Impact of DNA-binding position variants on yeast gene expression

Nucleic Acids Research

Volumn 37, Issue 21, 2009, Pages 6991-7001

  Swamy, Krishna B S ^a   Cho, Chung Yi ^a,b   Chiang, Sufeng ^a   Tsai, Zing Tsung Yeh ^a   Tsai, Huai Kuang ^a,b  

^a NATIONAL YANG MING UNIVERSITY   (Taiwan)

^b RESEARCH CENTER FOR INFORMATION TECHNOLOGY INNOVATION   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; TRANSCRIPTION FACTOR; DNA;

ARTICLE; CONTROLLED STUDY; DNA BINDING MOTIF; FUNCTIONAL GENOMICS; GENE CONTROL; GENE EXPRESSION REGULATION; GENE LOCATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC REGULATION; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE BINDING SITE; POSITION EFFECT VARIEGATION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN VARIANT; SACCHAROMYCES CEREVISIAE; CHEMISTRY; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; PROMOTER REGION;

SACCHAROMYCES CEREVISIAE;

DNA; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC VARIATION; PROMOTER REGIONS, GENETIC; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION FACTORS;

EID: 75349111445     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp743     Document Type: Article

References (57)

1. Mirny, L.A. and Gelfand, M.S. (2002) Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Res., 30, 1704-1711.
2. Moses, A.M., Chiang, D.Y., Kellis, M., Lander, E.S. and Eisen, M.B. (2003) Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol. Bio.l, 3, 19.
3. Su, G., Mao, B. and Wang, J. (2006) A web server for transcription factor binding site prediction. Bioinformation, 1, 156-157.
4. Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W.W. and Lenhard, B. (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res., 32, D91-D94.
5. 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.
6. MacIsaac, K.D., Wang, T., Gordon, D.B., Gifford, D.K., Stormo, G.D. and Fraenkel, E. (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics, 7, 113.
7. Stormo, G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
8. Berg, J., Willmann, S. and Lassig, M. (2004) Adaptive evolution of transcription factor binding sites. BMC Evol. Biol., 4, 42.
9. 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.
10. Moses, A.M., Pollard, D.A., Nix, D.A., Iyer, V.N., Li, X.Y., Biggin, M.D. and Eisen, M.B. (2006) Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput. Biol., 2, e130.
11. Michal, L., Mizrahi-Man, O. and Pilpel, Y. (2008) Functional characterization of variations on regulatory motifs. PLoS Genet., 4, e1000018.
12. Andersen, M.C., Engstrom, P.G., Lithwick, S., Arenillas, D., Eriksson, P., Lenhard, B., Wasserman, W.W. and Odeberg, J. (2008) In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput. Biol., 4, e5.
13. Stormo, G.D., Schneider, T.D. and Gold, L. (1986) Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res., 14, 6661-6679.
14. Tomovic, A. and Oakeley, E.J. (2007) Position dependencies in transcription factor binding sites. Bioinformatics, 23, 933-941.
15. Zhang, M.Q. and Marr, T.G. (1993) A weight array method for splicing signal analysis. Comput. Appl. Biosci., 9, 499-509.
16. Barrick, D., Villanueba, K., Childs, J., Kalil, R., Schneider, T.D., Lawrence, C.E., Gold, L. and Stormo, G.D. (1994) Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res., 22, 1287-1295.
17. Gaudet, J. and Mango, S.E. (2002) Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Science, 295, 821-825.
18. Gaudet, J., Muttumu, S., Horner, M. and Mango, S.E. (2004) Whole-genome analysis of temporal gene expression during foregut development. PLoS Biol., 2, e352.
19. Giordano, M., Godi, M., Giacopelli, F., Lessi, M., Mellone, S., Paracchini, R., Petri, A., Bellone, J., Ravazzolo, R., Bona, G. et al. (2006) A variation in a Pit-1 site in the growth hormone gene (GH1) promoter induces a differential transcriptional activity. Mol. Cell Endocrinol., 249, 51-57.
20. Tsai, H.K., Chou, M.Y., Shih, C.H., Huang, G.T., Chang, T.H. and Li, W.H. (2007) MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. Nucleic Acids Res., 35, W221-W226.
21. Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 9440-9445.
22. Demeter, J., Beauheim, C., Gollub, J., Hernandez-Boussard, T., Jin, H., Maier, D., Matese, J.C., Nitzberg, M., Wymore, F., Zachariah, Z.K. et al. (2007) The stanford microarray database: implementation of new analysis tools and open source release of software. Nucleic Acids Res., 35, D766-D770.
23. Ronen, M. and Botstein, D. (2006) Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. Proc. Natl Acad. Sci. USA, 103, 389-394.
24. Brauer, M.J., Saldanha, A.J., Dolinski, K. and Botstein, D. (2005) Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Mol. Biol. Cell, 16, 2503-2517.
25. Yoshimoto, H., Saltsman, K., Gasch, A.P., Li, H.X., Ogawa, N., Botstein, D., Brown, P.O. and Cyert, M.S. (2002) Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J. Biol. Chem., 277, 31079-31088.
26. Gasch, A.P., Huang, M., Metzner, S., Botstein, D., Elledge, S.J. and Brown, P.O. (2001) Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol. Biol. Cell, 12, 2987-3003.
