메뉴 건너뛰기




Volumn 22, Issue 10, 2012, Pages 1889-1898

Exploring the DNA-recognition potential of homeodomains

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN; HOMEODOMAIN PROTEIN;

EID: 84867157760     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.139014.112     Document Type: Article
Times cited : (23)

References (60)
  • 1
    • 0028108227 scopus 로고
    • Differential DNA-binding specificity of the engrailed homeodomain: The role of residue 50
    • Ades SE, Sauer RT. 1994. Differential DNA-binding specificity of the engrailed homeodomain: The role of residue 50. Biochemistry 33: 9187-9194. (Pubitemid 24272870)
    • (1994) Biochemistry , vol.33 , Issue.31 , pp. 9187-9194
    • Ades, S.E.1    Sauer, R.T.2
  • 2
    • 0028810470 scopus 로고
    • Specificity of minor-groove and major-groove interactions in a homeodomain-DNA complex
    • Ades SE, Sauer RT. 1995. Specificity of minor-groove and major-groove interactions in a homeodomain-DNA complex. Biochemistry 34: 14601-14608.
    • (1995) Biochemistry , vol.34 , pp. 14601-14608
    • Ades, S.E.1    Sauer, R.T.2
  • 5
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
    • (1994) Proc Int Conf Intell Syst Mol Biol , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 7
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57: 289-300.
    • (1995) J R Stat Soc ser B Methodol , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 8
    • 0036977044 scopus 로고    scopus 로고
    • Probabilistic code for DNA recognition by proteins of the EGR family
    • DOI 10.1016/S0022-2836(02)00917-8
    • Benos PV, Lapedes AS, Stormo GD. 2002. Probabilistic code for DNA recognition by proteins of the EGR family. J Mol Biol 323: 701-727. (Pubitemid 36160225)
    • (2002) Journal of Molecular Biology , vol.323 , Issue.4 , pp. 701-727
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 10
    • 79960836662 scopus 로고    scopus 로고
    • Homeodomain subtypes and functional diversity
    • Burglin TR. 2011. Homeodomain subtypes and functional diversity. Subcell Biochem 52: 95-122.
    • (2011) Subcell Biochem , vol.52 , pp. 95-122
    • Burglin, T.R.1
  • 12
    • 0033557227 scopus 로고    scopus 로고
    • Mutational analysis of the engrailed homeodomain recognition helix by phage display
    • DOI 10.1093/nar/27.4.1182
    • Connolly JP, Augustine JG, Francklyn C. 1999. Mutational analysis of the engrailed homeodomain recognition helix by phage display. Nucleic Acids Res 27: 1182-1189. (Pubitemid 29209524)
    • (1999) Nucleic Acids Research , vol.27 , Issue.4 , pp. 1182-1189
    • Connolly, J.P.1    Augustine, J.G.2    Francklyn, C.3
  • 15
    • 33748049771 scopus 로고    scopus 로고
    • Cross-species annotation of basic leucine zipper factor interactions: Insight into the evolution of closed interaction networks
    • DOI 10.1093/molbev/msl022
    • Deppmann CD, Alvania RS, Taparowsky EJ. 2006. Cross-species annotation of basic leucine zipper factor interactions: Insight into the evolution of closed interaction networks. Mol Biol Evol 23: 1480-1492. (Pubitemid 44297407)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.8 , pp. 1480-1492
    • Deppmann, C.D.1    Alvania, R.S.2    Taparowsky, E.J.3
  • 16
    • 0027936793 scopus 로고
    • The degree of variation in DNA sequence recognition among four Drosophila homeotic proteins
    • Ekker SC, Jackson DG, von Kessler DP, Sun BI, Young KE, Beachy PA. 1994. The degree of variation in DNA sequence recognition among four Drosophila homeotic proteins. EMBO J 13: 3551-3560. (Pubitemid 24246192)
    • (1994) EMBO Journal , vol.13 , Issue.15 , pp. 3551-3560
    • Ekker, S.C.1    Jackson, D.G.2    Von Kassler, D.P.3    Sun, B.I.4    Young, K.E.5    Beachy, P.A.6
  • 17
    • 58949084539 scopus 로고    scopus 로고
    • Adaptive evolution in zinc finger transcription factors
    • doi: 10.1371/journal.pgen.1000325.
    • Emerson RO, Thomas JH. 2009. Adaptive evolution in zinc finger transcription factors. PLoS Genet 5: e1000325. doi: 10.1371/journal.pgen. 1000325.
