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Volumn 323, Issue 4, 2002, Pages 701-727

Probabilistic code for DNA recognition by proteins of the EGR family

Author keywords

DNA binding specificity; DNA protein interactions; Recognition code; Zinc finger proteins

Indexed keywords

EARLY GROWTH RESPONSE FACTOR 1; EGR PROTEIN; PROTEIN DERIVATIVE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

EID: 0036977044     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00917-8     Document Type: Article
Times cited : (99)

References (51)
  • 1
    • 0000127073 scopus 로고
    • Sequence-specific recognition of double helical nucleic acids by proteins
    • Seeman, N. C., Rosenberg, J. M. & Rich, A. (1976). Sequence-specific 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
    • 0024294636 scopus 로고
    • Protein-DNA interaction. No code for recognition
    • Matthews, B. W. (1988). Protein-DNA interaction. No code for recognition. Nature, 335, 294-295.
    • (1988) Nature , vol.335 , pp. 294-295
    • Matthews, B.W.1
  • 4
    • 0026089185 scopus 로고
    • Base sequence discrimination by zinc-finger DNA-binding domains
    • Nardelli, J., Gibson, T. J., Vesque, C. & Charnay, P. (1991). Base sequence discrimination by zinc-finger DNA-binding domains. Nature, 349, 175-178.
    • (1991) Nature , vol.349 , pp. 175-178
    • Nardelli, J.1    Gibson, T.J.2    Vesque, C.3    Charnay, P.4
  • 5
    • 0026742626 scopus 로고
    • Toward rules relating zinc finger protein sequences and DNA binding site preferences
    • Desjarlais, J. R. & Berg, J. M. (1992). Toward rules relating zinc finger protein sequences and DNA binding site preferences. Proc. Natl Acad. Sci. USA, 89, 7345-7349.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 7345-7349
    • Desjarlais, J.R.1    Berg, J.M.2
  • 6
    • 0029822407 scopus 로고    scopus 로고
    • A zinc finger directory for high-affinity DNA recognition
    • Jamieson, A. C., Wang, H. & Kim, S. H. (1996). A zinc finger directory for high-affinity DNA recognition. Proc. Natl Acad. Sci. USA, 93, 12834-12839.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 12834-12839
    • Jamieson, A.C.1    Wang, H.2    Kim, S.H.3
  • 7
    • 0032524713 scopus 로고    scopus 로고
    • Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites
    • Mandel-Gutfreund, Y. & Margalit, H. (1998). Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. Nucl. Acids Res. 26, 2306-2312.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 2306-2312
    • Mandel-Gutfreund, Y.1    Margalit, H.2
  • 9
    • 0035393302 scopus 로고    scopus 로고
    • Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
    • Luscombe, N. M., Laskowski, R. A. & Thornton, J. M. (2001). Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucl. Acids Res. 29, 2860-2874.
    • (2001) Nucl. Acids Res. , vol.29 , pp. 2860-2874
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3
  • 10
  • 11
    • 0031042082 scopus 로고    scopus 로고
    • Physical basis of a protein-DNA recognition code
    • Choo, Y. & Klug, A. (1997). Physical basis of a protein-DNA recognition code. Curr. Opin. Struct. Biol. 7, 117-125.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 117-125
    • Choo, Y.1    Klug, A.2
  • 12
    • 0033120215 scopus 로고    scopus 로고
    • Structure-based prediction of DNA target sites by regulatory proteins
    • Kono, H. & Sarai, A. (1999). Structure-based prediction of DNA target sites by regulatory proteins. Proteins: Struct. Funct. Genet. 35, 114-131.
    • (1999) Proteins: Struct. Funct. Genet. , vol.35 , pp. 114-131
    • Kono, H.1    Sarai, A.2
  • 13
    • 0035221367 scopus 로고    scopus 로고
    • A structure-based approach for prediction of protein binding sites in gene-upstream regions
    • Mandel-Gutfreund, Y., Baron, A. & Margalit, H. (2001). A structure-based approach for prediction of protein binding sites in gene-upstream regions. Pac. Symp. Biocomput. 6, 139-150.
    • (2001) Pac. Symp. Biocomput. , vol.6 , pp. 139-150
    • Mandel-Gutfreund, Y.1    Baron, A.2    Margalit, H.3
  • 14
    • 0033524954 scopus 로고    scopus 로고
    • Analysis of zinc fingers optimized via phage display: Evaluating the utility of a recognition code
