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Volumn 147, Issue 6, 2011, Pages 1408-1419

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution

Author keywords

[No Author keywords available]

Indexed keywords

EXONUCLEASE; RIBOSOME PROTEIN; TANSCRIPTION FACTOR PHD1; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CTCF; TRANSCRIPTION FACTOR GAL4; TRANSCRIPTION FACTOR RAP1; TRANSCRIPTION FACTOR REB1; UNCLASSIFIED DRUG;

EID: 83255164884     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2011.11.013     Document Type: Article
Times cited : (598)

References (57)
  • 1
    • 34047111213 scopus 로고    scopus 로고
    • Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
    • I. Albert, T.N. Mavrich, L.P. Tomsho, J. Qi, S.J. Zanton, S.C. Schuster, and B.F. Pugh Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome Nature 446 2007 572 576
    • (2007) Nature , vol.446 , pp. 572-576
    • Albert, I.1    Mavrich, T.N.2    Tomsho, L.P.3    Qi, J.4    Zanton, S.J.5    Schuster, S.C.6    Pugh, B.F.7
  • 2
    • 43349089437 scopus 로고    scopus 로고
    • GeneTrack - A genomic data processing and visualization framework
    • I. Albert, S. Wachi, C. Jiang, and B.F. Pugh GeneTrack - a genomic data processing and visualization framework Bioinformatics 24 2008 1305 1306
    • (2008) Bioinformatics , vol.24 , pp. 1305-1306
    • Albert, I.1    Wachi, S.2    Jiang, C.3    Pugh, B.F.4
  • 6
    • 38549161074 scopus 로고    scopus 로고
    • CTCFBSDB: A CTCF-binding site database for characterization of vertebrate genomic insulators
    • L. Bao, M. Zhou, and Y. Cui CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators Nucleic Acids Res. 36 Database issue 2008 D83 D87
    • (2008) Nucleic Acids Res. , vol.36 , Issue.DATABASE ISSUE
    • Bao, L.1    Zhou, M.2    Cui, Y.3
  • 9
    • 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 NISC Comparative Sequencing Program Baylor College of Medicine Human Genome Sequencing Center Washington University Genome Sequencing Center Broad Institute Children's Hospital Oakland Research Institute
    • E. Birney, J.A. Stamatoyannopoulos, A. Dutta, R. Guigó, T.R. Gingeras, E.H. Margulies, Z. Weng, M. Snyder, E.T. Dermitzakis, R.E. Thurman ENCODE Project Consortium NISC Comparative Sequencing Program Baylor College of Medicine Human Genome Sequencing Center Washington University Genome Sequencing Center Broad Institute Children's Hospital Oakland Research Institute Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 447 2007 799 816
    • (2007) Nature , vol.447 , pp. 799-816
    • Birney, E.1    Stamatoyannopoulos, J.A.2    Dutta, A.3    Guigó, R.4    Gingeras, T.R.5    Margulies, E.H.6    Weng, Z.7    Snyder, M.8    Dermitzakis, E.T.9    Thurman, R.E.10
  • 12
    • 60149095014 scopus 로고    scopus 로고
    • Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
    • S. Cuddapah, R. Jothi, D.E. Schones, T.Y. Roh, K. Cui, and K. Zhao Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains Genome Res. 19 2009 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
  • 13
    • 0035986888 scopus 로고    scopus 로고
    • Evolution of transcription factor binding sites in Mammalian gene regulatory regions: Conservation and turnover
    • E.T. Dermitzakis, and A.G. Clark Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover Mol. Biol. Evol. 19 2002 1114 1121
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1114-1121
    • Dermitzakis, E.T.1    Clark, A.G.2
  • 14
    • 33947137710 scopus 로고    scopus 로고
    • Dynamics of replication-independent histone turnover in budding yeast
    • M.F. Dion, T. Kaplan, M. Kim, S. Buratowski, N. Friedman, and O.J. Rando Dynamics of replication-independent histone turnover in budding yeast Science 315 2007 1405 1408
    • (2007) Science , vol.315 , pp. 1405-1408
    • Dion, M.F.1    Kaplan, T.2    Kim, M.3    Buratowski, S.4    Friedman, N.5    Rando, O.J.6
  • 15
    • 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
    • G.N. Filippova, S. Fagerlie, E.M. Klenova, C. Myers, Y. Dehner, G. Goodwin, P.E. Neiman, S.J. Collins, and V.V. Lobanenkov 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 1996 2802 2813
    • (1996) Mol. Cell. Biol. , vol.16 , 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
  • 16
    • 0028265881 scopus 로고
    • Induction of pseudohyphal growth by overexpression of PHD1, a Saccharomyces cerevisiae gene related to transcriptional regulators of fungal development