    • (2009) PLoS Genet , vol.5
    • Emerson, R.O.1    Thomas, J.H.2
  • 18
    • 0032573434 scopus 로고    scopus 로고
    • Engrailed homeodomain-DNA complex at 2.2 A resolution: A detailed view of the interface and comparison with other engrailed structures
    • DOI 10.1006/jmbi.1998.2147
    • Fraenkel E, Rould MA, Chambers KA, Pabo CO. 1998. Engrailed homeodomain-DNA complex at 2.2 A resolution: A detailed view of the interface and comparison with other engrailed structures. J Mol Biol 284: 351-361. (Pubitemid 28542459)
    • (1998) Journal of Molecular Biology , vol.284 , Issue.2 , pp. 351-361
    • Fraenkel, E.1    Rould, M.A.2    Chambers, K.A.3    Pabo, C.O.4
  • 20
    • 0034682619 scopus 로고    scopus 로고
    • Exploring the role of glutamine 50 in the homeodomain-DNA interface: Crystal structure of engrailed (Gln50 → Ala) complex at 2.0 A
    • DOI 10.1021/bi000071a
    • Grant RA, Rould MA, Klemm JD, Pabo CO. 2000. Exploring the role of glutamine 50 in the homeodomain-DNA interface: Crystal structure of engrailed (Gln50 → ala) complex at 2.0 A. Biochemistry 39: 8187-8192. (Pubitemid 30460968)
    • (2000) Biochemistry , vol.39 , Issue.28 , pp. 8187-8192
    • Grant, R.A.1    Rould, M.A.2    Klemm, J.D.3    Pabo, C.O.4
  • 21
    • 78651341148 scopus 로고    scopus 로고
    • Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases
    • Gupta A, Meng X, Zhu LJ, Lawson ND, Wolfe SA. 2010. Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res 39: 381-392.
    • (2010) Nucleic Acids Res , vol.39 , pp. 381-392
    • Gupta, A.1    Meng, X.2    Zhu, L.J.3    Lawson, N.D.4    Wolfe, S.A.5
  • 22
    • 0026023608 scopus 로고
    • A genetic model for interaction of the homeodomain recognition helix with DNA
    • Hanes SD, Brent R. 1991. A genetic model for interaction of the homeodomain recognition helix with DNA. Science 251: 426-430. (Pubitemid 21916904)
    • (1991) Science , vol.251 , Issue.4992 , pp. 426-430
    • Hanes, S.D.1    Brent, R.2
  • 23
    • 0035834053 scopus 로고    scopus 로고
    • Crystal structure of the Msx-1 homeodomain/DNA complex
    • DOI 10.1021/bi0108148
    • Hovde S, Abate-Shen C, Geiger JH. 2001. Crystal structure of the Msx-1 homeodomain/DNA complex. Biochemistry 40: 12013-12021. (Pubitemid 32946543)
    • (2001) Biochemistry , vol.40 , Issue.40 , pp. 12013-12021
    • Hovde, S.1    Abate-Shen, C.2    Geiger, J.H.3
  • 24
    • 0030305457 scopus 로고    scopus 로고
    • R: A language for data analysis and graphics
    • Ihaka R, Gentleman R. 1996. R: A language for data analysis and graphics. J Comput Graph Statist 5: 299-314.
    • (1996) J Comput Graph Statist , vol.5 , pp. 299-314
    • Ihaka, R.1    Gentleman, R.2
  • 25
    • 35548931586 scopus 로고    scopus 로고
    • Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure
    • DOI 10.1016/j.cell.2007.09.024, PII S0092867407012123
    • Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS. 2007. Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131: 530-543. (Pubitemid 350007697)
    • (2007) Cell , vol.131 , Issue.3 , pp. 530-543
    • Joshi, R.1    Passner, J.M.2    Rohs, R.3    Jain, R.4    Sosinsky, A.5    Crickmore, M.A.6    Jacob, V.7    Aggarwal, A.K.8    Honig, B.9    Mann, R.S.10
  • 26
    • 29444434700 scopus 로고    scopus 로고
    • Ab initio prediction of transcription factor targets using structural knowledge
    • doi: 10.1371/journal.pcbi.0010001
    • Kaplan T, Friedman N, Margalit H. 2005. Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput Biol 1: e1. doi: 10.1371/journal.pcbi.0010001.
    • (2005) PLoS Comput Biol , vol.1
    • Kaplan, T.1    Friedman, N.2    Margalit, H.3
  • 27
    • 0025188837 scopus 로고
    • Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: A framework for understanding homeodomain-DNA interactions
    • Kissinger CR, Liu BS, Martin-Blanco E, Kornberg TB, Pabo CO. 1990. Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: A framework for understanding homeodomain-DNA interactions. Cell 63: 579-590.
