메뉴 건너뛰기




Volumn 9, Issue 4, 2014, Pages

Characterization of genomic vitamin D receptor binding sites through chromatin looping and opening

Author keywords

[No Author keywords available]

Indexed keywords

CALCITRIOL; MESSENGER RNA; TRANSCRIPTION FACTOR CTCF; VITAMIN D RECEPTOR; CALCITRIOL RECEPTOR; CCCTC-BINDING FACTOR; CHROMATIN; REPRESSOR PROTEIN; VDR PROTEIN, HUMAN;

EID: 84899713429     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0096184     Document Type: Article
Times cited : (28)

References (52)
  • 1
    • 21744435965 scopus 로고    scopus 로고
    • Controlling nuclear receptors: The circular logic of cofactor cycles
    • DOI 10.1038/nrm1680
    • Perissi V, Rosenfeld MG (2005) Controlling nuclear receptors: the circular logic of cofactor cycles. Nat Rev Mol Cell Biol 6: 542-554. (Pubitemid 40943045)
    • (2005) Nature Reviews Molecular Cell Biology , vol.6 , Issue.7 , pp. 542-554
    • Perissi, V.1    Rosenfeld, M.G.2
  • 2
    • 84857735521 scopus 로고    scopus 로고
    • Current status of vitamin D signaling and its therapeutic applications
    • Carlberg C, Molnár F (2012) Current status of vitamin D signaling and its therapeutic applications. Curr Top Med Chem 12: 528-547.
    • (2012) Curr Top Med Chem , vol.12 , pp. 528-547
    • Carlberg, C.1    Molnár, F.2
  • 3
    • 16244418604 scopus 로고    scopus 로고
    • Overview of general physiologic features and functions of vitamin D
    • DeLuca HF (2004) Overview of general physiologic features and functions of vitamin D. Am J Clin Nutr 80: 1689S-1696S.
    • (2004) Am J Clin Nutr , vol.80
    • DeLuca, H.F.1
  • 4
    • 38549125522 scopus 로고    scopus 로고
    • Molecular basis of the potential of vitamin D to prevent cancer
    • DOI 10.1185/030079907X253519
    • Ingraham BA, Bragdon B, Nohe A (2008) Molecular basis of the potential of vitamin D to prevent cancer. Curr Med Res Opin 24: 139-149. (Pubitemid 351160247)
    • (2008) Current Medical Research and Opinion , vol.24 , Issue.1 , pp. 139-149
    • Ingraham, B.A.1    Bragdon, B.2    Nohe, A.3
  • 6
    • 79957571086 scopus 로고    scopus 로고
    • Antibacterial effects of vitamin D
    • Hewison M (2011) Antibacterial effects of vitamin D. Nat Rev Endocrinol 7: 337-345.
    • (2011) Nat Rev Endocrinol , vol.7 , pp. 337-345
    • Hewison, M.1
  • 10
    • 65149083962 scopus 로고    scopus 로고
    • The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
    • FANTOM-Consortium
    • FANTOM-Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, et al. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41: 553-562.
    • (2009) Nat Genet , vol.41 , pp. 553-562
    • Suzuki, H.1    Forrest, A.R.2    Van Nimwegen, E.3    Daub, C.O.4
  • 11
    • 84856072305 scopus 로고    scopus 로고
    • The first genome-wide view of vitamin D receptor locations and their mechanistic implications
    • Carlberg C, Seuter S, Heikkinen S (2012) The first genome-wide view of vitamin D receptor locations and their mechanistic implications. Anticancer Res 32: 271-282.
    • (2012) Anticancer Res , vol.32 , pp. 271-282
    • Carlberg, C.1    Seuter, S.2    Heikkinen, S.3
  • 12
    • 0025812291 scopus 로고
    • 3 receptors
    • Umesono K, Murakami KK, Thompson CC, Evans RM (1991) Direct repeats as selective response elements for the thyroid hormone, retinoic acid, and vitamin D3 receptors. Cell 65: 1255-1266. (Pubitemid 121001338)
    • (1991) Cell , vol.65 , Issue.7 , pp. 1255-1266
    • Umesono, K.1    Murakami, K.K.2    Thompson, C.C.3    Evans, R.M.4
  • 14
    • 77957672846 scopus 로고    scopus 로고
    • Dynamics of nuclear receptor target gene regulation
    • Carlberg C, Seuter S (2010) Dynamics of nuclear receptor target gene regulation. Chromosoma 119: 479-484.
    • (2010) Chromosoma , vol.119 , pp. 479-484
    • Carlberg, C.1    Seuter, S.2
  • 15
    • 0036211013 scopus 로고    scopus 로고
    • Histone acetylation: A switch between repressive and permissive chromatin. Second in review on chromatin dynamics
    • DOI 10.1093/embo-reports/kvf053
