIN; CELL NUCLEUS RECEPTOR; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN BINDING PROTEIN; ESTRADIOL; ESTROGEN RECEPTOR ALPHA; ESTROGEN RELATED RECEPTOR ALPHA; ESTROGEN RELATED RECEPTOR GAMMA; GLUCOCORTICOID RECEPTOR; HEPATOCYTE NUCLEAR FACTOR 3ALPHA; HEPATOCYTE NUCLEAR FACTOR 4ALPHA; OCTAMER TRANSCRIPTION FACTOR 1; RETINOIC ACID RECEPTOR ALPHA; RETINOID X RECEPTOR; RNA POLYMERASE II; STAT3 PROTEIN; STEROID RECEPTOR COACTIVATOR 1; TRANSCRIPTION FACTOR AP 1; TRANSCRIPTION FACTOR SP1; UNCLASSIFIED DRUG; VITAMIN D RECEPTOR; WNT11 PROTEIN;

EID: 50649092225     PISSN: 08888809     EISSN: None     Source Type: Journal    
DOI: 10.1210/me.2007-0546     Document Type: Short Survey
Times cited : (32)

References (75)
  • 3
    • 0032580207 scopus 로고    scopus 로고
    • Allosteric effects of DNA on transcriptional regulators
    • Lefstin JA, Yamamoto KR 1998 Allosteric effects of DNA on transcriptional regulators. Nature 392:885-888
    • (1998) Nature , vol.392 , pp. 885-888
    • Lefstin, J.A.1    Yamamoto, K.R.2
  • 4
    • 0023948705 scopus 로고
    • Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene
    • Solomon MJ, Larsen PL, Varshavsky A 1988 Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53:937-947
    • (1988) Cell , vol.53 , pp. 937-947
    • Solomon, M.J.1    Larsen, P.L.2    Varshavsky, A.3
  • 5
    • 33845925394 scopus 로고    scopus 로고
    • Chromatin immunoprecipitation and microarray-based analysis of protein location
    • Lee TI, Johnstone SE, Young RA 2006 Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1:729-748
    • (2006) Nat Protoc , vol.1 , pp. 729-748
    • Lee, T.I.1    Johnstone, S.E.2    Young, R.A.3
  • 6
    • 0037177857 scopus 로고    scopus 로고
    • Reciprocal recruitment of DRIP/Mediator and p160 coactivator complexes in vivo by estrogen receptor
    • Burakov D, Crofts LA, Chang CP, Freedman LP 2002 Reciprocal recruitment of DRIP/Mediator and p160 coactivator complexes in vivo by estrogen receptor. J Biol Chem 277:14359-14362
    • (2002) J Biol Chem , vol.277 , pp. 14359-14362
    • Burakov, D.1    Crofts, L.A.2    Chang, C.P.3    Freedman, L.P.4
  • 7
    • 0036208492 scopus 로고    scopus 로고
    • Formation of the androgen receptor transcription complex
    • Shang Y, Myers M, Brown M 2002 Formation of the androgen receptor transcription complex. Mol Cell 9:601-610
    • (2002) Mol Cell , vol.9 , pp. 601-610
    • Shang, Y.1    Myers, M.2    Brown, M.3
  • 8
    • 0033637703 scopus 로고    scopus 로고
    • Cofactor dynamics and sufficiency in estrogen receptor-regulated transcription
    • Shang Y, Hu X, DiRenzo J, Lazar MA, Brown M 2000 Cofactor dynamics and sufficiency in estrogen receptor-regulated transcription. Cell 103:843-852
    • (2000) Cell , vol.103 , pp. 843-852
    • Shang, Y.1    Hu, X.2    DiRenzo, J.3    Lazar, M.A.4    Brown, M.5
  • 10
    • 2642544592 scopus 로고    scopus 로고
    • Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter
    • Metivier R, Penot G, Hubner MR, Reid G, Brand H, Kos M, Gannon F 2003 Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115:751-763
    • (2003) Cell , vol.115 , pp. 751-763
    • Metivier, R.1    Penot, G.2    Hubner, M.R.3    Reid, G.4    Brand, H.5    Kos, M.6    Gannon, F.7
  • 11
    • 24044540381 scopus 로고    scopus 로고
    • Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking
    • Wang Q, Carroll JS, Brown M 2005 Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking. Mol Cell 19:631-642
    • (2005) Mol Cell , vol.19 , pp. 631-642
    • Wang, Q.1    Carroll, J.S.2    Brown, M.3
  • 16