    • Wolfe, S. A., Greisman, H. A., Ramm, E. I. & Pabo, C. O. (1999). Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J. Mol. Biol. 285, 1917-1934.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1917-1934
    • Wolfe, S.A.1    Greisman, H.A.2    Ramm, E.I.3    Pabo, C.O.4
  • 15
    • 0031042082 scopus 로고    scopus 로고
    • Physical basis of a protein-DNA recognition code
    • Choo, Y. & Klug, A. (1997). Physical basis of a protein-DNA recognition code. Curr. Opin. Struct. Biol. 7, 117-125.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 117-125
    • Choo, Y.1    Klug, A.2
  • 16
    • 0035914475 scopus 로고    scopus 로고
    • Rearrangement of side-chains in Zif268 mutant highlights the complexities of zinc-finger DNA recognition
    • Miller, J. C. & Pabo, C. O. (2001). Rearrangement of side-chains in Zif268 mutant highlights the complexities of zinc-finger DNA recognition. J. Mol. Biol. 313, 309-315.
    • (2001) J. Mol. Biol. , vol.313 , pp. 309-315
    • Miller, J.C.1    Pabo, C.O.2
  • 18
    • 0035875327 scopus 로고    scopus 로고
    • Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay
    • Man, T.-K. & Stormo, G. D. (2001). Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucl. Acids Res. 15, 2471-2478.
    • (2001) Nucl. Acids Res. , vol.15 , pp. 2471-2478
    • Man, T.-K.1    Stormo, G.D.2
  • 19
    • 0036493201 scopus 로고    scopus 로고
    • Nucleotides of transcription factor binding sites exert inter-dependent effects on the binding affinities of transcription factors
    • Bulyk, M. L., Johnson, P. L. F. & Church, G. M. (2002). Nucleotides of transcription factor binding sites exert inter-dependent effects on the binding affinities of transcription factors. Nucl. Acids Res. 30, 1255-1261.
    • (2002) Nucl. Acids Res. , vol.30 , pp. 1255-1261
    • Bulyk, M.L.1    Johnson, P.L.F.2    Church, G.M.3
  • 20
    • 0037109192 scopus 로고    scopus 로고
    • Additivity on protein-DNA interactions: How good an approximation is it?
    • In press
    • Benos, P. V., Bulyk, M. L. & Stormo, G. D. (2002). Additivity on protein-DNA interactions: how good an approximation is it? Nucl. Acids Res. In press.
    • (2002) Nucl. Acids Res.
    • Benos, P.V.1    Bulyk, M.L.2    Stormo, G.D.3
  • 21
    • 0023491356 scopus 로고
    • A nerve growth factor-induced gene encodes a possible transcriptional regulatory factor
    • Milbrandt, J. (1987). A nerve growth factor-induced gene encodes a possible transcriptional regulatory factor. Science, 238, 797-799.
    • (1987) Science , vol.238 , pp. 797-799
    • Milbrandt, J.1
  • 22
    • 0024281381 scopus 로고
    • A zinc finger-encoding gene coregulated with c-fos during growth and differentiation, and after cellular depolarization
    • Sukhatme, V. P., Cao, X., Chang, L. C., Tsai-Morris, C-H., Stamenkovich, D., Ferreira, P. C. P. et al. (1988). A zinc finger-encoding gene coregulated with c-fos during growth and differentiation, and after cellular depolarization. Cell, 53, 37-43.
    • (1988) Cell , vol.53 , pp. 37-43
    • Sukhatme, V.P.1    Cao, X.2    Chang, L.C.3    Tsai-Morris, C.-H.4    Stamenkovich, D.5    Ferreira, P.C.P.6
  • 23
    • 0026511496 scopus 로고
    • A gene coding for a zinc finger protein is induced during 12-O-tetradecanoylphorbol-13-acetate-stimulated HL-60 cell differentiation
    • Shimizu, N., Ohta, M., Fujiwara, C., Sagara, J., Mochizuki, N., Oda, T. & Utiyama, H. (1992). A gene coding for a zinc finger protein is induced during 12-O-tetradecanoylphorbol-13-acetate-stimulated HL-60 cell differentiation. J. Biochem. 111, 272-277.
    • (1992) J. Biochem. , vol.111 , pp. 272-277
    • Shimizu, N.1    Ohta, M.2    Fujiwara, C.3    Sagara, J.4    Mochizuki, N.5    Oda, T.6    Utiyama, H.7
  • 24
    • 0027089949 scopus 로고
    • The structure and expression of the Xenopus Krox-20 gene: Conserved and divergent patterns of expression in rhombomeres and neural crest
    • Bradley, L. C., Snape, A., Bhatt, S. & Wilkinson, D. G. (1993). The structure and expression of the Xenopus Krox-20 gene: conserved and divergent patterns of expression in rhombomeres and neural crest. Mech. Dev. 40, 73-84.
    • (1993) Mech. Dev. , vol.40 , pp. 73-84
    • Bradley, L.C.1    Snape, A.2    Bhatt, S.3    Wilkinson, D.G.4
  • 25
    • 0028043420 scopus 로고
    • The zebrafish EGR1 gene encodes a highly conserved, zinc-finger transcriptional regulator