    • Eberharter A, Becker PB (2002) Histone acetylation: a switch between repressive and permissive chromatin. Second in review series on chromatin dynamics. EMBO Rep 3: 224-229. (Pubitemid 34269514)
    • (2002) EMBO Reports , vol.3 , Issue.3 , pp. 224-229
    • Eberharter, A.1    Becker, P.B.2
  • 16
    • 34250369627 scopus 로고    scopus 로고
    • FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
    • DOI 10.1101/gr.5533506
    • Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD (2007) FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 17: 877-885. (Pubitemid 46919722)
    • (2007) Genome Research , vol.17 , Issue.6 , pp. 877-885
    • Giresi, P.G.1    Kim, J.2    McDaniell, R.M.3    Iyer, V.R.4    Lieb, J.D.5
  • 17
    • 67649524640 scopus 로고    scopus 로고
    • Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
    • Giresi PG, Lieb JD (2009) Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods 48: 233-239.
    • (2009) Methods , vol.48 , pp. 233-239
    • Giresi, P.G.1    Lieb, J.D.2
  • 18
    • 80053539409 scopus 로고    scopus 로고
    • Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
    • Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, et al. (2011) Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 21: 1757-1767.
    • (2011) Genome Res , vol.21 , pp. 1757-1767
    • Song, L.1    Zhang, Z.2    Grasfeder, L.L.3    Boyle, A.P.4    Giresi, P.G.5
  • 21
    • 8844262660 scopus 로고    scopus 로고
    • Principles for modulation of the nuclear receptor superfamily
    • DOI 10.1038/nrd1551
    • Gronemeyer H, Gustafsson JA, Laudet V (2004) Principles for modulation of the nuclear receptor superfamily. Nat Rev Drug Discov 3: 950-964. (Pubitemid 39534319)
    • (2004) Nature Reviews Drug Discovery , vol.3 , Issue.11 , pp. 950-964
    • Gronemeyer, H.1    Gustafsson, J.-A.2    Laudet, V.3
  • 22
    • 84876838711 scopus 로고    scopus 로고
    • The hierarchy of the 3D genome
    • Gibcus JH, Dekker J (2013) The hierarchy of the 3D genome. Mol Cell 49: 773-782.
    • (2013) Mol Cell , vol.49 , pp. 773-782
    • Gibcus, J.H.1    Dekker, J.2
  • 23
    • 84871431768 scopus 로고    scopus 로고
    • Vitamin D receptor signaling mechanisms: Integrated actions of a well-defined transcription factor
    • Carlberg C, Campbell MJ (2013) Vitamin D receptor signaling mechanisms: Integrated actions of a well-defined transcription factor. Steroids 78: 127-136.
    • (2013) Steroids , vol.78 , pp. 127-136
    • Carlberg, C.1    Campbell, M.J.2
  • 24
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: Advantages and challenges of a maturing technology
    • Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680.
    • (2009) Nat Rev Genet , vol.10 , pp. 669-680
    • Park, P.J.1
  • 25
    • 77956885532 scopus 로고    scopus 로고
    • A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution
    • Ramagopalan SV, Heger A, Berlanga AJ, Maugeri NJ, Lincoln MR, et al. (2010) A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. Genome Res 20: 1352-1360.
    • (2010) Genome Res , vol.20 , pp. 1352-1360
    • Ramagopalan, S.V.1    Heger, A.2    Berlanga, A.J.3    Maugeri, N.J.4    Lincoln, M.R.5
  • 26
    • 84855225831 scopus 로고    scopus 로고
    • VDR/RXR and TCF4/beta-catenin cistromes in colonic cells of colorectal tumor origin: Impact on c-FOS and c-MYC gene expression
    • Meyer MB, Goetsch PD, Pike JW (2012) VDR/RXR and TCF4/beta-catenin cistromes in colonic cells of colorectal tumor origin: impact on c-FOS and c-MYC gene expression. Mol Endocrinol 26: 37-51.
    • (2012) Mol Endocrinol , vol.26 , pp. 37-51
    • Meyer, M.B.1    Goetsch, P.D.2    Pike, J.W.3
  • 27
    • 84876928036 scopus 로고    scopus 로고
    • A vitamin D receptor/SMAD genomic circuit gates hepatic fibrotic response
    • Ding N, Yu RT, Subramaniam N, Sherman MH, Wilson C, et al. (2013) A vitamin D receptor/SMAD genomic circuit gates hepatic fibrotic response. Cell 153: 601-613.
    • (2013) Cell , vol.153 , pp. 601-613
    • Ding, N.1    Yu, R.T.2    Subramaniam, N.3    Sherman, M.H.4    Wilson, C.5
  • 29
    • 59349086115 scopus 로고    scopus 로고
    • Chromatin loops in gene regulation
