메뉴 건너뛰기




Volumn 110, Issue 30, 2013, Pages 12349-12354

DNA-binding specificity changes in the evolution of forkhead transcription factors

Author keywords

Protein DNA interactions; Transcription factor binding site motif

Indexed keywords

AMINO ACID; FORKHEAD TRANSCRIPTION FACTOR;

EID: 84880681583     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1310430110     Document Type: Article
Times cited : (135)

References (49)
  • 2
    • 14044252090 scopus 로고    scopus 로고
    • Conservation and evolution of cis-regulatory systems in ascomycete fungi
    • Gasch AP, et al. (2004) Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol 2(12):e398.
    • (2004) PLoS Biol , vol.2 , Issue.12
    • Gasch, A.P.1
  • 3
    • 2442537233 scopus 로고    scopus 로고
    • Gene regulatory network growth by duplication
    • Teichmann SA, Babu MM (2004) Gene regulatory network growth by duplication. Nat Genet 36(5):492-496.
    • (2004) Nat Genet , vol.36 , Issue.5 , pp. 492-496
    • Teichmann, S.A.1    Babu, M.M.2
  • 4
    • 0034708205 scopus 로고    scopus 로고
    • Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding
    • Gajiwala KS, et al. (2000) Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Nature 403(6772):916-921.
    • (2000) Nature , vol.403 , Issue.6772 , pp. 916-921
    • Gajiwala, K.S.1
  • 5
    • 0027402969 scopus 로고
    • Crystal structure of globular domain of histone H5 and its implications for nucleosome binding
    • Ramakrishnan V, Finch JT, Graziano V, Lee PL, Sweet RM (1993) Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature 362(6417):219-223.
    • (1993) Nature , vol.362 , Issue.6417 , pp. 219-223
    • Ramakrishnan, V.1    Finch, J.T.2    Graziano, V.3    Lee, P.L.4    Sweet, R.M.5
  • 6
    • 77952008658 scopus 로고    scopus 로고
    • Evolutionary genomics of the Fox genes: Origin of gene families and the ancestry of gene clusters
    • Shimeld SM, Degnan B, Luke GN (2010) Evolutionary genomics of the Fox genes: Origin of gene families and the ancestry of gene clusters. Genomics 95(5):256-260.
    • (2010) Genomics , vol.95 , Issue.5 , pp. 256-260
    • Shimeld, S.M.1    Degnan, B.2    Luke, G.N.3
  • 7
    • 0342614209 scopus 로고    scopus 로고
    • Unified nomenclature for the winged helix/forkhead transcription factors
    • Kaestner KH, Knochel W, Martinez DE (2000) Unified nomenclature for the winged helix/forkhead transcription factors. Genes Dev 14(2):142-146.
    • (2000) Genes Dev , vol.14 , Issue.2 , pp. 142-146
    • Kaestner, K.H.1    Knochel, W.2    Martinez, D.E.3
  • 8
    • 79952143437 scopus 로고    scopus 로고
    • Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki
    • Sebé-Pedrós A, de Mendoza A, Lang BF, Degnan BM, Ruiz-Trillo I (2011) Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki. Mol Biol Evol 28(3):1241-1254.
    • (2011) Mol Biol Evol , vol.28 , Issue.3 , pp. 1241-1254
    • Sebé-Pedrós, A.1    De Mendoza, A.2    Lang, B.F.3    Degnan, B.M.4    Ruiz-Trillo, I.5
  • 9
    • 0027270989 scopus 로고
    • Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5
    • Clark KL, Halay ED, Lai E, Burley SK (1993) Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5. Nature 364(6436):412-420.
    • (1993) Nature , vol.364 , Issue.6436 , pp. 412-420
    • Clark, K.L.1    Halay, E.D.2    Lai, E.3    Burley, S.K.4
  • 10
    • 33745204667 scopus 로고    scopus 로고
    • Crystal structure of the human FOXK1a-DNA complex and its implications on the diverse binding specificity of winged helix/forkhead proteins
    • Tsai KL, et al. (2006) Crystal structure of the human FOXK1a-DNA complex and its implications on the diverse binding specificity of winged helix/forkhead proteins. J Biol Chem 281(25):17400-17409.
    • (2006) J Biol Chem , vol.281 , Issue.25 , pp. 17400-17409
    • Tsai, K.L.1
  • 11
    • 33644800026 scopus 로고    scopus 로고
    • Structure of the forkhead domain of FOXP2 bound to DNA
    • Stroud JC, et al. (2006) Structure of the forkhead domain of FOXP2 bound to DNA. Structure 14(1):159-166.