    • Drummond, I. A., Rohwer-Nutter, P. & Sukhatme, V. P. (1994). The zebrafish EGR1 gene encodes a highly conserved, zinc-finger transcriptional regulator. DNA Cell Biol. 13, 1047-1055.
    • (1994) DNA Cell Biol. , vol.13 , pp. 1047-1055
    • Drummond, I.A.1    Rohwer-Nutter, P.2    Sukhatme, V.P.3
  • 27
    • 0025773296 scopus 로고
    • Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 Å
    • Pavletich, N. P. & Pabo, C. O. (1991). Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å. Science, 252, 809-817.
    • (1991) Science , vol.252 , pp. 809-817
    • Pavletich, N.P.1    Pabo, C.O.2
  • 28
    • 0030587774 scopus 로고    scopus 로고
    • Zif268 protein-DNA complex refined at 1.6 Å: A model system for understanding zinc finger-DNA interactions
    • Elrod-Erickson, M., Rould, M. A., Nekludova, L. & Pabo, C. O. (1996). Zif268 protein-DNA complex refined at 1.6 Å: a model system for understanding zinc finger-DNA interactions. Structure, 4, 1171-1180.
    • (1996) Structure , vol.4 , pp. 1171-1180
    • Elrod-Erickson, M.1    Rould, M.A.2    Nekludova, L.3    Pabo, C.O.4
  • 29
    • 0032522662 scopus 로고    scopus 로고
    • High-resolution structures of variant Zif268-DNA complexes: Implications for understanding zinc finger-DNA recognition
    • Elrod-Erickson, M., Benson, T. E. & Pabo, C. O. (1998). High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. Structure, 6, 451-464.
    • (1998) Structure , vol.6 , pp. 451-464
    • Elrod-Erickson, M.1    Benson, T.E.2    Pabo, C.O.3
  • 30
    • 0027994717 scopus 로고
    • Toward a code for the interactions of zinc fingers with DNA: Selection of randomized fingers displayed on phage
    • Choo, Y. & Klug, A. (1994). Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage. Proc. Natl Acad. Sci. USA, 91, 11163-11167.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 11163-11167
    • Choo, Y.1    Klug, A.2
  • 31
    • 0028046895 scopus 로고
    • Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions
    • Choo, Y. & Klug, A. (1994). Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc. Natl Acad. Sci. USA, 91, 11168-11172.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 11168-11172
    • Choo, Y.1    Klug, A.2
  • 32
    • 0024531901 scopus 로고
    • Facilitated target location in biological systems
    • von Hippel, P. H. & Berg, O. G. (1989). Facilitated target location in biological systems. J. Biol. Chem. 264, 675-678.
    • (1989) J. Biol. Chem. , vol.264 , pp. 675-678
    • Von Hippel, P.H.1    Berg, O.G.2
  • 34
    • 0031053362 scopus 로고    scopus 로고
    • A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites
    • Greisman, H. A. & Pabo, C. O. (1997). A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science, 275, 657-661.
    • (1997) Science , vol.275 , pp. 657-661
    • Greisman, H.A.1    Pabo, C.O.2
  • 35
    • 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
  • 37
    • 0029779351 scopus 로고    scopus 로고
    • Egr-1 activates basic fibroblast growth factor transcription
    • Biesiada, E., Razandi, M. & Levin, E. R. (1996). Egr-1 activates basic fibroblast growth factor transcription. J. Biol. Chem. 271, 18576-18581.
    • (1996) J. Biol. Chem. , vol.271 , pp. 18576-18581
    • Biesiada, E.1    Razandi, M.2    Levin, E.R.3
  • 38
    • 0029090347 scopus 로고
    • A regulatory element in the human interleukin 2 gene promoter is a binding site for the zinc finger proteins sp1 and EGR-1
    • Skerka, C., Decker, E. L. & Zipfel, P. F. (1995). A regulatory element in the human interleukin 2 gene promoter is a binding site for the zinc finger proteins sp1 and EGR-1. J. Biol. Chem. 270, 22500-22506.
    • (1995) J. Biol. Chem. , vol.270 , pp. 22500-22506
    • Skerka, C.1    Decker, E.L.2    Zipfel, P.F.3
  • 39
    • 0025965525 scopus 로고
    • Two monomers of yeast transcription factor ADR1 bind a palindromic sequence symmetrically to activate ADH2 expression
    • Thukral, S. K., Eisen, A. & Young, E. T. (1991). Two monomers of yeast transcription factor ADR1 bind a palindromic sequence symmetrically to activate ADH2 expression. Mol. Cell. Biol. 11, 1566-1577.
    • (1991) Mol. Cell. Biol. , vol.11 , pp. 1566-1577
    • Thukral, S.K.1    Eisen, A.2    Young, E.T.3
