메뉴 건너뛰기




Volumn 42, Issue 1, 2014, Pages 430-441

Covariation between homeodomain transcription factors and the shape of their DNA binding sites

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; HOMEODOMAIN PROTEIN;

EID: 84891777143     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt862     Document Type: Article
Times cited : (38)

References (54)
  • 1
    • 0000127073 scopus 로고
    • Sequencespecific recognition of double helical nucleic acids by proteins
    • Seeman, N.C., Rosenberg, J.M. and Rich, A. (1976) Sequencespecific recognition of double helical nucleic acids by proteins. Proc. Natl Acad. Sci. USA, 73, 804-808
    • (1976) Proc. Natl Acad. Sci. USA , vol.73 , pp. 804-808
    • Seeman, N.C.1    Rosenberg, J.M.2    Rich, A.3
  • 3
    • 84872522659 scopus 로고    scopus 로고
    • Opposites attract: Shape and electrostatic complementarity in protein-DNA complexes. Chapter 3
    • vol. II In: T. Schlick (ed). The Royal Society of Chemistry. Cambridge, UK.
    • Harris, R.C., Mackoy, T., Dantas Machado, A.C., Xu, D., Rohs, R. and Fenley, M.O. (2012) Opposites attract: Shape and electrostatic complementarity in protein-DNA complexes. Chapter 3, vol. II In: T. Schlick (ed). Innovations in Biomolecular Modeling and Simulations, 53-80. The Royal Society of Chemistry. Cambridge, UK
    • (2012) Innovations in Biomolecular Modeling and Simulations , pp. 53-80
    • Harris, R.C.1    Mackoy, T.2    Dantas Machado, A.C.3    Xu, D.4    Rohs, R.5    Fenley, M.O.6
  • 6
    • 84870397179 scopus 로고    scopus 로고
    • DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation
    • Chen, Y., Bates, D.L., Dey, R., Chen, P-H., Dantas Machado, A.C., Laird-Offringa, I.A., Rohs, R. and Chen, L. (2012) DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation. Cell Rep., 2, 1197-1206
    • (2012) Cell Rep , Issue.2 , pp. 1197-1206
    • Chen, Y.1    Bates, D.L.2    Dey, R.3    Chen, P.-H.4    Dantas Machado, A.C.5    Laird-Offringa, I.A.6    Rohs, R.7    Chen, L.8
  • 7
    • 84876955991 scopus 로고    scopus 로고
    • Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape
    • Gordâ n, R., Shen, N., Dror, I., Zhou, T., Horton, J., Rohs, R. and Bulyk, M.L. (2013) Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep., 3, 1093-1104
    • (2013) Cell Rep , Issue.3 , pp. 1093-1104
    • Gordân, R.1    Shen, N.2    Dror, I.3    Zhou, T.4    Horton, J.5    Rohs, R.6    Bulyk, M.L.7
  • 8
    • 70350686719 scopus 로고    scopus 로고
    • The role of DNA shape in protein-DNA recognition
    • Rohs, R., West, S.M., Sosinsky, A., Liu, P., Mann, R.S. and Honig, B. (2009) The role of DNA shape in protein-DNA recognition. Nature, 461, 1248-1253
    • (2009) Nature , vol.461 , pp. 1248-1253
    • Rohs, R.1    West, S.M.2    Sosinsky, A.3    Liu, P.4    Mann, R.S.5    Honig, B.6
  • 9
    • 77950934795 scopus 로고    scopus 로고
    • The shape of the DNA minor groove directs binding by the DNA-bending protein Fis
    • Stella, S., Cascio, D. and Johnson, R.C. (2010) The shape of the DNA minor groove directs binding by the DNA-bending protein Fis. Genes Dev., 24, 814-826
    • (2010) Genes Dev , Issue.24 , pp. 814-826
    • Stella, S.1    Cascio, D.2    Johnson, R.C.3
  • 11
    • 84876982103 scopus 로고    scopus 로고
    • Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen
    • Chang, Y.P., Xu, M., Dantas Machado, A.C., Yu, X.J., Rohs, R. and Chen, X.S. (2013) Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen. Cell Rep., 3, 1117-1127
    • (2013) Cell Rep , Issue.3 , pp. 1117-1127
    • Chang, Y.P.1    Xu, M.2    Dantas Machado, A.C.3    Yu, X.J.4    Rohs, R.5    Chen, X.S.6
  • 12
    • 0035912721 scopus 로고    scopus 로고
    • Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