    • 0037080674 scopus 로고    scopus 로고
    • Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis
    • Weinmann AS, Yan PS, Oberley MJ, Huang TH, Farnham PJ 2002 Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev 16:235-244
    • (2002) Genes Dev , vol.16 , pp. 235-244
    • Weinmann, A.S.1    Yan, P.S.2    Oberley, M.J.3    Huang, T.H.4    Farnham, P.J.5
  • 17
    • 33745140886 scopus 로고    scopus 로고
    • Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome
    • Bieda M, Xu X, Singer MA, Green R, Farnham PJ 2006 Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res 16:595-605
    • (2006) Genome Res , vol.16 , pp. 595-605
    • Bieda, M.1    Xu, X.2    Singer, M.A.3    Green, R.4    Farnham, P.J.5
  • 19
    • 34447098370 scopus 로고    scopus 로고
    • A chromatin landmark and transcription initiation at most promoters in human cells
    • Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA 2007 A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77-88
    • (2007) Cell , vol.130 , pp. 77-88
    • Guenther, M.G.1    Levine, S.S.2    Boyer, L.A.3    Jaenisch, R.4    Young, R.A.5
  • 24
    • 0242558354 scopus 로고    scopus 로고
    • Nuclear receptor target gene discovery using high throughput chromatin immunoprecipitation
    • Russell DW, Mangelsdorf DJ, eds, San Diego: Academic Press;
    • Laganière J, Deblois G, Giguère V 2003 Nuclear receptor target gene discovery using high throughput chromatin immunoprecipitation. In: Russell DW, Mangelsdorf DJ, eds. Methods in enzymology. San Diego: Academic Press; 339-350
    • (2003) Methods in enzymology , pp. 339-350
    • Laganière, J.1    Deblois, G.2    Giguère, V.3
  • 25
    • 22344438888 scopus 로고    scopus 로고
    • Functional genomics identifies a mechanism for estrogen activation of the retinoic acid receptor α1 gene in breast cancer cells
    • Laganière J, Deblois G, Giguère V 2005 Functional genomics identifies a mechanism for estrogen activation of the retinoic acid receptor α1 gene in breast cancer cells. Mol Endocrinol 19:1584-1592
    • (2005) Mol Endocrinol , vol.19 , pp. 1584-1592
    • Laganière, J.1    Deblois, G.2    Giguère, V.3
  • 26
    • 0028819989 scopus 로고
    • 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
    • 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
    • (1995) Cancer Res , vol.55 , pp. 4999-5006
    • Rishi, A.K.1    Shao, Z.M.2    Baumann, R.G.3    Li, X.S.4    Sheikh, M.S.5    Kimura, S.6    Bashirelahi, N.7    Fontana, J.A.8
  • 27
    • 0032230246 scopus 로고    scopus 로고
    • Estrogen-induced retinoic acid receptor α 1 gene expression: Role of estrogen receptor-Sp1 complex
    • Sun G, Porter W, Safe S 1998 Estrogen-induced retinoic acid receptor α 1 gene expression: role of estrogen receptor-Sp1 complex. Mol Endocrinol 12:882-890
    • (1998) Mol Endocrinol , vol.12 , pp. 882-890
    • Sun, G.1    Porter, W.2    Safe, S.3
  • 28
    • 33847330324 scopus 로고    scopus 로고
    • Estrogen receptor regulates expression of the breast cancer 1 associated ring domain 1 (BARD1) gene through intronic DNA sequence
    • Creekmore AL, Ziegler YS, Boney JL, Nardulli AM 2007 Estrogen receptor regulates expression of the breast cancer 1 associated ring domain 1 (BARD1) gene through intronic DNA sequence. Mol Cell Endocrinol 267:106-115
    • (2007) Mol Cell Endocrinol , vol.267 , pp. 106-115
    • Creekmore, A.L.1    Ziegler, Y.S.2    Boney, J.L.3    Nardulli, A.M.4
  • 29
    • 34250363896 scopus 로고    scopus 로고
    • Novel estrogen receptor-α binding sites and estradiol target genes identified by chromatin immunoprecipitation cloning in breast cancer