    • (2006) Structure , vol.14 , Issue.1 , pp. 159-166
    • Stroud, J.C.1
  • 12
    • 77955264230 scopus 로고    scopus 로고
    • Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence
    • Littler DR, et al. (2010) Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence. Nucleic Acids Res 38(13):4527-4538.
    • (2010) Nucleic Acids Res , vol.38 , Issue.13 , pp. 4527-4538
    • Littler, D.R.1
  • 13
    • 78649897656 scopus 로고    scopus 로고
    • Structure of the human FOXO4-DBD-DNA complex at 1.9 A resolution reveals new details of FOXO binding to the DNA
    • Boura E, Rezabkova L, Brynda J, Obsilova V, Obsil T (2010) Structure of the human FOXO4-DBD-DNA complex at 1.9 A resolution reveals new details of FOXO binding to the DNA. Acta Crystallogr D Biol Crystallogr 66(Pt 12):1351-1357.
    • (2010) Acta Crystallogr D Biol Crystallogr , vol.66 , Issue.PART 12 , pp. 1351-1357
    • Boura, E.1    Rezabkova, L.2    Brynda, J.3    Obsilova, V.4    Obsil, T.5
  • 14
    • 44649163941 scopus 로고    scopus 로고
    • Genesis and expansion of metazoan transcription factor gene classes
    • Larroux C, et al. (2008) Genesis and expansion of metazoan transcription factor gene classes. Mol Biol Evol 25(5):980-996.
    • (2008) Mol Biol Evol , vol.25 , Issue.5 , pp. 980-996
    • Larroux, C.1
  • 15
    • 58549105347 scopus 로고    scopus 로고
    • Evolutionary selection pressure of forkhead domain and functional divergence
    • Wang M, Wang Q, Zhao H, Zhang X, Pan Y (2009) Evolutionary selection pressure of forkhead domain and functional divergence. Gene 432(1-2):19-25.
    • (2009) Gene , vol.432 , Issue.1-2 , pp. 19-25
    • Wang, M.1    Wang, Q.2    Zhao, H.3    Zhang, X.4    Pan, Y.5
  • 16
    • 0029023801 scopus 로고
    • DNA recognition site analysis of Xenopus winged helix proteins
    • Kaufmann E, Müller D, Knöchel W (1995) DNA recognition site analysis of Xenopus winged helix proteins. J Mol Biol 248(2):239-254.
    • (1995) J Mol Biol , vol.248 , Issue.2 , pp. 239-254
    • Kaufmann, E.1    Müller, D.2    Knöchel, W.3
  • 17
    • 0028353904 scopus 로고
    • The DNA-binding specificity of the hepatocyte nuclear factor 3/forkhead domain is influenced by amino-acid residues adjacent to the recognition helix
    • Overdier DG, Porcella A, Costa RH (1994) The DNA-binding specificity of the hepatocyte nuclear factor 3/forkhead domain is influenced by amino-acid residues adjacent to the recognition helix. Mol Cell Biol 14(4):2755-2766.
    • (1994) Mol Cell Biol , vol.14 , Issue.4 , pp. 2755-2766
    • Overdier, D.G.1    Porcella, A.2    Costa, R.H.3
  • 18
    • 0028046675 scopus 로고
    • Cloning and characterization of seven human forkhead proteins: Binding site specificity and DNA bending
    • Pierrou S, Hellqvist M, Samuelsson L, Enerbäck S, Carlsson P (1994) Cloning and characterization of seven human forkhead proteins: Binding site specificity and DNA bending. EMBO J 13(20):5002-5012.
    • (1994) EMBO J , vol.13 , Issue.20 , pp. 5002-5012
    • Pierrou, S.1    Hellqvist, M.2    Samuelsson, L.3    Enerbäck, S.4    Carlsson, P.5
  • 19
    • 63849315606 scopus 로고    scopus 로고
    • High-resolution DNA-binding specificity analysis of yeast transcription factors
    • Zhu C, et al. (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-566.
    • (2009) Genome Res , vol.19 , Issue.4 , pp. 556-566
    • Zhu, C.1
  • 20
    • 67649982744 scopus 로고    scopus 로고
    • Diversity and complexity in DNA recognition by transcription factors
    • Badis G, et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324(5935):1720-1723.
    • (2009) Science , vol.324 , Issue.5935 , pp. 1720-1723
    • Badis, G.1
  • 21
    • 57749121616 scopus 로고    scopus 로고
    • A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters
    • Badis G, et al. (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32(6): 878-887.
    • (2008) Mol Cell , vol.32 , Issue.6 , pp. 878-887
    • Badis, G.1
  • 22
    • 84863338247 scopus 로고    scopus 로고
    • Differential regulation ofmesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors
    • Zhu X, et al. (2012) Differential regulation ofmesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors. Development 139(8):1457-1466.
    • (2012) Development , vol.139 , Issue.8 , pp. 1457-1466
    • Zhu, X.1
  • 23
    • 0030991733 scopus 로고    scopus 로고
    • The nude gene encodes a sequencespecific DNA binding protein with homologs in organisms that lack an anticipatory immune system
    • Schlake T, Schorpp M, Nehls M, Boehm T (1997) The nude gene encodes a sequencespecific DNA binding protein with homologs in organisms that lack an anticipatory immune system. Proc Natl Acad Sci USA 94(8):3842-3847.
    • (1997) Proc Natl Acad Sci USA , vol.94 , Issue.8 , pp. 3842-3847
    • Schlake, T.1    Schorpp, M.2    Nehls, M.3    Boehm, T.4
  • 24
    • 84863289661 scopus 로고    scopus 로고
    • Forkhead box N4 (Foxn4) activates Dll4-Notch signaling to suppress photoreceptor cell fates of early retinal progenitors
    • Luo H, et al. (2012) Forkhead box N4 (Foxn4) activates Dll4-Notch signaling to suppress photoreceptor cell fates of early retinal progenitors. Proc Natl Acad Sci USA 109 (9):E553-E562.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.9
    • Luo, H.1
  • 26
    • 0030853056 scopus 로고    scopus 로고
    • Evidence that the DNA binding specificity of winged helix proteins is mediated by a structural change in the amino acid sequence adjacent to the principal DNA binding helix
    • Marsden I, Chen Y, Jin C, Liao X (1997) Evidence that the DNA binding specificity of winged helix proteins is mediated by a structural change in the amino acid sequence adjacent to the principal DNA binding helix. Biochemistry 36(43):13248-13255.
    • (1997) Biochemistry , vol.36 , Issue.43 , pp. 13248-13255
    • Marsden, I.1    Chen, Y.2    Jin, C.3    Liao, X.4
  • 27
    • 34547883900 scopus 로고    scopus 로고
    • Toward resolving the eukaryotic tree: The phylogenetic positions of jakobids and cercozoans
    • Rodríguez-Ezpeleta N, et al. (2007) Toward resolving the eukaryotic tree: The phylogenetic positions of jakobids and cercozoans. Curr Biol 17(16):1420-1425.
    • (2007) Curr Biol , vol.17 , Issue.16 , pp. 1420-1425
    • Rodríguez-Ezpeleta, N.1
  • 28
    • 33750882505 scopus 로고    scopus 로고
    • Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • Berger MF, et al. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol 24(11): 1429-1435.
    • (2006) Nat Biotechnol , vol.24 , Issue.11 , pp. 1429-1435
    • Berger, M.F.1
  • 29
    • 84858077472 scopus 로고    scopus 로고
    • The Pfam protein families database
    • (Database issue, D1
    • Punta M, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40(Database issue, D1)D290-D301.
    • (2012) Nucleic Acids Res , vol.40
    • Punta, M.1
  • 30
    • 6944226171 scopus 로고    scopus 로고
    • Identification and characterization of human FOXN5 and rat Foxn5 genes in silico
    • Katoh M, Katoh M (2004) Identification and characterization of human FOXN5 and rat Foxn5 genes in silico. Int J Oncol 24(5):1339-1344.
    • (2004) Int J Oncol , vol.24 , Issue.5 , pp. 1339-1344
    • Katoh, M.1    Katoh, M.2
  • 31
    • 65249167505 scopus 로고    scopus 로고
    • DNA binding site sequence directs glucocorticoid receptor structure and activity
    • Meijsing SH, et al. (2009) DNA binding site sequence directs glucocorticoid receptor structure and activity. Science 324(5925):407-410.
    • (2009) Science , vol.324 , Issue.5925 , pp. 407-410
    • Meijsing, S.H.1
  • 32
    • 0034634340 scopus 로고    scopus 로고
    • Allosteric effects of Pit-1 DNA sites on long-term repression in cell type specification
    • Scully KM, et al. (2000) Allosteric effects of Pit-1 DNA sites on long-term repression in cell type specification. Science 290(5494):1127-1131.
    • (2000) Science , vol.290 , Issue.5494 , pp. 1127-1131
    • Scully, K.M.1
  • 33
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated profile HMM searches
    • Eddy SR (2011) Accelerated Profile HMM Searches. PLOS Comput Biol 7(10):e1002195.
    • (2011) PLOS Comput Biol , vol.7 , Issue.10