    • (1990) Cell , vol.63 , pp. 579-590
    • Kissinger, C.R.1    Liu, B.S.2    Martin-Blanco, E.3    Kornberg, T.B.4    Pabo, C.O.5
  • 28
    • 0027751867 scopus 로고
    • Understanding the homeodomain
    • Kornberg TB. 1993. Understanding the homeodomain. J Biol Chem 268: 26813-26816. (Pubitemid 24006384)
    • (1993) Journal of Biological Chemistry , vol.268 , Issue.36 , pp. 26813-26816
    • Kornberg, T.B.1
  • 29
    • 0015530179 scopus 로고
    • Lac repressor binding to non-operator DNA: Detailed studies and a comparison of equilibrium and rate competition methods
    • Lin SY, Riggs AD. 1972. Lac repressor binding to non-operator DNA: Detailed studies and a comparison of equilibrium and rate competition methods. J Mol Biol 72: 671-690.
    • (1972) J Mol Biol , vol.72 , pp. 671-690
    • Lin, S.Y.1    Riggs, A.D.2
  • 30
    • 50549103329 scopus 로고    scopus 로고
    • 2 zinc-finger transcription factors
    • 2 zinc-finger transcription factors. Bioinformatics 24: 1850-1857.
    • (2008) Bioinformatics , vol.24 , pp. 1850-1857
    • Liu, J.1    Stormo, G.D.2
  • 31
    • 34547830863 scopus 로고    scopus 로고
    • Inferring protein-DNA dependencies using motif alignments and mutual information
    • DOI 10.1093/bioinformatics/btm215
    • Mahony S, Auron PE, Benos PV. 2007. Inferring protein-DNA dependencies using motif alignments and mutual information. Bioinformatics 23: i297-i304. (Pubitemid 47244413)
    • (2007) Bioinformatics , vol.23 , Issue.13
    • Mahony, S.1    Auron, P.E.2    Benos, P.V.3
  • 32
    • 67749095703 scopus 로고    scopus 로고
    • Hox specificity unique roles for cofactors and collaborators
    • Mann RS, Lelli KM, 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
    • 45449111373 scopus 로고    scopus 로고
    • Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites
    • DOI 10.1016/j.cell.2008.05.023, PII S009286740800682X
    • Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA. 2008a. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133: 1277-1289. (Pubitemid 351852912)
    • (2008) Cell , vol.133 , Issue.7 , 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
  • 35
    • 43349107222 scopus 로고    scopus 로고
    • A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
    • DOI 10.1093/nar/gkn048
    • Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA. 2008b. A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res 36: 2547-2560. (Pubitemid 351659570)
    • (2008) Nucleic Acids Research , vol.36 , Issue.8 , pp. 2547-2560
    • Noyes, M.B.1    Meng, X.2    Wakabayashi, A.3    Sinha, S.4    Brodsky, M.H.5    Wolfe, S.A.6
  • 36
    • 0033602242 scopus 로고    scopus 로고
    • Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex
    • Passner JM, Ryoo HD, Shen L, Mann RS, Aggarwal AK. 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
  • 37
    • 0025155089 scopus 로고
    • The interaction with DNA of wild-type and mutant fushi tarazu homeodomains
    • Percival-Smith A, Muller M, Affolter M, Gehring WJ. 1990. The interaction with DNA of wild-type and mutant fushi tarazu homeodomains. EMBO J 9: 3967-3974.
    • (1990) EMBO J , vol.9 , pp. 3967-3974
    • Percival-Smith, A.1    Muller, M.2    Affolter, M.3    Gehring, W.J.4
  • 38
    • 79956206770 scopus 로고    scopus 로고
    • 2 zinc finger protein-DNA interfaces
    • doi: 10.1088/1478-3975/8/3/035010
    • 2 zinc finger protein-DNA interfaces. Phys Biol 8: 035010. doi: 10.1088/1478-3975/8/3/035010.