  • 40
    • 0031761689 scopus 로고    scopus 로고
    • Characterization of three related glucose repressors and genes they regulate in S. cerevisiae
    • Lutfiyya, L. L., Iyer, V. R., DeRisi, J., DeVit, M. J., Brown, P. O. & Johnston, M. (1998). Characterization of three related glucose repressors and genes they regulate in S. cerevisiae. Genetics, 150, 1377-1391.
    • (1998) Genetics , vol.150 , pp. 1377-1391
    • Lutfiyya, L.L.1    Iyer, V.R.2    DeRisi, J.3    DeVit, M.J.4    Brown, P.O.5    Johnston, M.6
  • 41
    • 0023042012 scopus 로고
    • Information content of binding sites on nucleotide sequences
    • Schneider, T. D., Stormo, G. D., Gold, L. & Ehrenfeucht, A. (1986). Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188, 415-431.
    • (1986) J. Mol. Biol. , vol.188 , pp. 415-431
    • Schneider, T.D.1    Stormo, G.D.2    Gold, L.3    Ehrenfeucht, A.4
  • 42
    • 0034711731 scopus 로고    scopus 로고
    • An accessory DNA binding motif in the zinc finger protein Adr1 assists stable binding to DNA and can be replaced by a third finger
    • Young, E. T., Kacherovsky, N. & Cheng, C. (2000). An accessory DNA binding motif in the zinc finger protein Adr1 assists stable binding to DNA and can be replaced by a third finger. Biochemistry, 39, 567-574.
    • (2000) Biochemistry , vol.39 , pp. 567-574
    • Young, E.T.1    Kacherovsky, N.2    Cheng, C.3
  • 43
    • 0027749348 scopus 로고
    • The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recongition
    • Fairall, L., Schwabe, J. W. R., Chapman, L., Finch, J. T. & Rhodes, D. (1993). The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recongition. Nature, 366, 483-487.
    • (1993) Nature , vol.366 , pp. 483-487
    • Fairall, L.1    Schwabe, J.W.R.2    Chapman, L.3    Finch, J.T.4    Rhodes, D.5
  • 44
    • 0032539651 scopus 로고    scopus 로고
    • Comparison of the DNA binding characteristics of the related zinc finger proteins WT1 and EGR1
    • Hamilton, T. B., Borel, F. & Romaniuk, P. J. (1998). Comparison of the DNA binding characteristics of the related zinc finger proteins WT1 and EGR1. Biochemistry, 37, 2051-2058.
    • (1998) Biochemistry , vol.37 , pp. 2051-2058
    • Hamilton, T.B.1    Borel, F.2    Romaniuk, P.J.3
  • 45
    • 0032981699 scopus 로고    scopus 로고
    • Toward controlling gene expression at will: Selecting and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences
    • Segal, D. J., Dreier, B., Beerli, R. R. & Barbas, C. F., III (1999). Toward controlling gene expression at will: selecting and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences. Proc. Natl Acad. Sci. USA, 96, 2758-2763.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 2758-2763
    • Segal, D.J.1    Dreier, B.2    Beerli, R.R.3    Barbas C.F. III4
  • 46
    • 0035912721 scopus 로고    scopus 로고
    • Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
    • Bulyk, M. L., Huang, X., Choo, Y. & 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
  • 47
    • 0028609064 scopus 로고
    • DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families
    • Suzuki, M. & Yagi, N. (1994). DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families. Proc. Natl Acad. Sci. USA, 91, 12357-12361.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 12357-12361
    • Suzuki, M.1    Yagi, N.2
  • 48
    • 0028948325 scopus 로고
    • Structure-based design of transcription factors
    • Pomerantz, J. L., Sharp, P. A. & Pabo, C. O. (1995). Structure-based design of transcription factors. Science, 267, 93-96.
    • (1995) Science , vol.267 , pp. 93-96
    • Pomerantz, J.L.1    Sharp, P.A.2    Pabo, C.O.3
  • 49
    • 0028839860 scopus 로고
    • Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles
    • Mandel-Gutfreund, Y., Schueler, O. & Margalit, H. (1995). Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. J. Mol. Biol. 253, 370-382.
    • (1995) J. Mol. Biol. , vol.253 , pp. 370-382
    • Mandel-Gutfreund, Y.1    Schueler, O.2    Margalit, H.3
  • 51
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F. & Wootton, J. C. (1993). Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, C.E.1    Altschul, S.F.2    Boguski, M.S.3    Liu, J.S.4    Neuwald, A.F.5    Wootton, J.C.6


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