Yeast: An experimental organism for 21st century biology

Genetics

Volumn 189, Issue 3, 2011, Pages 695-704

  Botstein, David ^a   Fink, Gerald R ^b  

^a PRINCETON UNIVERSITY   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN;

ARTICLE; EXPERIMENTAL ORGANISM; FUNGAL GENETICS; GENE EXPRESSION; GENE FUNCTION; GENE INTERACTION; GENE REGULATORY NETWORK; HISTORY OF MEDICINE; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; SACCHAROMYCES CEREVISIAE;

ANIMALS; DISEASE; EVOLUTION, MOLECULAR; GENE REGULATORY NETWORKS; GENETIC VARIATION; HUMANS; PROTEIN INTERACTION MAPS; SACCHAROMYCES CEREVISIAE;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 81255197643     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.111.130765     Document Type: Article

References (75)

1. Aaltonen, L. A., P. Peltomaki, F. S. Leach, P. Sistonen, L. Pylkkanen et al., 1993 Clues to the pathogenesis of familial colorectal cancer. Science 260: 812-816.
2. Alter, O., P. O. Brown, and D. Botstein, 2000 Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. USA 97: 10101-10106.
3. Ames, B. N., I. Elson-Schwab, and E. A. Silver, 2002 High-dose vitamin therapy stimulates variant enzymes with decreased coenzyme binding affinity (increased K(m)): relevance to genetic disease and polymorphisms. Am. J. Clin. Nutr. 75: 616-658.
4. Andalis, A. A., Z. Storchova, C. Styles, T. Galitski, D. Pellman et al., 2004 Defects arising from whole-genome duplications in Saccharomyces cerevisiae. Genetics 167: 1109-1121.
5. Ashburner, M., C. A. Ball, J. A. Blake, D. Botsteini, H. Butler et al., 2000 Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. title typejournalNat. Genet/title. 25: 25-29.
6. Baryshnikova, A., M. Costanzo, Y. Kim, H. Ding, J. Koh et al., 2010 Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat. Methods 7: 1017-1024.
7. Bender, A., and J. R. Pringle, 1991 Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae. Mol. Cell. Biol. 11: 1295-1305.
8. Botstein, D., 2010 It's the data! Mol. Biol. Cell 21: 4-6.
9. Botstein, D., and G. R. Fink, 1988 Yeast: an experimental organism for modern biology. Science 240: 1439-1443.
10. Brem, R. B., G. Yvert, R. Clinton, and L. Kruglyak, 2002 Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
11. Brown, P. O., and D. Botstein, 1999 Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21: 33-37.
12. Byrne, K. P., and K. H. Wolfe, 2005 The yeast gene order browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15: 1456-1461.
13. Cheung, V. G., and R. S. Spielman, 2009 Genetics of human gene expression. mapping DNA variants that influence gene expression. Nat. Rev. Genet. 10: 595-604.
14. Chu, S., J. DeRisi, M. Eisen, J. Mulholland, D. Botstein et al., 1998 The transcriptional program of sporulation in budding yeast. Science 282: 699-705.
15. Clayton, P. T., 2006 B6-responsive disorders: a model of vitamin dependency. J. Inherit. Metab. Dis. 29: 317-326.
16. Conant, G. C., and K. H. Wolfe, 2007 Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Mol. Syst. Biol. 3: 129
17. Conant, G. C., and K. H. Wolfe, 2008 Turning a hobby into a job: how duplicated genes find new functions. Nat. Rev. Genet. 9: 938-950.
18. Costanzo, M., A. Baryshnikova, J. Bellay, Y. Kim, E. D. Spear et al., 2010 The genetic landscape of a cell. Science 327: 425-431.
19. DeRisi, J. L., V. R. Iyer, and P. O. Brown, 1997 Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
20. Dobzhansky, T., 1946 Genetics of natural populations. Xiii. Recombination and variability in populations of Drosophila pseudoobscura. Genetics 31: 269-290.
21. Dolinski, K., and D. Botstein, 2005 Changing perspectives in yeast research nearly a decade after the genome sequence. Genome Res. 15: 1611-1619.
22. Dolinski, K., and D. Botstein, 2007 Orthology and functional conservation in eukaryotes. Annu. Rev. Genet. 41: 465-507.
