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Volumn 22, Issue 1, 2012, Pages 9-24

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

Author keywords

[No Author keywords available]

Indexed keywords

MYC PROTEIN; RNA POLYMERASE II; SPACER DNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CTCF;

EID: 84655173624     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.127597.111     Document Type: Article
Times cited : (94)

References (66)
  • 1
    • 23144464363 scopus 로고    scopus 로고
    • Transcriptional regulation and transformation by Myc proteins
    • DOI 10.1038/nrm1703
    • Adhikary S, Eilers M. 2005. Transcriptional regulation and transformation by Myc proteins. Nat Rev Mol Cell Biol 6: 635-645. (Pubitemid 41081267)
    • (2005) Nature Reviews Molecular Cell Biology , vol.6 , Issue.8 , pp. 635-645
    • Adhikary, S.1    Eilers, M.2
  • 3
    • 44449158814 scopus 로고    scopus 로고
    • Splicing, transcription, and chromatin: A ménage a trois
    • DOI 10.1016/j.gde.2008.01.006, PII S0959437X08000105
    • Allemand E, Batsche E, Muchardt C. 2008. Splicing, transcription, and chromatin: A menage a trois. Curr Opin Genet Dev 18: 145-151. (Pubitemid 351756536)
    • (2008) Current Opinion in Genetics and Development , vol.18 , Issue.2 , pp. 145-151
    • Allemand, E.1    Batsche, E.2    Muchardt, C.3
  • 4
    • 70349333201 scopus 로고    scopus 로고
    • Nucleosomes are well positioned in exons and carry characteristic histone modifications
    • Andersson R, Enroth S, Rada-Iglesias A, Wadelius C, Komorowski J. 2009. Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res 19: 1732-1741.
    • (2009) Genome Res , vol.19 , pp. 1732-1741
    • Andersson, R.1    Enroth, S.2    Rada-Iglesias, A.3    Wadelius, C.4    Komorowski, J.5
  • 5
    • 34249026300 scopus 로고    scopus 로고
    • High-Resolution Profiling of Histone Methylations in the Human Genome
    • DOI 10.1016/j.cell.2007.05.009, PII S0092867407006009
    • Barski A, Cuddapah S, Cui K, Roh TY, Schones DE,Wang Z,Wei G, Chepelev I, Zhao K. 2007.High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837. (Pubitemid 46802390)
    • (2007) Cell , vol.129 , Issue.4 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Roh, T.-Y.4    Schones, D.E.5    Wang, Z.6    Wei, G.7    Chepelev, I.8    Zhao, K.9
  • 10
    • 0031029141 scopus 로고    scopus 로고
    • Negative protein 1, which is required for function of the chicken lysozyme gene silencer in conjunction with hormone receptors, is identical to the multivalent zinc finger repressor CTCF
    • Burcin M, Arnold R, Lutz M, Kaiser B, Runge D, Lottspeich F, Filippova GN, Lobanenkov VV, Renkawitz R. 1997. Negative protein 1, which is required for function of the chicken lysozyme gene silencer in conjunction with hormone receptors, is identical to the multivalent zinc finger repressor CTCF. Mol Cell Biol 17: 1281-1288. (Pubitemid 27097357)
    • (1997) Molecular and Cellular Biology , vol.17 , Issue.3 , pp. 1281-1288
    • Burcin, M.1    Arnold, R.2    Lutz, M.3    Kaiser, B.4    Runge, D.5    Lottspeich, F.6    Filippova, G.N.7    Lobanenkov, V.V.8    Renkawitz, R.9
  • 13
    • 33947285072 scopus 로고    scopus 로고
    • The Myc transactivation domain promotes global phosphorylation of the RNA polymerase II carboxy-terminal domain independently of direct DNA binding
    • DOI 10.1128/MCB.01828-06
    • Cowling VH, Cole MD. 2007. The Myc transactivation domain promotes global phosphorylation of the RNA polymerase II carboxy-terminal domain independently of direct DNA binding. Mol Cell Biol 27: 2059-2073. (Pubitemid 46418464)
    • (2007) Molecular and Cellular Biology , vol.27 , Issue.6 , pp. 2059-2073
    • Cowling, V.H.1    Cole, M.D.2
  • 14
    • 60149095014 scopus 로고    scopus 로고
    • Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
    • Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K. 2009. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res 19: 24-32.
