Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics

Genome Research

Volumn 15, Issue 8, 2005, Pages 1145-1152

  Gertz, Jason ^a   Riles, Linda ^a   Turnbaugh, Peter ^a   Ho, Su Wen ^a   Cohen, Barak A ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PERMEASE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR SFP1; TRANSCRIPTION FACTOR STP1; TRANSCRIPTION FACTOR STP2; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; BINDING SITE; CELL GROWTH; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; GENOME; NONHUMAN; NUTRIENT UPTAKE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; REGULATORY SEQUENCE; SACCHAROMYCES CEREVISIAE; VALIDATION PROCESS;

ARYLSULFOTRANSFERASE; BASE SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION; GENOMICS; MOLECULAR SEQUENCE DATA; MUTATION; PROMOTER REGIONS (GENETICS); REPRODUCIBILITY OF RESULTS; TRANSCRIPTION FACTORS;

SACCHAROMYCES CEREVISIAE;

EID: 23744490071     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3859605     Document Type: Article

References (55)

1. Aach, J., Rindone, W., and Church, G.M. 2000. Systematic management and analysis of yeast gene expression data. Genome Res. 10: 431-445.
2. Aerts, S., Van Loo, P., Moreau, Y., and De Moor, B. 2004. A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes. Bioinformatics 20: 1974-1976.
3. Alexander, M.K., Bourns, B.D., and Zakian, V.A. 2001. One-hybrid systems for detecting protein-DNA interactions. Methods Mol. Biol. 177: 241-259.
4. Blumberg, H. and Silver, P. 1991. A split zinc-finger protein is required for normal yeast growth. Gene 107: 101-110.
5. Brachmann, C.B., Davies, A., Cost, G.J., Caputo, E., Li, J., Hieter, P., and Boeke, J.D. 1998. Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 115-132.
6. Cho, R.J., Cambell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J., et al. 1998. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2: 65-73.
7. Cho, J.H., Seok Sung, K., and Ryong Ha, S. 2004. A river water quality management model for optimising regional wastewater treatment using a genetic algorithm. J. Environ. Manage. 73: 229-242.
8. Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B.A., and Johnston, M. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
9. Dandekar, T. and Argos, P. 1992. Potential of genetic algorithms in protein folding and protein engineering simulations. Protein Eng. 5: 637-645.
10. De Boer, M., Bebelman, J.P., Goncalves, P.M., Maat, J., Van Heerikhuizen, H., and Planta, R.J. 1998. Regulation of expression of the amino acid transporter gene BAP3 in Saccharomyces cerevisiae. Mol. Microbiol. 30: 603-613.
11. de Boer, M., Nielsen, P.S., Bebelman, J.P., Heerikhuizen, H., Andersen, H.A., and Planta, R.J. 2000. Stp1p, Stp2p and Abf1p are involved in regulation of expression of the amino acid transporter gene BAP3 of Saccharomyces cerevisiae. Nucleic Acids Res. 28: 974-981.
12. Dudley, A.M., Aach, J., Steffen, M.A., and Church, G.M. 2002. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. 99: 7554-7559.
13. Eddy, S.R. 2005. A model of the statistical power of comparative genome sequence analysis. PLoS Biol. 3: e10.
14. Fields, S. and Song, O. 1989. A novel genetic system to detect protein-protein interactions. Nature 340: 245-246.
15. Fingerman, I., Nagaraj, V., Norris, D., and Vershon, A.K. 2003. Sfp1 plays a key role in yeast ribosome biogenesis. Eukaryot. Cell 2: 1061-1068.
16. Fisher, R.A. 1936. The use of multiple measures in taxonomic problems. Ann. Eugenics 7: 179-188.
17. Fogel, G.B., Weekes, D.G., Varga, G., Dow, E.R., Harlow, H.B., Onyia, J.E., and Su, C. 2004. Discovery of sequence motifs related to coexpression of genes using evolutionary computation. Nucleic Acids Res. 32: 3826-3835.
18. Gietz, R.D. and Sugino, A. 1988. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74: 527-534.
19. GuhaThakurta, D., Schriefer, L.A., Waterston, R.H., and Stormo, G.D. 2004. Novel transcription regulatory elements in Caenorhabditis elegans muscle genes. Genome Res. 14: 2457-2468.
20. Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N.J., Macisaac, K.D., Danford, T.W., Hannett, N.M., Tagne, J.B., Reynolds, D.B., Yoo, J., et al. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
21. Hardison, R.C., Oeltjen, J., and Miller, W. 1997. Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome. Genome Res. 7: 959-966.
22. Hertz, G.Z. and Stormo, G.D. 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15: 563-577.