23. Dunham, M. J., H. Badrane, T. Ferea, J. Adams, P. O. Brown et al., 2002 Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 99: 16144-16149.
24. Ehrenreich, I. M., N. Torabi, Y. Jia, J. Kent, S. Martis et al., 2010 Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature 464: 1039-1042.
25. Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein, 1998 Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95: 14863-14868.
26. Ferea, T. L., D. Botstein, P. O. Brown, and R. F. Rosenzweig, 1999 Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. USA 96: 9721-9726.
27. Fields, S., 2009 Interactive learning: lessons from two hybrids over two decades. Proteomics 9: 5209-5213.
28. Fields, S., and O. Song, 1989 A novel genetic system to detect protein-protein interactions. Nature 340: 245-246.
29. Fishel, R., M. K. Lescoe, M. R. Rao, N. G. Copeland, N. A. Jenkins et al., 1993 The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer. Cell 75: 1027-1038.
30. Friis, E. M., W. G. Chaloner, and P. R. Crane, 1987 The Origins of Angiosperms and Their Biological Consequences. Cambridge University Press, Cambridge, UK
31. Galitski, T., A. J. Saldanha, C. A. Styles, E. S. Lander, and G. R. Fink, 1999 Ploidy regulation of gene expression. Science 285: 251-254.
32. Gammie, A. E., N. Erdeniz, J. Beaver, B. Devlin, A. Nanji et al., 2007 Functional characterization of pathogenic human MSH2 missense mutations in Saccharomyces cerevisiae. Genetics 177: 707-721.
33. Gasch, A. P., P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen et al., 2000 Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11: 4241-4257.
34. Ghaemmaghami, S., W. K. Huh, K. Bower, R. W. Howson, A. Belle et al., 2003 Global analysis of protein expression in yeast. Nature 425: 737-741.
35. Giaever, G., A. M. Chu, L. Ni, C. Connelly, L. Riles et al., 2002 Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
36. Gresham, D., M. M. Desai, C. M. Tucker, H. T. Jenq, D. A. Pai et al., 2008 The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet. 4: e1000303
37. Guarente, L., 1993 Synthetic enhancement in gene interaction: a genetic tool come of age. Trends Genet. 9: 362-366.
38. Hamilton, S. R., P. Bobrowicz, B. Bobrowicz, R. C. Davidson, H. Li et al., 2003 Production of complex human glycoproteins in yeast. Science 301: 1244-1246.
39. Hamilton, S. R., R. C. Davidson, N. Sethuraman, J. H. Nett, Y. Jiang et al., 2006 Humanization of yeast to produce complex terminally sialylated glycoproteins. Science 313: 1441-1443.
40. Heinicke, S., M. S. Livstone, C. Lu, R. Oughtred, F. Kang et al., 2007 The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. PLoS ONE 2: e766
41. Hibbs, M. A., D. C. Hess, C. L. Myers, C. Huttenhower, K. Li et al., 2007 Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics 23: 2692-2699.
42. Hibbs, M. A., C. L. Myers, C. Huttenhower, D. C. Hess, K. Li et al., 2009 Directing experimental biology: a case study in mitochondrial biogenesis. PLoS Comput. Biol. 5: e1000322
43. Huh, W. K., J. V. Falvo, L. C. Gerke, A. S. Carroll, R. W. Howson et al., 2003 Global analysis of protein localization in budding yeast. Nature 425: 686-691.
44. Huttenhower, C., M. A. Hibbs, C. L. Myers, A. A. Caudy, D. C. Hess et al., 2009 The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinformatics 25: 2404-2410.
45. Ingolia, N. T., S. Ghaemmaghami, J. R. Newman, and J. S. Weissman, 2009 Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218-223.
46. Ito, T., T. Chiba, R. Ozawa, M. Yoshida, M. Hattori et al., 2001 A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98: 4569-4574.
47. Iyer, V. R., C. E. Horak, C. S. Scafe, D. Botstein, M. Snyder et al., 2001 Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538.
48. Kao, K. C., and G. Sherlock, 2008 Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Nat. Genet. 40: 1499-1504.
