A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding site in Escherichia coli

Genome Research

Volumn 14, Issue 2, 2004, Pages 201-208

  Bulyk, Martha L ^a,b   McGuire, Abigail M ^a   Masuda, Nobuhisa ^a   Church, George M ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; DNA; MESSENGER RNA; PRIMER DNA; TRANSCRIPTION FACTOR;

ARTICLE; BACTERIAL GENOME; BINDING SITE; BIOLOGY; COMPUTER SYSTEM; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA MICROARRAY; ESCHERICHIA COLI; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE MUTATION; GENETIC TRANSCRIPTION; GENETICS; GENOME; KNOCKOUT GENE; METHODOLOGY; NONHUMAN; OPEN READING FRAME; POLYMERASE CHAIN REACTION; PREDICTION; PREDICTION AND FORECASTING; PRIORITY JOURNAL; PROBABILITY; PROKARYOTE; REAL TIME POLYMERASE CHAIN REACTION; REGULON; SITE DIRECTED MUTAGENESIS; STATISTICAL SIGNIFICANCE; STRUCTURAL GENE;

BASE COMPOSITION; BINDING SITES; COMPUTATIONAL BIOLOGY; COMPUTER SYSTEMS; DNA PRIMERS; DNA, BACTERIAL; ESCHERICHIA COLI; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; GENOME, BACTERIAL; MUTAGENESIS, SITE-DIRECTED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; PREDICTIVE VALUE OF TESTS; RNA, BACTERIAL; RNA, MESSENGER; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 0742333984     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1448004     Document Type: Article

References (56)