    • C.J. Gimeno, and G.R. Fink Induction of pseudohyphal growth by overexpression of PHD1, a Saccharomyces cerevisiae gene related to transcriptional regulators of fungal development Mol. Cell. Biol. 14 1994 2100 2112
    • (1994) Mol. Cell. Biol. , vol.14 , pp. 2100-2112
    • Gimeno, C.J.1    Fink, G.R.2
  • 18
    • 65249164132 scopus 로고    scopus 로고
    • Mechanisms that specify promoter nucleosome location and identity
    • P.D. Hartley, and H.D. Madhani Mechanisms that specify promoter nucleosome location and identity Cell 137 2009 445 458
    • (2009) Cell , vol.137 , pp. 445-458
    • Hartley, P.D.1    Madhani, H.D.2
  • 20
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • D.S. Johnson, A. Mortazavi, R.M. Myers, and B. Wold Genome-wide mapping of in vivo protein-DNA interactions Science 316 2007 1497 1502
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 21
    • 52649132425 scopus 로고    scopus 로고
    • Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    • R. Jothi, S. Cuddapah, A. Barski, K. Cui, and K. Zhao Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data Nucleic Acids Res. 36 2008 5221 5231
    • (2008) Nucleic Acids Res. , vol.36 , pp. 5221-5231
    • Jothi, R.1    Cuddapah, S.2    Barski, A.3    Cui, K.4    Zhao, K.5
  • 23
    • 70349173215 scopus 로고    scopus 로고
    • Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome
    • R.T. Koerber, H.S. Rhee, C. Jiang, and B.F. Pugh Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome Mol. Cell 35 2009 889 902
    • (2009) Mol. Cell , vol.35 , pp. 889-902
    • Koerber, R.T.1    Rhee, H.S.2    Jiang, C.3    Pugh, B.F.4
  • 25
    • 0029938794 scopus 로고    scopus 로고
    • DNA sequence preferences of GAL4 and PPR1: How a subset of Zn2 Cys6 binuclear cluster proteins recognizes DNA
    • S.D. Liang, R. Marmorstein, S.C. Harrison, and M. Ptashne DNA sequence preferences of GAL4 and PPR1: how a subset of Zn2 Cys6 binuclear cluster proteins recognizes DNA Mol. Cell. Biol. 16 1996 3773 3780
    • (1996) Mol. Cell. Biol. , vol.16 , pp. 3773-3780
    • Liang, S.D.1    Marmorstein, R.2    Harrison, S.C.3    Ptashne, M.4
  • 26
    • 0034934774 scopus 로고    scopus 로고
    • Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
    • J.D. Lieb, X. Liu, D. Botstein, and P.O. Brown Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association Nat. Genet. 28 2001 327 334
    • (2001) Nat. Genet. , vol.28 , pp. 327-334
    • Lieb, J.D.1    Liu, X.2    Botstein, D.3    Brown, P.O.4
  • 27
    • 0016640172 scopus 로고
    • The general affinity of lac repressor for E. coli DNA: Implications for gene regulation in procaryotes and eucaryotes
    • S. Lin, and A.D. Riggs The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eucaryotes Cell 4 1975 107 111
    • (1975) Cell , vol.4 , pp. 107-111
    • Lin, S.1    Riggs, A.D.2
  • 29
    • 0026547747 scopus 로고
    • DNA recognition by GAL4: Structure of a protein-DNA complex
    • R. Marmorstein, M. Carey, M. Ptashne, and S.C. Harrison DNA recognition by GAL4: structure of a protein-DNA complex Nature 356 1992 408 414
    • (1992) Nature , vol.356 , pp. 408-414
    • Marmorstein, R.1    Carey, M.2    Ptashne, M.3    Harrison, S.C.4
  • 30
    • 0026320245 scopus 로고
    • Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae
    • C.M. Moehle, and A.G. Hinnebusch Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae Mol. Cell. Biol. 11 1991 2723 2735
    • (1991) Mol. Cell. Biol. , vol.11 , pp. 2723-2735
    • Moehle, C.M.1    Hinnebusch, A.G.2
  • 32
    • 0035451090 scopus 로고    scopus 로고
    • CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease
    • R. Ohlsson, R. Renkawitz, and V. Lobanenkov CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease Trends Genet. 17 2001 520 527
    • (2001) Trends Genet. , vol.17 , pp. 520-527
    • Ohlsson, R.1    Renkawitz, R.2    Lobanenkov, V.3
  • 33
    • 74949102277 scopus 로고    scopus 로고
    • Does CTCF mediate between nuclear organization and gene expression?
    • R. Ohlsson, V. Lobanenkov, and E. Klenova Does CTCF mediate between nuclear organization and gene expression? Bioessays 32 2010 37 50
    • (2010) Bioessays , vol.32 , pp. 37-50
    • Ohlsson, R.1    Lobanenkov, V.2    Klenova, E.3
  • 35
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: Master weaver of the genome
    • J.E. Phillips, and V.G. Corces CTCF: master weaver of the genome Cell 137 2009 1194 1211
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 38
  • 40
    • 0001473216 scopus 로고
    • Formaldehyde-mediated DNA-protein crosslinking: A probe for in vivo chromatin structures