    • Eddy, S.R.1
  • 34
    • 0035878724 scopus 로고    scopus 로고
    • Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
    • Schäffer AA, et al. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 29(14):2994-3005.
    • (2001) Nucleic Acids Res , vol.29 , Issue.14 , pp. 2994-3005
    • Schäffer, A.A.1
  • 35
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33(2):511-518.
    • (2005) Nucleic Acids Res , vol.33 , Issue.2 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 36
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302(1):205-217.
    • (2000) J Mol Biol , vol.302 , Issue.1 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 37
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 38
    • 80054078476 scopus 로고    scopus 로고
    • Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
    • Sievers F, et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539.
    • (2011) Mol Syst Biol , vol.7 , pp. 539
    • Sievers, F.1
  • 39
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 40
    • 82255185493 scopus 로고    scopus 로고
    • FastSP: Linear time calculation of alignment accuracy
    • Mirarab S, Warnow T (2011) FastSP: Linear time calculation of alignment accuracy. Bioinformatics 27(23):3250-3258.
    • (2011) Bioinformatics , vol.27 , Issue.23 , pp. 3250-3258
    • Mirarab, S.1    Warnow, T.2
  • 41
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • Le SQ, Gascuel O (2008) An improved general amino acid replacement matrix. Mol Biol Evol 25(7):1307-1320.
    • (2008) Mol Biol Evol , vol.25 , Issue.7 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 42
    • 79954529507 scopus 로고    scopus 로고
    • ProtTest 3: Fast selection of best-fit models of protein evolution
    • Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: Fast selection of best-fit models of protein evolution. Bioinformatics 27(8):1164-1165.
    • (2011) Bioinformatics , vol.27 , Issue.8 , pp. 1164-1165
    • Darriba, D.1    Taboada, G.L.2    Doallo, R.3    Posada, D.4
  • 43
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
    • Guindon S, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst Biol 59(3):307-321.
    • (2010) Syst Biol , vol.59 , Issue.3 , pp. 307-321
    • Guindon, S.1
  • 44
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39(4):783-791.
    • (1985) Evolution , vol.39 , Issue.4 , pp. 783-791
    • Felsenstein, J.1
  • 45
    • 33745256005 scopus 로고    scopus 로고
    • Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
    • Anisimova M, Gascuel O (2006) Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol 55(4):539-552.
    • (2006) Syst Biol , vol.55 , Issue.4 , pp. 539-552
    • Anisimova, M.1    Gascuel, O.2
  • 46
    • 80052014395 scopus 로고    scopus 로고
    • Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihoodbased approximation schemes
    • Anisimova M, Gil M, Dufayard J-F, Dessimoz C, Gascuel O (2011) Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihoodbased approximation schemes. Syst Biol 60(5):685-699.
    • (2011) Syst Biol , vol.60 , Issue.5 , pp. 685-699
    • Anisimova, M.1    Gil, M.2    Dufayard, J.-F.3    Dessimoz, C.4    Gascuel, O.5
  • 47
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688-2690.
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2688-2690
    • Stamatakis, A.1
  • 48
    • 59949083631 scopus 로고    scopus 로고
    • Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors
    • Berger MF, Bulyk ML (2009) Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc 4(3):393-411.
    • (2009) Nat Protoc , vol.4 , Issue.3 , pp. 393-411
    • Berger, M.F.1    Bulyk, M.L.2
  • 49
    • 22344457014 scopus 로고    scopus 로고
    • EnoLOGOS: A versatile web tool for energy normalized sequence logos
    • (Web Server issue
    • Workman CT, et al. (2005) enoLOGOS: A versatile web tool for energy normalized sequence logos. Nucleic Acids Res 33(Web Server issue):W389-W392.
    • (2005) Nucleic Acids Res , vol.33
    • Workman, C.T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.