    • Bulyk, M.L., Huang, X., Choo, Y. and Church, G.M. (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl Acad. Sci. USA, 98, 7158-7163
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 7158-7163
    • Bulyk, M.L.1    Huang, X.2    Choo, Y.3    Church, G.M.4
  • 13
    • 59949083631 scopus 로고    scopus 로고
    • Universal protein binding microarrays for the comprehensive characterization of the DNA binding specificities of transcription factors
    • Berger, M.F. and Bulyk, M.L. (2009) Universal protein binding microarrays for the comprehensive characterization of the DNA binding specificities of transcription factors. Nat. Protoc., 4, 393-411
    • (2009) Nat. Protoc , vol.4 , pp. 393-411
    • Berger, M.F.1    Bulyk, M.L.2
  • 15
    • 23444446753 scopus 로고    scopus 로고
    • A bacterial onehybrid system for determining the DNA-binding specificity of transcription factors
    • Meng, X., Brodsky, M.H. and Wolfe, S.A. (2005) A bacterial onehybrid system for determining the DNA-binding specificity of transcription factors. Nat. Biotechnol., 23, 988-994
    • (2005) Nat. Biotechnol , vol.23 , pp. 988-994
    • Meng, X.1    Brodsky, M.H.2    Wolfe, S.A.3
  • 16
    • 45449111373 scopus 로고    scopus 로고
    • Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
    • Noyes, M.B., Christensen, R.G., Wakabayashi, A., Stormo, G.D., Brodsky, M.H. and Wolfe, S.A. (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell, 133, 1277-1289
    • (2008) Cell , vol.133 , pp. 1277-1289
    • Noyes, M.B.1    Christensen, R.G.2    Wakabayashi, A.3    Stormo, G.D.4    Brodsky, M.H.5    Wolfe, S.A.6
  • 17
    • 74549209548 scopus 로고    scopus 로고
    • Inferring binding energies from selected binding sites
    • Zhao, Y., Granas, D. and Stormo, G.D. (2009) Inferring binding energies from selected binding sites. PLoS Comput. Biol., 5, e1000590
    • (2009) PLoS Comput. Biol , vol.5
    • Zhao, Y.1    Granas, D.2    Stormo, G.D.3
  • 18
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo, G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 19
    • 79958115193 scopus 로고    scopus 로고
    • Quantitative analysis demonstrates most transcription factors require only simple models of specificity
    • Zhao, Y. and Stormo, G.D. (2011) Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat. Biotechnol., 29, 480-483
    • (2011) Nat. Biotechnol , Issue.29 , pp. 480-483
    • Zhao, Y.1    Stormo, G.D.2
  • 22
    • 0035945567 scopus 로고    scopus 로고
    • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    • Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M. and Brown, P.O. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature, 409, 533-538
    • (2001) Nature , vol.409 , pp. 533-538
    • Iyer, V.R.1    Horak, C.E.2    Scafe, C.S.3    Botstein, D.4    Snyder, M.5    Brown, P.O.6
  • 23
    • 57449100870 scopus 로고    scopus 로고
    • Design and analysis of ChIP-seq experiments for DNA-binding proteins
    • Kharchenko, P.V., Tolstorukov, M.Y. and Park, P.J. (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol., 26, 1351-1359
    • (2008) Nat. Biotechnol , vol.26 , pp. 1351-1359
    • Kharchenko, P.V.1    Tolstorukov, M.Y.2    Park, P.J.3
  • 26
    • 0026504525 scopus 로고
    • Homeobox genes and axial patterning
    • McGinnis, W. and Krumlauf, R. (1992) Homeobox genes and axial patterning. Cell, 68, 283-302
    • (1992) Cell , vol.68 , pp. 283-302
    • McGinnis, W.1    Krumlauf, R.2
  • 27
    • 0027237596 scopus 로고
    • Tinman and bagpipe: Two homeo box genes that determine cell fates in the dorsal mesoderm of Drosophila
    • Azpiazu, N. and Frasch, M. (1993) tinman and bagpipe: Two homeo box genes that determine cell fates in the dorsal mesoderm of Drosophila. Genes Dev., 7, 1325-1340
