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  • 1
    Online Resource
    Online Resource
    Genomic Expression Responses to DNA-damaging Agents and the Regulatory Role of the Yeast ATR Homolog Mec1p
    American Society for Cell Biology (ASCB) ; 2001
    In:  Molecular Biology of the Cell Vol. 12, No. 10 ( 2001-10), p. 2987-3003
    Details
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 12, No. 10 ( 2001-10), p. 2987-3003
    Abstract: Eukaryotic cells respond to DNA damage by arresting the cell cycle and modulating gene expression to ensure efficient DNA repair. The human ATR kinase and its homolog in yeast, MEC1, play central roles in transducing the damage signal. To characterize the role of the Mec1 pathway in modulating the cellular response to DNA damage, we used DNA microarrays to observe genomic expression inSaccharomyces cerevisiae responding to two different DNA-damaging agents. We compared the genome-wide expression patterns of wild-type cells and mutants defective in Mec1 signaling, includingmec1, dun1, and crt1 mutants, under normal growth conditions and in response to the methylating-agent methylmethane sulfonate (MMS) and ionizing radiation. Here, we present a comparative analysis of wild-type and mutant cells responding to these DNA-damaging agents, and identify specific features of the gene expression responses that are dependent on the Mec1 pathway. Among the hundreds of genes whose expression was affected by Mec1p, one set of genes appears to represent an MEC1-dependent expression signature of DNA damage. Other aspects of the genomic responses were independent of Mec1p, and likely independent of DNA damage, suggesting the pleiotropic effects of MMS and ionizing radiation. The complete data set as well as supplemental materials is available at http://www-genome.stanford.edu/mec1 .
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    URL: Article
    DOI: 10.1091/mbc.12.10.2987
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2001
    detail.hit.zdb_id: 1474922-1
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes
    American Society for Cell Biology (ASCB) ; 2000
    In:  Molecular Biology of the Cell Vol. 11, No. 12 ( 2000-12-01), p. 4241-4257
    Details
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 11, No. 12 ( 2000-12-01), p. 4241-4257
    Abstract: We explored genomic expression patterns in the yeastSaccharomyces 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.
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    URL: Article
    DOI: 10.1091/mbc.11.12.4241
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2000
    detail.hit.zdb_id: 1474922-1
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Genome-wide Analysis of Gene Expression Regulated by the Calcineurin/Crz1p Signaling Pathway in Saccharomyces cerevisiae
    Elsevier BV ; 2002
    In:  Journal of Biological Chemistry Vol. 277, No. 34 ( 2002-08), p. 31079-31088
    Details
    In: Journal of Biological Chemistry, Elsevier BV, Vol. 277, No. 34 ( 2002-08), p. 31079-31088
    Type of Medium: Online Resource
    ISSN: 0021-9258
    URL: Article
    DOI: 10.1074/jbc.M202718200
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2002
    detail.hit.zdb_id: 2141744-1
    detail.hit.zdb_id: 1474604-9
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast
    Proceedings of the National Academy of Sciences ; 2000
    In:  Proceedings of the National Academy of Sciences Vol. 97, No. 14 ( 2000-07-05), p. 7957-7962
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 97, No. 14 ( 2000-07-05), p. 7957-7962
    Abstract: The Zap1p transcription factor senses cellular zinc status and increases expression of its target genes in response to zinc deficiency. Previously known Zap1p-regulated genes encode the Zrt1p, Zrt2p, and Zrt3p zinc transporter genes and Zap1p itself. To allow the characterization of additional genes in yeast important for zinc homeostasis, a systematic study of gene expression on the genome-wide scale was used to identify other Zap1p target genes. Using a combination of DNA microarrays and a computer-assisted analysis of shared motifs in the promoters of similarly regulated genes, we identified 46 genes that are potentially regulated by Zap1p. Zap1p-regulated expression of seven of these newly identified target genes was confirmed independently by using lacZ reporter fusions, suggesting that many of the remaining candidate genes are also Zap1p targets. Our studies demonstrate the efficacy of this combined approach to define the regulon of a specific eukaryotic transcription factor.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.97.14.7957
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2000
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 5
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    Online Resource
    Role of thioredoxin reductase in the Yap1p‐dependent response to oxidative stress in Saccharomyces cerevisiae
    Wiley ; 2001
    In:  Molecular Microbiology Vol. 39, No. 3 ( 2001-02), p. 595-605
    Details
    In: Molecular Microbiology, Wiley, Vol. 39, No. 3 ( 2001-02), p. 595-605
    Abstract: The Saccharomyces cerevisiae Yap1p transcription factor is required for the H 2 O 2 ‐dependent activation of many antioxidant genes including the TRX2 gene encoding thioredoxin 2. To identify factors that regulate Yap1p activity, we carried out a genetic screen for mutants that show elevated expression of a TRX2–HIS3 fusion in the absence of H 2 O 2 . Two independent mutants isolated in this screen carried mutations in the TRR1 gene encoding thioredoxin reductase. Northern blot and whole‐genome expression analysis revealed that the basal expression of most Yap1p targets and many other H 2 O 2 ‐inducible genes is elevated in Δ trr1 mutants in the absence of external stress. In Δ trr1 mutants treated with H 2 O 2 , the Yap1p targets, as well as genes comprising a general environmental stress response and genes encoding protein‐folding chaperones, are hyperinduced. However, despite the elevated expression of genes encoding antioxidant enzymes, Δ trr1 mutants are extremely sensitive to H 2 O 2 . The results suggest that cells lacking thioredoxin reductase have diminished capacity to detoxify oxidants and/or to repair oxidative stress‐induced damage and that the thioredoxin system is involved in the redox regulation of Yap1p transcriptional activity.
    Type of Medium: Online Resource
    ISSN: 0950-382X , 1365-2958
    URL: Article
    DOI: 10.1046/j.1365-2958.2001.02255.x
    Language: English
    Publisher: Wiley
    Publication Date: 2001
    detail.hit.zdb_id: 1501537-3
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  • 6
    Online Resource
    Online Resource
    Stability Improvement of Motion of a Rotor With an Active Control Method
    SAGE Publications ; 2000
    In:  Journal of Vibration and Control Vol. 6, No. 2 ( 2000-02), p. 291-308
    Details
    In: Journal of Vibration and Control, SAGE Publications, Vol. 6, No. 2 ( 2000-02), p. 291-308
    Abstract: The so-called phase-locked delayed feedback control method is applied to a Jeffcott rotor supported by rolling-element bearings but with negative damping and then to the same rotor supported hy journal bear ings, to improve the stability of motion of the rotor. The control parameters arc determined in terms of the characteristic equation of the controlled rotor. The results of numerical simulations show that the stability of motion of the rotor is greatly improved with the help of the phase-locked delayed feedback control method.
    Type of Medium: Online Resource
    ISSN: 1077-5463 , 1741-2986
    URL: Article
    DOI: 10.1177/107754630000600208
    Language: English
    Publisher: SAGE Publications
    Publication Date: 2000
    detail.hit.zdb_id: 2070247-4
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