Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors

Genome Research

Volumn 17, Issue 8, 2007, Pages 1161-1169

  Wang, Daryi ^a   Sung, Huang Mo ^b   Wang, Tzi Yuan ^b   Huang, Chih Jen ^b   Yang, Peggy ^b   Chang, Tiffany ^b   Wang, Yang Chao ^b   Tseng, Da Lun ^b   Wu, Jen Pey ^c   Lee, Tso Ching ^c   Shih, Ming Che ^d   Li, Wen Hsiung ^b,e  

^a BIODIVERSITY RESEARCH CENTER   (Taiwan)

^b GENOMICS RESEARCH CENTER   (Taiwan)

^c TAICHUNG VETERANS GENERAL HOSPITAL   (Taiwan)

^d UNIVERSITY OF IOWA   (United States)

^e UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANS ACTING FACTOR;

ALLELE; ARTICLE; COCULTURE; DIPLOIDY; DNA MICROARRAY; GENE EXPRESSION; HYBRID; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; QUANTITATIVE ANALYSIS; RANDOMIZATION; SACCHAROMYCES CEREVISIAE; YEAST;

ALLELES; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, GENETIC; PROMOTER REGIONS (GENETICS); SACCHAROMYCES CEREVISIAE; TRANS-ACTIVATORS;

EID: 34547637236     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.6328907     Document Type: Article

References (35)

1. Brem, R.B., Yvert, G., Clinton, R., and Kruglyak, L. 2002. Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
2. Bush, R.M. and Paigen, K. 1992. Evolution of β-glucuronidase regulation in the genus Mus. Evolution Int. J. Org. Evolution 46: 1-15.
3. Carroll, S.B. 2000. Endless forms: The evolution of gene regulation and morphological diversity. Cell 101: 577-580.
4. Carroll, S.B., Grenier, J.K., and Weatherbee, S.D. 2001. From DNA to diversity: Molecular genetics and the evolution of animal design. Blackwell Science, Malden MA.
5. Cowles, C.R., Hirschhorn, J.N., Altshuler, D., and Lander, E.S. 2002. Detection of regulatory variation in mouse genes. Nat. Genet. 32: 432-437.
6. Daborn, P.J., Yen, J.L., Bogwitz, M.R., Le Goff, G., Feil, E., Jeffers, S., Tijet, N., Perry, T., Heckel, D., Batterham, P., et al. 2002. A single p450 allele associated with insecticide resistance in Drosophila. Science 297: 2253-2256.
7. 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.
8. Forsburg, S.L. and Guarente, L. 1989. Identification and characterization of HAP4: A third component of the CCAAT-bound HAP2/HAP3 heteromer. Genes & Dev. 3: 1166-1178.
9. Gerhart, J. and Kirschner, M. 1997. Cell, embryos, and evolution: Toward a cellular and developmental understanding of phenotypic variation and evolutionary adaptability. Blackwell Science, Malden, MA.
10. Gietz, R.D. and Woods, R.A. 2002. Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. In Methods in enzymology (eds. C. Guthrie and G.R. Fink), pp. 87-96. Academic Press, San Diego, CA.
11. Gray, M., Kupiec, M., and Honigberg, S.M. 2004. Site-specific genomic (SSG) and random domain-localized (RDL) mutagenesis in yeast. BMC Biotechnol. 4: 7. doi: 10.1186/1472-6750-4-7.
12. Gu, Z., David, L., Petrov, D., Jones, T., Davis, R.W., and Steinmetz, L.M. 2005. Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 102: 1092-1097.
13. 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.
14. Hughes, K.A., Ayroles, J.F., Reedy, M.M., Drnevich, J.M., Rowe, K.C., Ruedi, E.A., Caceres, C.E., and Paige, K.N. 2006. Segregating variation in the transcriptome: cis regulation and additivity of effects. Genetics 173: 1347-1355.
15. Landgrebe, J., Bretz, F., and Brunner, E. 2006. Efficient design and analysis of two colour factorial microarray experiments. Comput. Stat. Data Anal. 50: 499-517.
16. Laurie-Ahlberg, C.C. and Bewley, G.C. 1983. Naturally occurring genetic variation affecting the expression of sn-glycerol-3-phosphate dehydrogenase in Drosophila melanogaster. Biochem. Genet. 21: 943-961.
17. 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.
18. Li, W.H. 1997. Molecular evolution. Sinauer Associated, Inc., Sunderland, MA.
19. Morley, M., Molony, C.M., Weber, T.M., Devlin, J.L., Ewens, K.G., Spielman, R.S., and Cheung, V.G. 2004. Genetic analysis of genome-wide variation in human gene expression. Nature 430: 743-747.
20. Mortimer, R.K., Romano, P., Suzzi, G., and Polsinelli, M. 1994. Genome renewal: A new phenomenon revealed from a genetic study of 43 strains of Saccharomyces cerevisiae derived from natural fermentation of grape musts. Yeast 10: 1543-1552.
21. Osada, N., Kohn, M.H., and Wu, C.I. 2006. Genomic inferences of the cis-regulatory nucleotide polymorphisms underlying gene expression differences between Drosophila melanogaster mating races. Mol. Biol. Evol. 23: 1585-1591.
22. Purugganan, M.D. 2000. The molecular population genetics of regulatory genes. Mol. Ecol. 9: 1451-1461.
23. Rifkin, S.A., Kim, J., and White, K.P. 2003. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat. Genet. 33: 138-144.
24. Rockman, M.V. and Wray, G.A. 2002. Abundant raw material for cis-regulatory evolution in humans. Mol. Biol. Evol. 19: 1991-2004.
25. Rockman, M.V. and Kruglyak, L. 2006. Genetics of global gene expression. Nat. Rev. Genet. 7: 862-872.
26. Ronald, J., Brem, R.B., Whittle, J., and Kruglyak, L. 2005. Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet. 1: e25. doi: 10.1371/journal.pgen.0010025.
27. Schadt, E.E., Monks, S.A., Drake, T.A., Lusis, A.J., Che, N., Colinayo, V., Ruff, T.G., Milligan, S.B., Lamb, J.R., Cavet, G., et al. 2003. Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
28. Stern, D.L. 2000. Evolutionary developmental biology and the problem of variation. Evolution Int. J. Org. Evolution 54: 1079-1091.
29. Streelman, J.T. and Kocher, T.D. 2002. Microsatellite variation associated with prolactin expression and growth of salt-challenged tilapia. Physiol. Genomics 9: 1-4.
30. Tautz, D. 2000. Evolution of transcriptional regulation. Curr. Opin. Genet. Dev. 10: 575-579.
31. Wittkopp, P.J., Haerum, B.K., and Clark, A.G. 2004. Evolutionary changes in cis and trans gene regulation. Nature 430: 85-88.
32. Wray, G.A., Hahn, M.W., Abouheif, E., Balhoff, J.P., Pizer, M., Rockman, M.V., and Romano, L.A. 2003. The evolution of transcriptional regulation in eukaryotes. Mol. Biol. Evol. 20: 1377-1419.
33. Yang, Y.H. and Speed, T. 2002. Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3: 579-588.
34. Yang, Y.H., Dudoit, S., Luu, P., Lin, D.M., Peng, V., Ngai, J., and Speed, T.P. 2002. Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30: e15.
35. Yvert, G., Brem, R.B., Whittle, J., Akey, J.M., Foss, E., Smith, E.N., Mackelprang, R., and Kruglyak, L. 2003. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat. Genet. 35: 57-64.