    • (1993) Genes Dev , vol.7 , pp. 1325-1340
    • Azpiazu, N.1    Frasch, M.2
  • 28
    • 0033602242 scopus 로고    scopus 로고
    • Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex
    • Passner, J.M., Ryoo, H.D., Shen, L., Mann, R.S. and Aggarwal, A.K. (1999) Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex. Nature, 397, 714-719
    • (1999) Nature , vol.397 , pp. 714-719
    • Passner, J.M.1    Ryoo, H.D.2    Shen, L.3    Mann, R.S.4    Aggarwal, A.K.5
  • 29
    • 0032573434 scopus 로고    scopus 로고
    • Engrailed homeodomain-DNA complex at 2.2 å resolution: A detailed view of the interface and comparison with other engrailed structures
    • Fraenkel, E., Rould, M.A., Chambers, K.A. and Pabo, C.O. (1998) Engrailed homeodomain-DNA complex at 2.2 å resolution: A detailed view of the interface and comparison with other engrailed structures. J. Mol. Biol., 284, 351-361
    • (1998) J. Mol. Biol , vol.284 , pp. 351-361
    • Fraenkel, E.1    Rould, M.A.2    Chambers, K.A.3    Pabo, C.O.4
  • 30
    • 0028828745 scopus 로고
    • Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA
    • Li, T., Stark, M.R., Johnson, A.D. and Wolberger, C. (1995) Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA. Science, 270, 262-269
    • (1995) Science , vol.270 , pp. 262-269
    • Li, T.1    Stark, M.R.2    Johnson, A.D.3    Wolberger, C.4
  • 31
    • 0031851485 scopus 로고    scopus 로고
    • Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex
    • Fraenkel, E. and Pabo, C.O. (1998) Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex. Nat. Struct. Biol., 5, 692-697
    • (1998) Nat. Struct. Biol , vol.5 , pp. 692-697
    • Fraenkel, E.1    Pabo, C.O.2
  • 32
    • 0042161874 scopus 로고    scopus 로고
    • Structure of HoxA9 and Pbx1 bound to DNA: Hox hexapeptide and DNA recognition anterior to posterior
    • LaRonde-LeBlanc, N.A. and Wolberger, C. (2003) Structure of HoxA9 and Pbx1 bound to DNA: Hox hexapeptide and DNA recognition anterior to posterior. Genes Dev., 17, 2060-2072
    • (2003) Genes Dev , vol.17 , pp. 2060-2072
    • LaRonde-LeBlanc, N.A.1    Wolberger, C.2
  • 33
    • 67749095703 scopus 로고    scopus 로고
    • Hox specificity unique roles for cofactors and collaborators
    • Mann, R.S., Lelli, K.M. and Joshi, R. (2009) Hox specificity unique roles for cofactors and collaborators. Curr. Top. Dev. Biol., 88, 63-101
    • (2009) Curr. Top. Dev. Biol , vol.88 , pp. 63-101
    • Mann, R.S.1    Lelli, K.M.2    Joshi, R.3
  • 34
    • 0032524713 scopus 로고    scopus 로고
    • Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites
    • Mandel-Gutfreund, Y. and Margalit, H. (1998) Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites. Nucleic Acids Res., 26, 2306-2312
    • (1998) Nucleic Acids Res , vol.26 , pp. 2306-2312
    • Mandel-Gutfreund, Y.1    Margalit, H.2
  • 38
    • 34547830863 scopus 로고    scopus 로고
    • Inferring protein- DNA dependencies using motif alignments and mutual information
    • Mahony, S., Auron, P.E. and Benos, P.V. (2007) Inferring protein- DNA dependencies using motif alignments and mutual information. Bioinformatics, 23, i297-i304
    • (2007) Bioinformatics , vol.23
    • Mahony, S.1    Auron, P.E.2    Benos, P.V.3
  • 39
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh, K., Kuma, K., Toh, H. and Miyata, T. (2005) MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res., 33, 511-518
    • (2005) Nucleic Acids Res , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 40
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 41
    • 26444478194 scopus 로고    scopus 로고
    • Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites
    • Rohs, R., Sklenar, H. and Shakked, Z. (2005) Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites. Structure, 13, 1499-1509
