Coding limits on the number of transcription factors

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Itzkovitz, Shalev ^a   Tlusty, Tsvi ^a   Alon, Uri ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; GENE CONTROL; GENE FUNCTION; GENE SEQUENCE; GENETIC CODE; GENETIC DATABASE; GENOME; HUMAN; NONHUMAN; PREDICTION; PROTEIN BINDING; THEORY;

AMINO ACID MOTIFS; ANIMALS; BACTERIA; BACTERIAL PROTEINS; BINDING SITES; DIMERIZATION; DNA; FUNGAL PROTEINS; FUNGI; HUMANS; INFORMATION THEORY; INVERTEBRATES; MULTIGENE FAMILY; PLANT PROTEINS; PLANTS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SPECIES SPECIFICITY; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; TRANSCRIPTION FACTORS; VERTEBRATES;

EID: 33749451228     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-239     Document Type: Article

References (73)

1. Robison K, McGuire AM, Church GM: A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol 1998, 284:241-254.
2. Stormo GD: DNA binding sites: representation and discovery. Bioinformatics 2000, 16:16-23.
3. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254.
4. Bussemaker HJ, Li H, Siggia ED: Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc Natl Acad Sci U S A 2000, 97:10096-10100.
5. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Pruss M, Reuter I, Schacherer F: TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 2000, 28:316-319.
6. Sengupta AM, Djordjevic M, Shraiman BI: Specificity and robustness in transcription control networks. Proc Natl Acad Sci U S A 2002, 99:2072-2077.
7. Schneider TD, Stormo GD, Gold L, Ehrenfeucht A: Information content of binding sites on nucleotide sequences. J Mol Biol 1986, 188:415-431.
8. Gerland U, Moroz JD, Hwa T: Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc Natl Acad Sci U S A 2002, 99:12015-12020.
9. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA: Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431:99-104.
10. Berg J, Willmann S, Lassig M: Adaptive evolution of transcription factor binding sites. BMC Evol Biol 2004, 4:42.
11. Schneider TD, Stephens RM: Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 1990, 18:6097-6100.
12. Garvie CW, Wolberger C: Recognition of specific DNA sequences. Mol Cell 2001, 8:937-946.
13. Luscombe NM, Austin SE, Berman HM, Thornton JM: An overview of the structures of protein-DNA complexes. Genome Biol 2000, I:REVIEWS001.
14. Pabo CO, Sauer RT: Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem 1992, 61:1053-1095.
15. Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA: Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 2004, 14:283-291.
16. Aravind L, Anantharaman V, Balaji S, Babu MM, Iyer LM: The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol Rev 2005, 29:231-262.
17. Mandel-Gutfreund Y, Margalit H: Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. Nucleic Acids Res 1998, 26:2306-2312.
18. Benos PV, Lapedes AS, Stormo GD: Probabilistic code for DNA recognition by proteins of the EGR family. J Mol Biol 2002, 323:701-727.
19. Levine M, Tjian R: Transcription regulation and animal diversity. Nature 2003, 424:147-151.
20. van Nimwegen E: Scaling laws in the functional content of genomes. Trends Genet 2003, 19:479-484.
21. Luscombe NM, Thornton JM: Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J Mol Biol 2002, 320:991-1009.
22. Ptashne M: A genetic switch, cell press&blackwell science; 1992.
23. Massari ME, Murre C: Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol Cell Biol 2000, 20:429-440.
24. Beltran AC, Dawson PE, Gottesfeld JM: Role of DNA sequence in the binding specificity of synthetic basic-helix-loop-helix domains. Chembiochem 2005, 6:104-113.
25. Jones S: An overview of the basic helix-loop-helix proteins. Genome Biol 2004, 5:226.
26. Kaplan T, Friedman N, Margalit H: Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge. PLoS Computational Biology 2005, I:e1.
27. Marathe A, Condon AE, Corn RM: On combinatorial DNA word design. J Comput Biol 2001, 8:201-219.
28. Hamming RW: Coding and information theory. New Jersey, Prentice-Hall; 1980.
29. Tlusty T: Emergence of a genetic code as a phase transition induced by error-load topology. submitted.
30. Woese CR: Order in the genetic code. Proc Natl Acad Sci U S A 1965, 54:71-75.
31. Swanson R. A unifying concept for the amino acid code. Bull Math Biol 1984, 46:187-203.
32. Haig D, Hurst LD: A quantitative measure of error minimization in the genetic code. J Mol Evol 1991, 33:412-417.
33. Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munsterkotter M, Mewes HW: The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res 2004, 32:5539-5545.
34. Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M, Karp PD: EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res 2005, 33:D334-7.
35. Garten Y, Kaplan S, Pilpel Y: Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data. Nucleic Acids Res 2005, 33:605-615.
36. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804.
37. Tanaka N, Kawakami T, Taniguchi T: Recognition DNA sequences of interferon regulatory factor 1 (IRF-1) and IRF-2, regulators of cell growth and the interferon system. Mol Cell Biol 1993, 13:4531-4538.
38. Ray-Gallet D, Mao C, Tavitian A, Moreau-Gachelin F: DNA binding specificities of Spi-I/PU.1 and Spi-B transcription factors and identification of a Spi-I/Spi-B binding site in the c-fes/c-fps promoter. Oncogene 1995, 11:303-313.
39. Babu MM, Teichmann SA: Evolution of Transcription Factors and the Gene Regulatory Network in E. coli. Nucleic Acids Research 2003, 31:1234-1244.
40. Teichmann SA, Babu MM: Gene regulatory network growth by duplication. Nat Genet 2004, 36:492-496.
41. Papp B, Pal C, Hurst LD: Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet 2003, 19:417-422.
42. Tanay A, Gat-Viks I, Shamir R: A global view of the selection forces in the evolution of yeast cis-regulation. Genome Res 2004, 14:829-834.
43. Todd RB, Andrianopoulos A: Evolution of a fungal regulatory gene family: the Zn(II)2Cys6 binuclear cluster DNA binding motif. Fungal Genet Biol 1997, 21:388-405.
44. Volff JN: Genome evolution and biodiversity in teleost fish. Heredity 2005, 94:280-294.
45. Amores A, Force A, Yan YL, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang YL, Westerfield M, Ekker M, Postlethwait JH: Zebrafish hox clusters and vertebrate genome evolution. Science 1998, 282:1711-1714.
46. Meyer A, Schartl M: Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr Opin Cell Biol 1999, 11:699-704.
47. Seoighe C: Turning the clock back on ancient genome duplication. Curr Opin Genet Dev 2003, 13:636-643.
48. Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA: The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 2003, 20:1377-1419.
49. Yuh CH, Bolouri H, Davidson EH: Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 1998, 279:1896-1902.
50. Pilpel Y, Sudarsanam P, Church GM: Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 2001, 29:153-159.
51. Beer MA, Tavazoie S: Predicting gene expression from sequence. Cell 2004, 117:185-198.
52. Buchler NE, Gerland U, Hwa T: On schemes of combinatorial transcription logic. Proc Natl Acad Sci U S A 2003, 100:5136-5141.
53. Setty Y, Mayo AE, Surette MG, Alon U: Detailed map of a cis-regulatory input function. Proc Natl Acad Sci U S A 2003, 100:7702-7707.
54. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N: Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003, 34:166-176.
55. Balaji S, Babu MM, Iyer LM, Luscombe NM, Aravind L: Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J Mol Biol 2006, 360:213-227.
56. Muller J, Oehler S, Muller-Hill B: Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator. J Mol Biol 1996, 257:21-29.
57. Kolb A, Busby S, Buc H, Garges S, Adhya S: Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 1993, 62:749-795.
58. Ptashne M, Gann A: Transcriptional activation by recruitment. Nature 1997, 386:569-577.
59. Zhang Z, Gu J, Gu X: How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution? Trends Genet 2004, 20:403-407.
60. Struhl K: Yeast transcriptional regulatory mechanisms. Annu Rev Genet 1995, 29:651-674.
61. Kafri R, Bar-Even A, Pilpel Y: Transcription control reprogramming in genetic backup circuits. Nat Genet 2005, 37:295-299.
62. Dueber JE, Yeh BJ, Bhattacharyya RP, Lim WA: Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry. Curr Opin Struct Biol 2004, 14:690-699.
63. Zarrinpar A, Bhattacharyya RP, Lim WA: The structure and function of proline recognition domains. Sci STKE 2003, 2003:RE8.
64. Gough J, Karplus K, Hughey R, Chothia C: Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 2001, 313:903-919.
65. Kummerfeld SK, Teichmann SA: DBD: a transcription factor prediction database. Nucleic Acids Res 2006, 34:D74-81.
66. Salgado H, Gama-Castro S, Martinez-Antonio A, Diaz-Peredo E, Sanchez-Solano F, Peralta-Gil M, Garcia-Alonso D, Jimenez-Jacinto V, Santos-Zavaleta A, Bonavides-Martinez C, Collado-Vides J: RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res 2004, 32:D303-6.
67. Hughes JD, Estep PW, Tavazoie S, Church GM: Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000, 296:1205-1214.
68. Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B: JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 2004, 32:D91-4.
69. Wang T, Stormo GD: Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 2003, 19:2369-2380.
70. Lin J: Divergence measures based on Shannon entropy. IEEE Trans Inform Theory 1991, 37:145-151.
71. Kolkhof P, Teichmann D, Kisters-Woike B, von Wilcken-Bergmann B, Muller-Hill B: Lac repressor with the helix-turn-helix motif of lambda cro binds to lac operator. Embo J 1992, 11:3031-3038.
72. Sandelin A, Wasserman WW: Prediction of nuclear hormone receptor response elements. Mol Endocrinol 2005, 19:595-606.
73. Peterson WW, Weldon EJ: Error-Correcting Codes. The MIT Press; 1972.