    • (2009) Genome Res , vol.19 , pp. 24-32
    • Cuddapah, S.1    Jothi, R.2    Schones, D.E.3    Roh, T.Y.4    Cui, K.5    Zhao, K.6
  • 15
    • 54849406775 scopus 로고    scopus 로고
    • Crosstalk between c-Myc and ribosome in ribosomal biogenesis and cancer
    • Dai MS, Lu H. 2008. Crosstalk between c-Myc and ribosome in ribosomal biogenesis and cancer. J Cell Biochem 105: 670-677.
    • (2008) J Cell Biochem , vol.105 , pp. 670-677
    • Dai, M.S.1    Lu, H.2
  • 16
    • 0032905924 scopus 로고    scopus 로고
    • c-Myc target genes involved in cell growth, apoptosis, and metabolism
    • Dang CV. 1999. c-Myc target genes involved in cell growth, apoptosis, and metabolism. Mol Cell Biol 19: 1-11. (Pubitemid 29018404)
    • (1999) Molecular and Cellular Biology , vol.19 , Issue.1 , pp. 1-11
    • Dang, C.V.1
  • 20
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • ENCODE Project Consortium
    • ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
    • (2007) Nature , vol.447 , pp. 799-816
  • 21
    • 79955550445 scopus 로고    scopus 로고
    • A user's guide to the encyclopedia of DNA elements (ENCODE)
    • ENCODE Project Consortium. doi: 10.1371/journal.pbio.1001046
    • ENCODE Project Consortium. 2011. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046. doi: 10.1371/journal.pbio.1001046.
    • (2011) PLoS Biol , vol.9
  • 23
    • 0029929793 scopus 로고    scopus 로고
    • An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes
    • Filippova GN, Fagerlie S, Klenova EM, Myers C, Dehner Y, Goodwin G, Neiman PE, Collins SJ, Lobanenkov VV. 1996. An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes. Mol Cell Biol 16: 2802-2813. (Pubitemid 26161284)
    • (1996) Molecular and Cellular Biology , vol.16 , Issue.6 , pp. 2802-2813
    • Filippova, G.N.1    Fagerlie, S.2    Klenova, E.M.3    Myers, C.4    Dehner, Y.5    Goodwin, G.6    Neiman, P.E.7    Collins, S.J.8    Lobanenkov, V.V.9
  • 24
    • 78149477660 scopus 로고    scopus 로고
    • Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
    • Gilchrist DA, Dos Santos G, Fargo DC, Xie B, Gao Y, Li L, Adelman K. 2010. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 143: 540-551.
    • (2010) Cell , vol.143 , pp. 540-551
    • Gilchrist, D.A.1    Dos Santos, G.2    Fargo, D.C.3    Xie, B.4    Gao, Y.5    Li, L.6    Adelman, K.7
  • 26
    • 0034713275 scopus 로고    scopus 로고
    • CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus
    • DOI 10.1038/35013106
    • Hark AT, Schoenherr CJ, Katz DJ, Ingram RS, Levorse JM, Tilghman SM. 2000. CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 405: 486-489. (Pubitemid 30367428)
    • (2000) Nature , vol.405 , Issue.6785 , pp. 486-489
    • Hark, A.T.1    Schoenherr, C.J.2    Katz, D.J.3    Ingram, R.S.4    Levorse, J.M.5    Tilghman, S.M.6
  • 28
    • 78649836342 scopus 로고    scopus 로고
    • Reciprocal intronic and exonic histone modification regions in humans
    • Huff JT, Plocik AM, Guthrie C, Yamamoto KR. 2010. Reciprocal intronic and exonic histone modification regions in humans. Nat Struct Mol Biol 17: 1495-1499.
    • (2010) Nat Struct Mol Biol , vol.17 , pp. 1495-1499
    • Huff, J.T.1    Plocik, A.M.2    Guthrie, C.3    Yamamoto, K.R.4
  • 29
  • 30
    • 33847173310 scopus 로고    scopus 로고
    • Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs
    • doi: 10.1186/1471-2105-7-114
    • Jin VX, Singer GA, Agosto-Perez FJ, Liyanarachchi S, Davuluri RV. 2006. Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. BMC Bioinformatics 7: 114. doi: 10.1186/1471-2105-7-114.
    • (2006) BMC Bioinformatics , vol.7 , pp. 114
    • Jin, V.X.1    Singer, G.A.2    Agosto-Perez, F.J.3    Liyanarachchi, S.4    Davuluri, R.V.5
  • 31
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • DOI 10.1126/science.1141319