23. Hughes, J.D., Estep, P.W., Tavazoie, S., and Church, G.M. 2000. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296: 1205-1214.
24. Jacob, E., Sasikumar, R., and Nair, K.N. 2004. A fuzzy guided genetic algorithm for operon prediction. Bioinformatics 21: 1403-1407.
25. James, P., Halladay, J., and Craig, E.A. 1996. Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144: 1425-1436.
26. Jelinsky, S.A., Estep, P., Church, G.M., and Samson, L.D. 2000. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol. Cell Biol. 20: 8157-8167.
27. Jorgensen, P., Nishikawa, J.L., Breitkreutz, B.J., and Tyers, M. 2002. Systematic identification of pathways that couple cell growth and division in yeast. Science 297: 395-400.
28. Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
29. 1 to S phase. Science 261: 1551-1557.
30. Koza, J.R., Keane, M.A., and Streeter, M.J. 2003. Evolving inventions. Sci. Am. 288: 52-59.
31. Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., et al. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
32. Li, J.J. and Herskowitz, I. 1993. Isolation of ORC6, a component of the yeast origin recognition complex by a one-hybrid system. Science 262: 1870-1874.
33. Ludwig, M.Z., Patel, N.H., and Kreitman, M. 1998. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: Rules governing conservation and change. Development 125: 949-958.
34. Ludwig, M.Z., Bergman, C., Patel, N.H., and Kreitman, M. 2000. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403: 564-567.
35. McCue, L., Thompson, W., Carmack, C., Ryan, M.P., Liu, J.S., Derbyshire, V., and Lawrence, C.E. 2001. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res. 29: 774-782.
36. Mewes, H.W., Heumann, K., Kaps, A., Mayer, K., Pfeiffer, F., Stocker, S., and Frishman, D. 1999. MIPS: A database for genomes and protein sequences. Nucleic Acids Res. 27: 44-48.
37. Moses, A.M., Chiang, D.Y., Pollard, D.A., Iyer, V.N., and Eisen, M.B. 2004. MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol. 5: R98.
38. Nielsen, P.S., van den Hazel, B., Didion, T., de Boer, M., Jorgensen, M., Planta, R.J., Kielland-Brandt, M.C., and Andersen, H.A. 2001. Transcriptional regulation of the Saccharomyces cerevisiae amino acid permease gene BAP2. Mol. Gen. Genet. 264: 613-622.
39. Petricoin, E.F., Ardekani, A.M., Hitt, B.A., Levine, P.J., Fusaro, V.A., Steinberg, S.M., Mills, G.B., Simone, C., Fishman, D.A., Kohn, E.C., et al. 2002. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359: 572-577.
40. Pilpel, Y., Sudarsanam, P., and Church, G.M. 2001. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29: 153-159.
41. Pond, S.L. and Frost, S.D. 2004. A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol. Biol. Evol. 22: 478-485.
42. Reggia, J.A., Lohn, J.D., and Chou, H.H. 1998. Self-replicating structures: Evolution, emergence and computation. Artif. Life 4: 283-302.
43. Schneider, T.D. and Stephens, R.M. 1990. Sequence logos: A new way to display consensus sequences. Nucleic Acids Res. 18: 6097-6100.
44. Schneider, T.D., Stormo, G.D., Gold, L., and Ehrenfeucht, A. 1986. Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188: 415-431.
45. Sikorski, R.S. and Hieter, P. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27.
46. Spalek, T., Pietrzyk, P., and Sojka, Z. 2005. Application of the genetic algorithm joint with the Powell method to nonlinear least-squares fitting of powder EPR spectra. J. Chem. Inf. Comput. Sci. 45: 18-29.
47. Sudarsanam, P., Pilpel, Y., and Church, G.M. 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.
48. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J., and Church, G.M. 1999. Systematic determination of genetic network architecture. Nat. Genet. 22: 281-285.
49. Tompa, M., Li, N., Bailey, T.L., Church, G.M., De Moor, B., Eskin, E., Favorov, A.V., Frith, M.C., Fu, Y., Kent, W.J., et al. 2005. Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol. 23: 137-144.
50. Wang, T. and Stormo, G.D. 2003. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 19: 2369-2380.
51. 2/M transitions during the mitotic cell cycle and DNA-damage response. Genetics 150: 1419-1428.
52. Zhu, J. and Zhang, M.Q. 1999. SCPD: A promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15: 607-611.
53. http://atlas.med.harvard.edu/motifs/; input sequences for motif refinement.
54. http://www.proteome.wayne.edu/vectorsandstrains.html; Kpn1/BamH1 fragment from pRF4-6o.
55. http://oligos.qiagen.com/arrays/oligosets_yeast.php; S. cerevisiae oligonucleotide set manufactured by Qiagen-Operon.