49. Kim, D. U., J. Hayles, D. Kim, V. Wood, H. O. Park et al., 2010 Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nat. Biotechnol. 28: 617-623.
50. Krogan, N. J., G. Cagney, H. Yu, G. Zhong, X. Guo et al., 2006 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.
51. Lam, F. H., F. S. Hartner, G. R. Fink, and G. Stephanopoulos, 2010 Enhancing stress resistance and production phenotypes through transcriptome engineering. Methods Enzymol. 470: 509-532.
52. Lander, E. S., 2011 Initial impact of the sequencing of the human genome. Nature 470: 187-197.
53. Lee, J. H., W. Terzaghi, and X. W. Deng, 2011 DWA3, an Arabidopsis DWD protein, acts as a negative regulator in ABA signal transduction. Plant Sci. 180: 352-357.
54. Lieb, J. D., X. Liu, D. Botstein, and P. O. Brown, 2001 Promoterspecific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28: 327-334.
55. Myers, C. L., D. Robson, A. Wible, M. A. Hibbs, C. Chiriac et al., 2005 Discovery of biological networks from diverse functional genomic data. Genome Biol. 6: R114
56. Novick, P., B. C. Osmond, and D. Botstein, 1989 Suppressors of yeast actin mutations. Genetics 121: 659-674.
57. Ohno, S., 1970 Evolution by Gene Duplication. Springer-Verlag, London/New York
58. Pop, A., C. Huttenhower, A. Iyer-Pascuzzi, P. N. Benfey, and O. G. Troyanskaya, 2010 Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. BMC Syst. Biol. 4: 180
59. Robertson, G., M. Hirst, M. Bainbridge, M. Bilenky, Y. Zhao et al., 2007 Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4: 651-657.
60. Scannell, D. R., G. Butler, and K. H. Wolfe, 2007 Yeast genome evolution: the origin of the species. Yeast 24: 929-942.
61. Scherens, B., and A. Goffeau, 2004 The uses of genome-wide yeast mutant collections. Genome Biol. 5: 229
62. Spellman, P. T., G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders et al., 1998 Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9: 3273-3297.
63. Storchova, Z., A. Breneman, J. Cande, J. Dunn, K. Burbank et al., 2006 Genome-wide genetic analysis of polyploidy in yeast. Nature 443: 541-547.
64. Strand, M., T. A. Prolla, R. M. Liskay, and T. D. Petes, 1993 Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature 365: 274-276.
65. Sturtevant, A. H., 1956 A highly specific complementary lethal system in Drosophila melanogaster. Genetics 41: 118-123.
66. Tong, A. H., M. Evangelista, A. B. Parsons, H. Xu, G. D. Bader et al., 2001 Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368.
67. Uetz, P., L. Giot, G. Cagney, T. A. Mansfield, R. S. Judson et al., 2000 A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
68. Wang, Y., C. L. Liu, J. D. Storey, R. J. Tibshirani, D. Herschlag et al., 2002 Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99: 5860-5865.
69. Wapinski, I., J. Pfiffner, C. French, A. Socha, D. A. Thompson et al., 2010 Gene duplication and the evolution of ribosomal protein gene regulation in yeast. Proc. Natl. Acad. Sci. USA 107: 5505-5510.
70. Wickner, R. B., 1994 [URE3] As an altered URE2 protein: evidence for a prion analog in Saccharomyces cerevisiae. Science 264: 566-569.
71. Winzeler, E. A., D. D. Shoemaker, A. Astromoff, H. Liang, K. Anderson et al., 1999 Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901-906.
72. Wohlbach, D. J., D. A. Thompson, A. P. Gasch, and A. Regev, 2009 From elements to modules: regulatory evolution in Ascomycota fungi. Curr. Opin. Genet. Dev. 19: 571-578.
73. Wolfe, K. H., and D. C. Shields, 1997 Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
74. Wu, C. Y., P. A. Rolfe, D. K. Gifford, and G. R. Fink, 2010 Control of transcription by cell size. PLoS Biol. 8: e1000523
75. Yvert, G., R. B. Brem, J. Whittle, J. M. Akey, E. Foss et al., 2003 Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat. Genet. 35: 57-64