    • Johnson DS, Mortazavi A, Myers RM,Wold B. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502. (Pubitemid 46906620)
    • (2007) Science , vol.316 , Issue.5830 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 32
  • 37
    • 0036866596 scopus 로고    scopus 로고
    • Multifunctional zinc finger proteins in development and disease
    • Ladomery M, Dellaire G. 2002. Multifunctional zinc finger proteins in development and disease. Ann Hum Genet 66: 331-342. (Pubitemid 36004223)
    • (2002) Annals of Human Genetics , vol.66 , Issue.5-6 , pp. 331-342
    • Ladomery, M.1    Dellaire, G.2
  • 39
    • 79956053726 scopus 로고    scopus 로고
    • Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis
    • Lee BK, Bhinge AA, Iyer VR. 2011. Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis. Nucleic Acids Res 39: 3558-3573.
    • (2011) Nucleic Acids Res , vol.39 , pp. 3558-3573
    • Lee, B.K.1    Bhinge, A.A.2    Iyer, V.R.3
  • 40
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 41
    • 34250324685 scopus 로고    scopus 로고
    • Transcription factor binding and modified histones in human bidirectional promoters
    • DOI 10.1101/gr.5623407
    • Lin JM, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z. 2007. Transcription factor binding and modified histones in human bidirectional promoters. Genome Res 17: 818-827. (Pubitemid 46919717)
    • (2007) Genome Research , vol.17 , Issue.6 , pp. 818-827
    • Lin, J.M.1    Collins, P.J.2    Trinklein, N.D.3    Fu, Y.4    Xi, H.5    Myers, R.M.6    Weng, Z.7
  • 44
    • 56749184298 scopus 로고    scopus 로고
    • Reflecting on 25 years with MYC
    • Meyer N, Penn LZ. 2008. Reflecting on 25 years with MYC. Nat Rev Cancer 8: 976-990.
    • (2008) Nat Rev Cancer , vol.8 , pp. 976-990
    • Meyer, N.1    Penn, L.Z.2
  • 45
    • 77951962545 scopus 로고    scopus 로고
    • Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells
    • Moqtaderi Z,Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K. 2010. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat StructMol Biol 17: 635-640.
    • (2010) Nat StructMol Biol , vol.17 , pp. 635-640
    • Moqtaderi, Z.1    Wang, J.2    Raha, D.3    White, R.J.4    Snyder, M.5    Weng, Z.6    Struhl, K.7
  • 46
    • 0035451090 scopus 로고    scopus 로고
    • CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease
    • DOI 10.1016/S0168-9525(01)02366-6, PII S0168952501023666
    • Ohlsson R, Renkawitz R, Lobanenkov V. 2001. CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet 17: 520-527. (Pubitemid 32763050)
    • (2001) Trends in Genetics , vol.17 , Issue.9 , pp. 520-527
    • Ohlsson, R.1    Renkawitz, R.2    Lobanenkov, V.3
  • 52
    • 69949132191 scopus 로고    scopus 로고
    • Chromatin organization marks exonintron structure
    • Schwartz S, Meshorer E, Ast G. 2009. Chromatin organization marks exonintron structure. Nat Struct Mol Biol 16: 990-995.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 990-995
    • Schwartz, S.1    Meshorer, E.2    Ast, G.3
  • 53
    • 41749091787 scopus 로고    scopus 로고
    • Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation
    • doi: 10.1371/journal.pbio.0060065
    • Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR. 2008. Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol 6: e65. doi: 10.1371/journal.pbio. 0060065.
    • (2008) PLoS Biol , vol.6
    • Shivaswamy, S.1    Bhinge, A.2    Zhao, Y.3    Jones, S.4    Hirst, M.5    Iyer, V.R.6
  • 54
    • 2342465953 scopus 로고    scopus 로고
    • Recent highlights of RNA-polymerase-II-mediated transcription
    • DOI 10.1016/j.ceb.2004.04.004, PII S0955067404000559
    • Sims RJ III, Mandal SS, Reinberg D. 2004. Recent highlights of RNA-polymerase-II-mediated transcription. Curr Opin Cell Biol 16: 263-271. (Pubitemid 38610406)
    • (2004) Current Opinion in Cell Biology , vol.16 , Issue.3 , pp. 263-271
    • Sims III, R.J.1    Mandal, S.S.2    Reinberg, D.3
  • 56
    • 70350013550 scopus 로고    scopus 로고