27. Zhu, G., Spellman, P.T., Volpe, T., Brown, P.O., Botstein, D., Davis, T.N. and Futcher, B. (2000) Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature, 406, 90-94.
28. Sudarsanam, P., Iyer, V.R., Brown, P.O. and Winston, F. (2000) Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 97, 3364-3369.
29. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
30. Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P.O. and Herskowitz, I. (1998) The transcriptional program of sporulation in budding yeast. Science, 282, 699-705.
31. DeRisi, J.L., Iyer, V.R. and Brown, P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680-686.
32. Quackenbush, J. (2002) Microarray data normalization and transformation. Nat. Genet., 32(Suppl), 496-501.
33. Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) A comparison of normalization methods or high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
34. Agresti, A. (1992) A survey of exact inference for contingency tables. Stat. Sci., 7, 131-153.
35. Tsai, H.K., Huang, G.T., Chou, M.Y., Lu, H.H. and Li, W.H. (2006) Method for identifying transcription factor binding sites in yeast. Bioinformatics, 22, 1675-1681.
36. Schlecht, U., Erb, I., Demougin, P., Robine, N., Borde, V., Nimwegen, E.V., Nicolas, A. and Primig, M. (2008) Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in Yeast. Mol. Biol. Cell, 19, 2193-2207.
37. Yarragudi, A., Miyake, T., Li, R. and Morse, R.H. (2004) Comparison of ABF1 and RAP1 in chromatin opening and transactivator potentiation in the budding yeast Saccharomyces cerevisiae. Mol. Cell Biol., 24, 9152-9164.
38. Casey, L., Patterson, E.E., Muller, U. and Fox, C.A. (2008) Conversion of a replication origin to a silencer through a pathway shared by a forkhead transcription factor and an S phase cyclin. Mol. Biol. Cell, 19, 608-622.
39. Lemmens, K., Dhollander, T., De Bie, T., Monsieurs, P., Engelen, K., Smets, B., Winderickx, J., De Moor, B. and Marchal, K. (2006) Inferring transcriptional modules from ChIP-chip, motif and microarray data. Genome Biol., 7, R37.
40. Jung, S.Y., Yoo, H.Y., Kim, Y.H., Kim, J. and Rho, H.M. (1995) The glucose-dependent transactivation activity of ABF1 on the expression of the TDH3 gene in yeast. Curr. Genet., 27, 312-317.
41. Bilu, Y. and Barkai, N. (2005) The design of transcription-factor binding sites is affected by combinatorial regulation. Genome Biol., 6, R103.
42. Andrews, B.J. and Moore, L.A. (1992) Interaction of the yeast Swi4 and Swi6 cell cycle regulatory proteins in vitro. Proc. Natl Acad. Sci. USA, 89, 11852-11856.
43. Hon, T., Lee, H.C., Hu, Z., Iyer, V.R. and Zhang, L. (2005) The heme activator protein Hap1 represses transcription by a heme-independent mechanism in Saccharomyces cerevisiae. Genetics, 169, 1343-1352.
44. Lombardia, L.J., Cadahia-Rodriguez, J.L., Freire-Picos, M.A., Gonzalez-Siso, M.I., Rodriguez-Torres, A.M. and Cerdan, M.E. (2000) Transcript analysis of 203 novel genes from Saccharomyces cerevisiae in hap1 and rox1 mutant backgrounds. Genome, 43, 881-886.
45. Verwaal, R., Arako, M., Kapur, R., Verkleij, A.J., Verrips, C.T. and Boonstra, J. (2004) HXT5 expression is under control of STRE and HAP elements in the HXT5 promoter. Yeast, 21, 747-757.
46. Tsai, H.K., Lu, H.H. and Li, W.H. (2005) Statistical methods for identifying yeast cell cycle transcription factors. Proc. Natl Acad. Sci. USA, 102, 13532-13537.
47. Workman, J.L. and Kingston, R.E. (1998) Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem., 67, 545-579.
48. Acton, T.B., Zhong, H. and Vershon, A.K. (1997) DNA-binding specificity of Mcm1: operator mutations that alter DNA-bending and transcriptional activities by a MADS box protein. Mol. Cell Biol., 17, 1881-1889.
49. Zhong, H., McCord, R. and Vershon, A.K. (1999) Identification of target sites of the alpha2-Mcm1 repressor complex in the yeast genome. Genome Res., 9, 1040-1047.
50. Kotelnikova, E.A., Makeev, V.J. and Gelfand, M.S. (2005) Evolution of transcription factor DNA binding sites. Gene, 347, 255-263.
51. King, D.A., Zhang, L., Guarente, L. and Marmorstein, R. (1999) Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein. Nat. Struct. Biol., 6, 64-71.
52. Tan, S. and Richmond, T.J. (1998) Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. Nature, 391, 660-666.
53. Konig, P., Giraldo, R., Chapman, L. and Rhodes, D. (1996) The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. Cell, 85, 125-136.
54. Tanay, A., Regev, A. and Shamir, R. (2005) Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc. Natl Acad. Sci. USA, 102, 7203-7208.
55. Wasserman, W.W. and Sandelin, A. (2004) Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet., 5, 276-287.
56. Tanay, A., Gat-Viks, I. and Shamir, R. (2004) A global view of the selection forces in the evolution of yeast cis-regulation. Genome Res., 14, 829-834.
57. Papatsenko, D. and Levine, M. (2005) Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. Proc. Natl Acad. Sci. USA, 102, 4966-4971.