    • (2011) Phys Biol , vol.8 , pp. 035010
    • Persikov, A.V.1    Singh, M.2
  • 40
    • 0033582545 scopus 로고    scopus 로고
    • Structure of a HoxB1-Pbx1 heterodimer bound to DNA: Role of the hexapeptide and a fourth homeodomain helix in complex formation
    • Piper DE, Batchelor AH, Chang CP, Cleary ML, Wolberger C. 1999. Structure of a HoxB1-Pbx1 heterodimer bound to DNA: Role of the hexapeptide and a fourth homeodomain helix in complex formation. Cell 96: 587-597. (Pubitemid 29106845)
    • (1999) Cell , vol.96 , Issue.4 , pp. 587-597
    • Piper, D.E.1    Batchelor, A.H.2    Chang, C.-P.3    Cleary, M.L.4    Wolberger, C.5
  • 41
    • 0028030691 scopus 로고
    • Homeodomain determinants of major groove recognition
    • Pomerantz JL, Sharp PA. 1994. Homeodomain determinants of major groove recognition. Biochemistry 33: 10851-10858. (Pubitemid 24296336)
    • (1994) Biochemistry , vol.33 , Issue.36 , pp. 10851-10858
    • Pomerantz, J.L.1    Sharp, P.A.2
  • 42
    • 0028948325 scopus 로고
    • Structure-based design of transcription factors
    • Pomerantz JL, Sharp PA, Pabo CO. 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
  • 47
    • 84934441299 scopus 로고    scopus 로고
    • Quantitative analysis of protein-RNA interactions by gel mobility shift
    • Ryder SP, Recht MI, Williamson JR. 2008. Quantitative analysis of protein-RNA interactions by gel mobility shift. Methods Mol Biol 488: 99-115.
    • (2008) Methods Mol Biol , vol.488 , pp. 99-115
    • Ryder, S.P.1    Recht, M.I.2    Williamson, J.R.3
  • 49
    • 0034660036 scopus 로고    scopus 로고
    • DNA-binding sequence of the human prostate-specific homeodomain protein NKX3.1
    • Steadman DJ, Giuffrida D, Gelmann EP. 2000. DNA-binding sequence of the human prostate-specific homeodomain protein NKX3.1. Nucleic Acids Res 28: 2389-2395. (Pubitemid 30349045)
    • (2000) Nucleic Acids Research , vol.28 , Issue.12 , pp. 2389-2395
    • Steadman, D.J.1    Giuffrida, D.2    Gelmann, E.P.3
  • 50
    • 0024397687 scopus 로고
    • A single amino acid can determine the DNA binding specificity of homeodomain proteins
    • DOI 10.1016/0092-8674(89)90038-X
    • Treisman J, Gonczy P, Vashishtha M, Harris E, Desplan C. 1989. A single amino acid can determine the DNA binding specificity of homeodomain proteins. Cell 59: 553-562. (Pubitemid 19284468)
    • (1989) Cell , vol.59 , Issue.3 , pp. 553-562
    • Treisman, J.1    Gonczy, P.2    Vashishtha, M.3    Harris, E.4    Desplan, C.5
  • 51
    • 0030609996 scopus 로고    scopus 로고
    • Engrailed (Gln50→Lys) homeodomain-DNA complex at 1.9 A resolution: Structural basis for enhanced affinity and altered specificity
    • Tucker-Kellogg L, Rould MA, Chambers KA, Ades SE, Sauer RT, Pabo CO. 1997. Engrailed (Gln50 → Lys) homeodomain-DNA complex at 1.9 A resolution: Structural basis for enhanced affinity and altered specificity. Structure 5: 1047-1054. (Pubitemid 27393089)
    • (1997) Structure , vol.5 , Issue.8 , pp. 1047-1054
    • Tucker-Kellogg, L.1    Rould, M.A.2    Chambers, K.A.3    Ades, S.E.4    Sauer, R.T.5    Pabo, C.O.6
  • 55
    • 0026002757 scopus 로고
    • Crystal structure of a MATα2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions
    • Wolberger C, Vershon AK, Liu B, Johnson AD, Pabo CO. 1991. Crystal structure of a MATα2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Cell 67: 517-528. (Pubitemid 121001466)
    • (1991) Cell , vol.67 , Issue.3 , pp. 517-528
    • Wolberger, C.1    Vershon, A.K.2    Liu, B.3    Johnson, A.D.4    Pabo, C.O.5
  • 57
    • 79958115193 scopus 로고    scopus 로고
    • Quantitative analysis demonstrates most transcription factors require only simple models of specificity
    • Zhao Y, Stormo GD. 2011. Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat Biotechnol 29: 480-483.
    • (2011) Nat Biotechnol , vol.29 , pp. 480-483
    • Zhao, Y.1    Stormo, G.D.2
  • 58
    • 77955034560 scopus 로고    scopus 로고
    • Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function
    • Zhao H, Yang Y, Zhou Y. 2010. Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinformatics 26: 1857-1863.
    • (2010) Bioinformatics , vol.26 , pp. 1857-1863
    • Zhao, H.1    Yang, Y.2    Zhou, Y.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.