    • (2005) Structure , vol.13 , pp. 1499-1509
    • Rohs, R.1    Sklenar, H.2    Shakked, Z.3
  • 42
    • 33750882505 scopus 로고    scopus 로고
    • Compact universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • Berger, M.F., Philippakis, A.A., Qureshi, A.M., He, F.S., Estep, P.W. and Bulyk, M.L. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol., 24, 1429-1435
    • (2006) Nat. Biotechnol , vol.24 , pp. 1429-1435
    • Berger, M.F.1    Philippakis, A.A.2    Qureshi, A.M.3    He, F.S.4    Estep, P.W.5    Bulyk, M.L.6
  • 44
    • 0024539180 scopus 로고
    • Defining the structure of irregular nucleic acids: Conventions and principles
    • Lavery, R. and Sklenar, H. (1989) Defining the structure of irregular nucleic acids: Conventions and principles. J. Biomol. Struct. Dyn., 6, 655-667
    • (1989) J. Biomol. Struct. Dyn , vol.6 , pp. 655-667
    • Lavery, R.1    Sklenar, H.2
  • 45
    • 0029595248 scopus 로고
    • Structure of the evenskipped homeodomain complexed to AT-rich DNA: New perspectives on homeodomain specificity
    • Hirsch, J.A. and Aggarwal, A.K. (1995) Structure of the evenskipped homeodomain complexed to AT-rich DNA: New perspectives on homeodomain specificity. EMBO J., 14, 6280-6291
    • (1995) EMBO J. , vol.14 , pp. 6280-6291
    • Hirsch, J.A.1    Aggarwal, A.K.2
  • 46
    • 0033569643 scopus 로고    scopus 로고
    • Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: Specific recognition of a protein-DNA interface
    • Chasman, D., Cepek, K., Sharp, P.A. and Pabo, C.O. (1999) Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: Specific recognition of a protein-DNA interface. Genes Dev., 13, 2650-2657
    • (1999) Genes Dev , vol.13 , pp. 2650-2657
    • Chasman, D.1    Cepek, K.2    Sharp, P.A.3    Pabo, C.O.4
  • 47
    • 77958096076 scopus 로고    scopus 로고
    • Determining the specificity of protein-DNA interactions
    • Stormo, G.D. and Zhao, Y. (2010) Determining the specificity of protein-DNA interactions. Nat. Rev. Genet., 11, 751-760
    • (2010) Nat. Rev. Genet , Issue.11 , pp. 751-760
    • Stormo, G.D.1    Zhao, Y.2
  • 49
    • 0036493201 scopus 로고    scopus 로고
    • Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
    • Bulyk, M.L., Johnson, P.L.F. and Church, G.M. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res., 30, 1255-1261
    • (2002) Nucleic Acids Res , vol.30 , pp. 1255-1261
    • Bulyk, M.L.1    Johnson, P.L.F.2    Church, G.M.3
  • 50
    • 0037109192 scopus 로고    scopus 로고
    • Additivity in protein-DNA interactions: How good an approximation is it?
    • Benos, P.V., Bulyk, M.L and Stormo, G.D. (2002) Additivity in protein-DNA interactions: How good an approximation is it? Nucleic Acids Res., 30, 4442-4451
    • (2002) Nucleic Acids Res , vol.30 , pp. 4442-4451
    • Benos, P.V.1    Bulyk, M.L.2    Stormo, G.D.3
  • 51
    • 50949097456 scopus 로고    scopus 로고
    • A feature-based approach to modeling protein-DNA interactions
    • Sharon, E., Lubliner, S. and Segal, E. (2008) A feature-based approach to modeling protein-DNA interactions. PLoS Comput. Biol., 4, e1000154
    • (2008) PLoS Comput. Biol , vol.4
    • Sharon, E.1    Lubliner, S.2    Segal, E.3
  • 52
    • 84863866025 scopus 로고    scopus 로고
    • Improved models for transcription factor binding site identification using nonindependent interactions
    • Zhao, Y., Ruan, S., Pandey, M. and Stormo, G.D. (2012) Improved models for transcription factor binding site identification using nonindependent interactions. Genetics, 191, 781-790
    • (2012) Genetics , vol.191 , pp. 781-790
    • Zhao, Y.1    Ruan, S.2    Pandey, M.3    Stormo, G.D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.