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Mol. Biol. Cell 11 (12): 4241-4257

Copyright © 2000 by The American Society for Cell Biology.

Vol. 11, Issue 12, 4241-4257, December 2000

Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes

Audrey P. Gasch,* Paul T. Spellman,dagger Camilla M. Kao,* Orna Carmel-Harel,Dagger Michael B. Eisen,§ Gisela Storz,Dagger David Botstein,dagger and Patrick O. Brown*||

 *Departments of Biochemistry and  dagger Genetics, Stanford University School of Medicine, Stanford, CA 94305-5428;  Dagger Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-5430;  §Lawrence Berkeley National Labs and Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, CA 94720; and  ||Howard Hughes Medical Institute, Stanford, CA

We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over time for almost every yeast gene, as cells responded to temperature shocks, hydrogen peroxide, the superoxide-generating drug menadione, the sulfhydryl-oxidizing agent diamide, the disulfide-reducing agent dithiothreitol, hyper- and hypo-osmotic shock, amino acid starvation, nitrogen source depletion, and progression into stationary phase. A large set of genes (~ 900) showed a similar drastic response to almost all of these environmental changes. Additional features of the genomic responses were specialized for specific conditions. Promoter analysis and subsequent characterization of the responses of mutant strains implicated the transcription factors Yap1p, as well as Msn2p and Msn4p, in mediating specific features of the transcriptional response, while the identification of novel sequence elements provided clues to novel regulators. Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell.

Online version of this article contains data set material, and is available at

Current address: Lawrence Berkeley National Labs, Berkeley, CA 94720. Dagger Dagger current address: Department of Chemical Engineering, Stanford University, Stanford, CA 94305-5428.

|| Corresponding author. E-mail address: pbrown{at}

Molecular Biology of the Cell
Vol. 11, 4241-4257, December 2000
Copyright © 2000 by The American Society for Cell Biology

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   Abstract »    Full Text »    PDF »
One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data.
S. Dumcke, M. Seizl, S. Etzold, N. Pirkl, D. E. Martin, P. Cramer, and A. Tresch (2012)
Nucleic Acids Res. 40, 8883-8892
   Abstract »    Full Text »    PDF »
Cellular Memory of Acquired Stress Resistance in Saccharomyces cerevisiae.
Q. Guan, S. Haroon, D. G. Bravo, J. L. Will, and A. P. Gasch (2012)
Genetics 192, 495-505
   Abstract »    Full Text »    PDF »

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