    • Kadauke S, Blobel GA (2009) Chromatin loops in gene regulation. Biochim Biophys Acta 1789: 17-25.
    • (2009) Biochim Biophys Acta , vol.1789 , pp. 17-25
    • Kadauke, S.1    Blobel, G.A.2
  • 30
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: Master weaver of the genome
    • Phillips JE, Corces VG (2009) CTCF: master weaver of the genome. Cell 137: 1194-1211.
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 31
    • 84863393570 scopus 로고    scopus 로고
    • Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages
    • Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, et al. (2012) Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148: 335-348.
    • (2012) Cell , vol.148 , pp. 335-348
    • Schmidt, D.1    Schwalie, P.C.2    Wilson, M.D.3    Ballester, B.4    Gonçalves, A.5
  • 32
    • 70449103609 scopus 로고    scopus 로고
    • An oestrogen-receptor-alpha-bound human chromatin interactome
    • Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, et al. (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462: 58-64.
    • (2009) Nature , vol.462 , pp. 58-64
    • Fullwood, M.J.1    Liu, M.H.2    Pan, Y.F.3    Liu, J.4    Xu, H.5
  • 33
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE-Project-Consortium
    • ENCODE-Project-Consortium, Bernstein BE, Birney E, Dunham I, Green ED, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Bernstein, B.E.1    Birney, E.2    Dunham, I.3    Green, E.D.4
  • 34
    • 0018871095 scopus 로고
    • Establishment and characterization of a human acute monocytic leukemia cell line (THP-1)
    • Tsuchiya S, Yamabe M, Yamaguchi Y, Kobayashi Y, Konno T, et al. (1980) Establishment and characterization of a human acute monocytic leukemia cell line (THP-1). Int J Cancer 26: 171-176. (Pubitemid 10086416)
    • (1980) International Journal of Cancer , vol.26 , Issue.2 , pp. 171-176
    • Tsuchiya, S.1    Yamabe, M.2    Yamaguchi, Y.3
  • 35
    • 84887574192 scopus 로고    scopus 로고
    • Dynamics of 1α,25-dihydroxyvitamin D-dependent chromatin accessibility of early vitamin D receptor target genes
    • Seuter S, Pehkonen P, Heikkinen S, Carlberg C (2013) Dynamics of 1α,25-dihydroxyvitamin D-dependent chromatin accessibility of early vitamin D receptor target genes. Biochim Biophys Acta 1829: 1266-1275.
    • (2013) Biochim Biophys Acta , vol.1829 , pp. 1266-1275
    • Seuter, S.1    Pehkonen, P.2    Heikkinen, S.3    Carlberg, C.4
  • 36
    • 84875634162 scopus 로고    scopus 로고
    • Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
    • Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14: 178-192.
    • (2013) Brief Bioinform , vol.14 , pp. 178-192
    • Thorvaldsdottir, H.1    Robinson, J.T.2    Mesirov, J.P.3
  • 38
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • Heinz S, Benner C, Spann N, Bertolino E, Lin YC, et al. (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38: 576-589.
    • (2010) Mol Cell , vol.38 , pp. 576-589
    • Heinz, S.1    Benner, C.2    Spann, N.3    Bertolino, E.4    Lin, Y.C.5
  • 39
    • 0037129827 scopus 로고    scopus 로고
    • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    • Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: R34.
    • (2002) Genome Biol , vol.3
    • Vandesompele, J.1    De Preter, K.2    Pattyn, F.3    Poppe, B.4    Van Roy, N.5
  • 40
    • 0017168760 scopus 로고
    • Properties of the K562 cell line, derived from a patient with chronic myeloid leukemia
    • Klein E, Ben-Bassat H, Neumann H, Ralph P, Zeuthen J, et al. (1976) Properties of the K562 cell line, derived from a patient with chronic myeloid leukemia. Int J Cancer 18: 421-431.
    • (1976) Int J Cancer , vol.18 , pp. 421-431
    • Klein, E.1    Ben-Bassat, H.2    Neumann, H.3    Ralph, P.4    Zeuthen, J.5
  • 41
    • 84872172430 scopus 로고    scopus 로고
    • Vorinostat induces apoptosis and differentiation in myeloid malignancies: Genetic and molecular mechanisms
    • Silva G, Cardoso BA, Belo H, Almeida AM (2013) Vorinostat induces apoptosis and differentiation in myeloid malignancies: genetic and molecular mechanisms. PLoS One 8: e53766.
    • (2013) PLoS One , vol.8