    • M.J. Solomon, and A. Varshavsky Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures Proc. Natl. Acad. Sci. USA 82 1985 6470 6474
    • (1985) Proc. Natl. Acad. Sci. USA , vol.82 , pp. 6470-6474
    • Solomon, M.J.1    Varshavsky, A.2
  • 41
  • 42
    • 60349122111 scopus 로고    scopus 로고
    • A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome
    • B.J. Venters, and B.F. Pugh A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome Genome Res. 19 2009 360 371
    • (2009) Genome Res. , vol.19 , pp. 360-371
    • Venters, B.J.1    Pugh, B.F.2
  • 43
    • 0016376109 scopus 로고
    • Non-specific DNA binding of genome regulating proteins as a biological control mechanism: I. The lac operon: Equilibrium aspects
    • P.H. von Hippel, A. Revzin, C.A. Gross, and A.C. Wang Non-specific DNA binding of genome regulating proteins as a biological control mechanism: I. The lac operon: equilibrium aspects Proc. Natl. Acad. Sci. USA 71 1974 4808 4812
    • (1974) Proc. Natl. Acad. Sci. USA , vol.71 , pp. 4808-4812
    • Von Hippel, P.H.1    Revzin, A.2    Gross, C.A.3    Wang, A.C.4
  • 45
    • 0029864437 scopus 로고    scopus 로고
    • DNA binding specificity of two homeodomain proteins in vitro and in Drosophila embryos
    • J. Walter, and M.D. Biggin DNA binding specificity of two homeodomain proteins in vitro and in Drosophila embryos Proc. Natl. Acad. Sci. USA 93 1996 2680 2685
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 2680-2685
    • Walter, J.1    Biggin, M.D.2
  • 47
    • 33847057887 scopus 로고    scopus 로고
    • Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells
    • A. Yang, Z. Zhu, P. Kapranov, F. McKeon, G.M. Church, T.R. Gingeras, and K. Struhl Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells Mol. Cell 24 2006 593 602
    • (2006) Mol. Cell , vol.24 , pp. 593-602
    • Yang, A.1    Zhu, Z.2    Kapranov, P.3    McKeon, F.4    Church, G.M.5    Gingeras, T.R.6    Struhl, K.7
  • 48
    • 77953740831 scopus 로고    scopus 로고
    • Genome-wide mapping of estrogen receptor-beta-binding regions reveals extensive cross-talk with transcription factor activator protein-1
    • C. Zhao, H. Gao, Y. Liu, Z. Papoutsi, S. Jaffrey, J.A. Gustafsson, and K. Dahlman-Wright Genome-wide mapping of estrogen receptor-beta-binding regions reveals extensive cross-talk with transcription factor activator protein-1 Cancer Res. 70 2010 5174 5183
    • (2010) Cancer Res. , vol.70 , pp. 5174-5183
    • Zhao, C.1    Gao, H.2    Liu, Y.3    Papoutsi, Z.4    Jaffrey, S.5    Gustafsson, J.A.6    Dahlman-Wright, K.7
  • 50
    • 34047111213 scopus 로고    scopus 로고
    • Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
    • Albert, I., Mavrich, T.N., Tomsho, L.P., Qi, J., Zanton, S.J., Schuster, S.C., and Pugh, B.F. (2007). Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446, 572-576.
    • (2007) Nature , vol.446 , pp. 572-576
    • Albert, I.1    Mavrich, T.N.2    Tomsho, L.P.3    Qi, J.4    Zanton, S.J.5    Schuster, S.C.6    Pugh, B.F.7
  • 51
    • 43349089437 scopus 로고    scopus 로고
    • GeneTrack - A genomic data processing and visualization framework
    • Albert, I., Wachi, S., Jiang, C., and Pugh, B.F. (2008). GeneTrack - a genomic data processing and visualization framework. Bioinformatics 24, 1305-1306.
    • (2008) Bioinformatics , vol.24 , pp. 1305-1306
    • Albert, I.1    Wachi, S.2    Jiang, C.3    Pugh, B.F.4
  • 52
    • 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, D.E., Roh, T.Y., Cui, K., and 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
  • 53
    • 70350731108 scopus 로고    scopus 로고
    • Distinguishing direct versus indirect transcription factor-DNA interactions
    • Gordân, R., Hartemink, A.J., and Bulyk, M.L. (2009). Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res. 19, 2090-2100.
    • (2009) Genome Res. , vol.19 , pp. 2090-2100
    • Gordân, R.1
  • 55
    • 70349173215 scopus 로고    scopus 로고
    • Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome
    • Koerber, R.T., Rhee, H.S., Jiang, C., and Pugh, B.F. (2009). Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome. Mol. Cell 35, 889-902.
    • (2009) Mol. Cell , vol.35 , pp. 889-902
    • Koerber, R.T.1    Rhee, H.S.2    Jiang, C.3    Pugh, B.F.4
  • 57
    • 60349122111 scopus 로고    scopus 로고
    • A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome
    • Venters, B.J., and Pugh, B.F. (2009). A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res. 19, 360-371.
    • (2009) Genome Res. , vol.19 , pp. 360-371
    • Venters, B.J.1    Pugh, B.F.2


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