    • Lin Z, Reierstad S, Huang CC, Bulun SE 2007 Novel estrogen receptor-α binding sites and estradiol target genes identified by chromatin immunoprecipitation cloning in breast cancer. Cancer Res 67:5017-5024
    • (2007) Cancer Res , vol.67 , pp. 5017-5024
    • Lin, Z.1    Reierstad, S.2    Huang, C.C.3    Bulun, S.E.4
  • 31
    • 33748900285 scopus 로고    scopus 로고
    • Chromatin immunoprecipitation-mediated target identification proved aquaporin 5 is regulated directly by estrogen in the uterus
    • Kobayashi M, Takahashi E, Miyagawa S, Watanabe H, Iguchi T 2006 Chromatin immunoprecipitation-mediated target identification proved aquaporin 5 is regulated directly by estrogen in the uterus. Genes Cells 11:1133-1143
    • (2006) Genes Cells , vol.11 , pp. 1133-1143
    • Kobayashi, M.1    Takahashi, E.2    Miyagawa, S.3    Watanabe, H.4    Iguchi, T.5
  • 32
    • 23844485897 scopus 로고    scopus 로고
    • Location analysis of estrogen receptor α target promoters reveals that FOXA1 defines a domain of the estrogen response
    • Laganière J, Deblois G, Lefebvre C, Bataille AR, Robert F, Giguère V 2005 Location analysis of estrogen receptor α target promoters reveals that FOXA1 defines a domain of the estrogen response. Proc Natl Acad Sci USA 102:11651-11656
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 11651-11656
    • Laganière, J.1    Deblois, G.2    Lefebvre, C.3    Bataille, A.R.4    Robert, F.5    Giguère, V.6
  • 37
    • 34447519218 scopus 로고    scopus 로고
    • Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters
    • 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
    • (2007) Mol Cell Biol , vol.27 , pp. 5090-5104
    • Kininis, M.1    Chen, B.S.2    Diehl, A.G.3    Isaacs, G.D.4    Zhang, T.5    Siepel, A.C.6    Clark, A.G.7    Kraus, W.L.8
  • 42
    • 13544265659 scopus 로고    scopus 로고
    • Identifying estrogen receptor α target genes using integrated computational genomics and chromatin immunoprecipitation microarray
    • Jin VX, Leu YW, Liyanarachchi S, Sun H, Fan M, Nephew KP, Huang TH, Davuluri RV 2004 Identifying estrogen receptor α target genes using integrated computational genomics and chromatin immunoprecipitation microarray. Nucleic Acids Res 32:6627-6635
    • (2004) Nucleic Acids Res , vol.32 , pp. 6627-6635
    • Jin, V.X.1    Leu, Y.W.2    Liyanarachchi, S.3    Sun, H.4    Fan, M.5    Nephew, K.P.6    Huang, T.H.7    Davuluri, R.V.8
  • 44
    • 34347324118 scopus 로고    scopus 로고
    • Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor
    • So AY, Chaivorapol C, Bolton EC, Li H, Yamamoto KR 2007 Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PLoS Genet 3:e94
    • (2007) PLoS Genet , vol.3
    • So, A.Y.1    Chaivorapol, C.2    Bolton, E.C.3    Li, H.4    Yamamoto, K.R.5
  • 46
    • 34547931715 scopus 로고    scopus 로고
    • Cell- and gene-specific regulation of primary target genes by the androgen receptor
    • Bolton EC, So AY, Chaivorapol C, Ha CM, Li H, Yamamoto KR 2007 Cell- and gene-specific regulation of primary target genes by the androgen receptor. Genes Dev 21:2005-2017
    • (2007) Genes Dev , vol.21 , pp. 2005-2017
    • Bolton, E.C.1    So, A.Y.2    Chaivorapol, C.3    Ha, C.M.4    Li, H.5    Yamamoto, K.R.6
  • 56
    • 22344449669 scopus 로고    scopus 로고
    • Constructing transcriptional regulatory networks
    • Blais A, Dynlacht BD 2005 Constructing transcriptional regulatory networks. Genes Dev 19:1499-1511
    • (2005) Genes Dev , vol.19 , pp. 1499-1511