    • Silva, G.1    Cardoso, B.A.2    Belo, H.3    Almeida, A.M.4
  • 43
    • 33847077659 scopus 로고    scopus 로고
    • Beyond the sequence: Cellular organization of genome function
    • Misteli T (2007) Beyond the sequence: cellular organization of genome function. Cell 128: 787-800.
    • (2007) Cell , vol.128 , pp. 787-800
    • Misteli, T.1
  • 44
    • 84862908850 scopus 로고    scopus 로고
    • Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
    • Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, et al. (2012) Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148: 84-98.
    • (2012) Cell , vol.148 , pp. 84-98
    • Li, G.1    Ruan, X.2    Auerbach, R.K.3    Sandhu, K.S.4    Zheng, M.5
  • 45
    • 80054088836 scopus 로고    scopus 로고
    • Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics
    • Mendoza-Parra MA, Walia M, Sankar M, Gronemeyer H (2011) Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics. Mol Syst Biol 7: 538.
    • (2011) Mol Syst Biol , vol.7 , pp. 538
    • Mendoza-Parra, M.A.1    Walia, M.2    Sankar, M.3    Gronemeyer, H.4
  • 46
    • 84875972572 scopus 로고    scopus 로고
    • Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries
    • Jakobsen JS, Waage J, Rapin N, Bisgaard HC, Larsen FS, et al. (2013) Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries. Genome Res.
    • (2013) Genome Res
    • Jakobsen, J.S.1    Waage, J.2    Rapin, N.3    Bisgaard, H.C.4    Larsen, F.S.5
  • 48
    • 0025001736 scopus 로고
    • A growth factor-inducible nuclear protein with a novel cysteine/histidine repetitive sequence
    • DuBois RN, McLane MW, Ryder K, Lau LF, Nathans D (1990) A growth factor-inducible nuclear protein with a novel cysteine/histidine repetitive sequence. J Biol Chem 265: 19185-19191.
    • (1990) J Biol Chem , vol.265 , pp. 19185-19191
    • DuBois, R.N.1    McLane, M.W.2    Ryder, K.3    Lau, L.F.4    Nathans, D.5
  • 49
    • 0032516626 scopus 로고    scopus 로고
    • Feedback inhibition of macrophage tumor necrosis factor-alpha production by tristetraprolin
    • Carballo E, Lai WS, Blackshear PJ (1998) Feedback inhibition of macrophage tumor necrosis factor-alpha production by tristetraprolin. Science 281: 1001-1005. (Pubitemid 28399252)
    • (1998) Science , vol.281 , Issue.5379 , pp. 1001-1005
    • Carballo, E.1    Lai, W.S.2    Blackshear, P.J.3
  • 50
    • 84877771544 scopus 로고    scopus 로고
    • Identification of a mitochondrial target of thiazolidinedione insulin sensitizers (mTOT)-relationship to newly identified mitochondrial pyruvate carrier proteins
    • Colca JR, McDonald WG, Cavey GS, Cole SL, Holewa DD, et al. (2013) Identification of a mitochondrial target of thiazolidinedione insulin sensitizers (mTOT)-relationship to newly identified mitochondrial pyruvate carrier proteins. PLoS One 8: e61551.
    • (2013) PLoS One , vol.8
    • Colca, J.R.1    McDonald, W.G.2    Cavey, G.S.3    Cole, S.L.4    Holewa, D.D.5
  • 51
    • 4344573131 scopus 로고    scopus 로고
    • Phosphorylation of septin 3 on Ser-91 by cGMP-dependent protein kinase-I in nerve terminals
    • DOI 10.1042/BJ20040455
    • Xue J, Milburn PJ, Hanna BT, Graham ME, Rostas JA, et al. (2004) Phosphorylation of septin 3 on Ser-91 by cGMP-dependent protein kinase-I in nerve terminals. Biochem J 381: 753-760. (Pubitemid 39120485)
    • (2004) Biochemical Journal , vol.381 , Issue.3 , pp. 753-760
    • Xue, J.1    Milburn, P.J.2    Hanna, B.T.3    Graham, M.E.4    Rostas, J.A.P.5    Robinson, P.J.6
  • 52
    • 0025633966 scopus 로고
    • Isolation and characterization of cDNA encoding a human nuclear antigen predominantly recognized by autoantibodies from patients with primary biliary cirrhosis
    • Szostecki C, Guldner HH, Netter HJ, Will H (1990) Isolation and characterization of cDNA encoding a human nuclear antigen predominantly recognized by autoantibodies from patients with primary biliary cirrhosis. J Immunol 145: 4338-4347.
    • (1990) J Immunol , vol.145 , pp. 4338-4347
    • Szostecki, C.1    Guldner, H.H.2    Netter, H.J.3    Will, H.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.