1. Affymetrix, Inc. 2002. Affymetrix GeneChip Expression Analysis Technical Manual. Affymetrix, Inc., Santa Clara, CA.
2. Bailey, T. and Elkan, C. 1995. The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3: 21-29.
3. Benos, P., Bulyk, M., and Stormo, G. 2002. Additivity in protein-DNA interactions: How good an approximation is it? Nucleic Acids Res. 30: 4442-4451.
4. Berg, O. and von Hippel, P. 1987. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193: 723-750.
5. Berman, B.P., Nibu, Y., Pfeiffer, B.D., Tomancak, P., Celniker, S.E., Levine, M., Rubin, G.M., and Eisen, M.B. 2002. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. 99: 757-762.
6. Blattner, F., Plunkett III, G., Bloch, C., Perna, N., Burland, V., Riley, M., Collado-Vides, J., Glasner, C., Rode, G., Mayhew, J., et al. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 14S3-1474.
7. Browning, D., Beatty, C., Wolfe, A., Cole, J., and Busby, S. 2002. Independent regulation of the divergent Escherichia coli nrfA and acsP1 promoters by a nucleoprotein assembly at a shared regulatory region. Mol. Microbiol. 43: 687-701.
8. Bulyk, M., Johnson, P., and Church, G. 2002. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 30: 1255-1261.
9. Bussemaker, H., Li, H., and Siggia, E. 2000. Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis. Proc. Natl. Acad. Sci. 97: 10096-10100.
10. Charlier, D., Roovers, M., Vliet, F.V., Boyen, A., Cumin, R., Nakamura, Y., Glansdorff, N., and Pierard, A. 1992. Arginine regulon of Escherichia coli K-12: A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression. J. Mol. Biol. 226: 367-386.
11. Frech, K. and Werner, T. 1997. Specific modelling of regulatory units in DNA sequences. Pac. Symp. Biocomput. 151-162.
12. Frith, M., Hansen, U., and Weng, Z. 2001. Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics 17: 878-889.
13. Frith, M., Spouge, J., Hansen, U., and Weng, Z. 2002. Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res. 30: 3214-3224.
14. Grundy, W., Bailey, T., and Elkan, C. 1996. ParaMEME: A parallel implementation and a web interface for a DNA and protein motif discovery tool. CABIOS 12: 303-310.
15. GuhaThakurta, D. and Stormo, G. 2001. Identifying target sites for cooperatively binding factors. Bioinformatics 17: 608-621.
16. Halfon, M., Grad, Y., Church, G., and Michelson, A. 2002. Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res. 12: 1019-1028.
17. Heid, C., Stevens, J., Livak, K., and Williams, P. 1996. Real time quantitative PCR. Genome Res. 6: 986-994.
18. Hengge-Aronis, R. 1999. Interplay of global regulators and cell physiology in the general stress response of Escherichia coli. Curr. Opin. Microbiol. 2: 148-152.
19. Hertz, G. and Stormo, G. 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15: 563-577.
20. Hughes, J., Estep, P., Tavazoie, S., and Church, G. 2000. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296: 1205-1214.
21. Kel-Margoulis, O., Ivanova, T., Wingender, E., and Kel, A. 2002a. Automatic annotation of genomic regulatory sequences by searching for composite Clusters. Pac. Symp. Biocomput. 187-198.
22. Kel-Margoulis, O., Kel, A., Reuter, I., Deineko, I., and Wingender, E. 2002b. TRANSCompel: A database on composite regulatory elements in eukaryotic genes. Nucleic Acids Res. 30: 332-334.
23. Klingenhoff, A., Frech, K., Quandt, K., and Werner, T. 1999. Functional promoter Modules can be detected by formal models independent of overall nucleotide sequence similarity. Bioinformatics 15: 180-186.
24. Kolchanov, N., Ignatieva, E., Ananko, E., Podkolodnaya, O., Stepanenko, I., Merkulova, T., Pozdnyakov, M., Podkolodny, N., Naumochkin, A., and Romashchenko, A. 2002. Transcription Regulatory Regions Database (TRRD): Its status in 2002. Nucleic Acids Res. 30: 312-317.
25. Lawrence, C., Altschul, S., Boguski, M., Liu, J., Neuwald, A., and Wootton, J. 1993. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science 262: 208-214.
26. Lee, M.-L., Bulyk, M., Whitmore, G., and Church, G. 2002. A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays. Biometrics 58: 981-988.
27. Lee, T., Rinaldi, N., Robert, F., Odom, D., Bar-Joseph, Z., Gerber, G., Hannett, N., Harbison, C., Thompson, C., Simon, I., et al. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
28. Li, H., Rhodius, V., Gross, C., and Siggia, E. 2002. Identification of the binding sites of regulatory proteins in bacterial genomes. Proc. Natl. Acad. Sci. 99: 11772-11777.
29. Link, A., Phillips, D., and Church, G. 1997. Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: Application to open reading frame characterization. J. Bacteriol. 179: 6228-6237.
30. Liu, X., Brutlag, D., and Liu, J. 2001. BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 127-138.
31. Liu, X., Brutlag, D., and Liu, J. 2002. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20: 835-839.
32. Man, T.K. and Stormo, G.D. 2001. Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res. 29: 2471-2478.
33. Mangan, J.A., Sole, K.M., Mitchison, D.A., and Butcher, P.D. 1997. An effective ruethod of RNA extraction from bacteria refractory to disruption, including mycobacteria. Nucleic Acids Res. 25: 675-677.
34. Markstein, M., Markstein, P., Markstein, V., and Levine, M. 2002. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl. Acad. Sci. 99: 763-768.
35. Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A., Kel-Margoulis, O., et al. 2003. TRANSFAC: Transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31: 374-378.
36. McGuire, A. 2000. "Computational studies of transcriptional regulation in prokaryotes." Ph.D. thesis, Harvard University, Cambridge.
37. Neidhardt, F. 1996. Escherichia coli and Salmonella: Cellular and molecular biology. American Society for Microbiology, Washington, DC.
38. Neidhardt, F., Bloch, P., and Smith, D. 1974. Culture medium for enterobacteria. J. Bacteriol. 119: 736-747.
39. Phillips, D. 2000. "Competitive growth analysis of E. coli in-frame deletion mutants across a spectrum of environmental conditions." Ph.D. thesis, Harvard University, Cambridge.
40. Pilpel, Y., Sudarsanam, P., and Church, G. 2001. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29: 153-159.
41. Quandt, K., Grote, K., and Werner, T. 1996. GenomeInspector: A new approach to detect correlation patterns of elements on genomic sequences. Comput. Appl. Biosci. 12: 405-413.
42. Rebeiz, M., Reeves, N., and Posakony, J. 2002. SCORE: A computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Proc. Natl. Acad. Sci. 99: 9888-9893.
43. Robin, S., Daudin, J., Richard, H., Sagot, M., and Schbath, S. 2002. Occurrence probability of structured motifs in random sequences. J. Comput. Biol. 9: 761-773.
44. Robison, K., McGuire, A.M., and Church, G.M. 1998. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 284: 241-254.
45. Rosenblueth, D.A., Thieffry, D., Huerta, A.M., Salgado, H., and Collado-Vides, J. 1996. Syntactic recognition of regulatory regions in Escherichia coli. Comput. Appl. Biosci. 12: 415-422.
46. Roth, F.P., Hughes, J.D., Estep, P.W., and Church, G.M. 1998. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotech. 16: 939-945.
47. Sambrook, J., Fritsch, E., and Maniatis, T. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
48. Sudarsanam, P., Pilpel, Y., and Church, G. 2002. Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res. 12: 1723-1731.
49. Thieffry, D., Salgado, H., Huerta, A., and Collado-Vides, J. 1998. Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. Bioinformatics 14: 391-400.
50. Tian, G., Lim, D., Oppenheim, J.D., and Maas, W.K. 1994. Explanation for different types of regulation of arginine biosynthesis in Escherichia coli B and Escherichia coli K12 caused by a difference between their arginine repressors. J. Mol. Biol. 235: 221-230.
51. van Helden, J., Andre, B., and Collado-Vides, J. 1998. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol. 281: 827-842.
52. van Helden, J., Rios, A., and Collado-Vides, J. 2000. Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res. 28: 1808-1818.
53. Wagner, A. 1999. Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics 15: 776-784.
54. Winer, J., Jung, C., Shackel, I., and Williams, P. 1999. Development and validation of real-time quantitative reverse transcriptase-polymerase chain reaction for monitoring gene expression in cardiac myocytes in vitro. Anal. Biochem. 270: 41-49.
55. Workman, C. and Stormo, G. 2000. ANN-Spec: A method for discovering transcription factor binding sites with improved specificity. Pac. Symp. Biocomput. 467-478.
56. Zacharias, M., Theissen, G., Bradaczek, C., and Wagner, R. 1991. Analysis of sequence elements important for the synthesis and control of ribosomal RNA in E. coli. Biochimie 73: 699-712.