    • Blais, A.1    Dynlacht, B.D.2
  • 57
    • 33845311536 scopus 로고    scopus 로고
    • Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping
    • Walhout AJ 2006 Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res 16:1445-1454
    • (2006) Genome Res , vol.16 , pp. 1445-1454
    • Walhout, A.J.1
  • 59
    • 34250322116 scopus 로고    scopus 로고
    • Trinklein ND, Karaoz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z 2007 Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res 17:720-731
    • Trinklein ND, Karaoz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z 2007 Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res 17:720-731
  • 61
    • 0023904316 scopus 로고
    • Action at a distance along a DNA
    • Wang JC, Giaever GN 1988 Action at a distance along a DNA. Science 240:300-304
    • (1988) Science , vol.240 , pp. 300-304
    • Wang, J.C.1    Giaever, G.N.2
  • 62
    • 0028801067 scopus 로고
    • Action at a distance: DNA-looping and initiation of transcription
    • Rippe K, von Hippel PH, Langowski J 1995 Action at a distance: DNA-looping and initiation of transcription. Trends Biochem Sci 20:500-506
    • (1995) Trends Biochem Sci , vol.20 , pp. 500-506
    • Rippe, K.1    von Hippel, P.H.2    Langowski, J.3
  • 64
    • 0030960672 scopus 로고    scopus 로고
    • Transcriptional activation by recruitment
    • Ptashne M, Gann A 1997 Transcriptional activation by recruitment. Nature 386:569-577
    • (1997) Nature , vol.386 , pp. 569-577
    • Ptashne, M.1    Gann, A.2
  • 65
    • 29444448047 scopus 로고    scopus 로고
    • On a chromosome far, far away: LCRs and gene expression
    • Dean A 2006 On a chromosome far, far away: LCRs and gene expression. Trends Genet 22:38-45
    • (2006) Trends Genet , vol.22 , pp. 38-45
    • Dean, A.1
  • 66
    • 33645887244 scopus 로고    scopus 로고
    • Chromatin looping and the probability of transcription
    • Li Q, Barkess G, Qian H 2006 Chromatin looping and the probability of transcription. Trends Genet 22:197-202
    • (2006) Trends Genet , vol.22 , pp. 197-202
    • Li, Q.1    Barkess, G.2    Qian, H.3
  • 67
    • 0042880630 scopus 로고    scopus 로고
    • Spatial organization of gene expression: The active chromatin hub
    • de Laat W, Grosveld F 2003 Spatial organization of gene expression: the active chromatin hub. Chromosome Res 11:447-459
    • (2003) Chromosome Res , vol.11 , pp. 447-459
    • de Laat, W.1    Grosveld, F.2
  • 70
    • 33750212321 scopus 로고    scopus 로고
    • Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
    • Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W 2006 Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38:1348-1354
    • (2006) Nat Genet , vol.38 , pp. 1348-1354
    • Simonis, M.1    Klous, P.2    Splinter, E.3    Moshkin, Y.4    Willemsen, R.5    de Wit, E.6    van Steensel, B.7    de Laat, W.8
  • 71
    • 34248524473 scopus 로고    scopus 로고
    • Mapping networks of physical interactions between genomic elements using 5C technology
    • Dostie J, Dekker J 2007 Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc 2:988-1002
    • (2007) Nat Protoc , vol.2 , pp. 988-1002
    • Dostie, J.1    Dekker, J.2
  • 73
    • 35748956435 scopus 로고    scopus 로고
    • An evaluation of 3C-based methods to capture DNA interactions
    • Simonis M, Kooren J, de Laat W 2007 An evaluation of 3C-based methods to capture DNA interactions. Nat Methods 4:895-901
    • (2007) Nat Methods , vol.4 , pp. 895-901
    • Simonis, M.1    Kooren, J.2    de Laat, W.3


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