    • Biased chromatin signatures around polyadenylation sites and exons
    • Spies N, Nielsen CB, Padgett RA, Burge CB. 2009. Biased chromatin signatures around polyadenylation sites and exons. Mol Cell 36: 245-254.
    • (2009) Mol Cell , vol.36 , pp. 245-254
    • Spies, N.1    Nielsen, C.B.2    Padgett, R.A.3    Burge, C.B.4
  • 57
    • 39049163024 scopus 로고    scopus 로고
    • Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site
    • doi: 10.1371/journal.pone.0000807
    • Tabach Y, Brosh R, Buganim Y, Reiner A, Zuk O, Yitzhaky A, Koudritsky M, Rotter V, Domany E. 2007. Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS ONE 2: e807. doi: 10.1371/journal.pone.0000807.
    • (2007) PLoS ONE , vol.2
    • Tabach, Y.1    Brosh, R.2    Buganim, Y.3    Reiner, A.4    Zuk, O.5    Yitzhaky, A.6    Koudritsky, M.7    Rotter, V.8    Domany, E.9
  • 60
    • 77949920493 scopus 로고    scopus 로고
    • MYC as a regulator of ribosome biogenesis and protein synthesis
    • van Riggelen J, Yetil A, Felsher DW. 2010. MYC as a regulator of ribosome biogenesis and protein synthesis. Nat Rev Cancer 10: 301-309.
    • (2010) Nat Rev Cancer , vol.10 , pp. 301-309
    • Van Riggelen, J.1    Yetil, A.2    Felsher, D.W.3
  • 62
    • 0031468080 scopus 로고    scopus 로고
    • The zinc finger protein CTCF binds to the APBb domain of the amyloid β-protein precursor promoter: Evidence for a role in transcriptional activation
    • DOI 10.1074/jbc.272.52.33353
    • Vostrov AA, Quitschke WW. 1997. The zinc finger protein CTCF binds to the APBb domain of the amyloid β-protein precursor promoter. Evidence for a role in transcriptional activation. J Biol Chem 272: 33353-33359. (Pubitemid 28023686)
    • (1997) Journal of Biological Chemistry , vol.272 , Issue.52 , pp. 33353-33359
    • Vostrov, A.A.1    Quitschke, W.W.2
  • 63
    • 0037059774 scopus 로고    scopus 로고
    • A region to the N-terminal side of the CTCF zinc finger domain is essential for activating transcription from the amyloid precursor protein promoter
    • DOI 10.1074/jbc.M109748200
    • Vostrov AA, Taheny MJ, Quitschke WW. 2002. A region to the N-terminal side of the CTCF zinc finger domain is essential for activating transcription from the amyloid precursor protein promoter. J Biol Chem 277: 1619-1627. (Pubitemid 34968922)
    • (2002) Journal of Biological Chemistry , vol.277 , Issue.2 , pp. 1619-1627
    • Vostrov, A.A.1    Taheny, M.J.2    Quitschke, W.W.3
  • 64
    • 36248934318 scopus 로고    scopus 로고
    • The c-myc Promoter: Still MysterY and Challenge
    • DOI 10.1016/S0065-230X(07)99004-1, PII S0065230X07990041
    • Wierstra I, Alves J. 2008. The c-myc promoter: Still MysterY and challenge. Adv Cancer Res 99: 113-333. (Pubitemid 350137254)
    • (2008) Advances in Cancer Research , vol.99 , pp. 113-333
    • Wierstra, I.1    Alves, J.2
  • 65
    • 36549013619 scopus 로고    scopus 로고
    • RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo
    • DOI 10.1038/ng.2007.26, PII NG200726
    • Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, Adelman K, Levine M, Young RA. 2007. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet 39: 1512-1516. (Pubitemid 350191345)
    • (2007) Nature Genetics , vol.39 , Issue.12 , pp. 1512-1516
    • Zeitlinger, J.1    Stark, A.2    Kellis, M.3    Hong, J.-W.4    Nechaev, S.5    Adelman, K.6    Levine, M.7    Young, R.A.8
  • 66
    • 67649671966 scopus 로고    scopus 로고
    • SR proteins in vertical integration of gene expression from transcription to RNA processing to translation
    • Zhong XY, Wang P, Han J, Rosenfeld MG, Fu XD. 2009. SR proteins in vertical integration of gene expression from transcription to RNA processing to translation. Mol Cell 35: 1-10.
    • (2009) Mol Cell , vol.35 , pp. 1-10
    • Zhong, X.Y.1    Wang, P.2    Han, J.3    Rosenfeld, M.G.4    Fu, X.D.5


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