Genomic Expression Responses to DNA-damaging Agents and the Regulatory Role of the Yeast ATR Homolog Mec1p

Gasch, Audrey P.; Huang, Mingxia; Metzner, Sandra; Botstein, David; Elledge, Stephen J.; Brown, Patrick O.

doi:10.1091/mbc.12.10.2987

Cited by 542DNA Repair MechanismsFungal and yeast genetics researchBacterial Genetics and Biotechnology

Genomic Expression Responses to DNA-damaging Agents and the Regulatory Role of the Yeast ATR Homolog Mec1p

Open access

Gasch, Audrey P., Huang, Mingxia, Metzner, Sandra, Botstein, David, Elledge, Stephen J., Brown, Patrick O.·2001·Molecular Biology of the Cell

DOI 10.1091/mbc.12.10.2987PMC PMC60150

Open this paper in CoChat — free account

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 .

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1091/mbc.12.10.2987

Cites

71 of 71 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Approximately 5% of the yeast genome is upregulated in response to various DNA-damaging agents.
“Indeed, approximately 5% of the yeast genome is upregulated in response to various DNA-damaging agents (15, 23, 24).”
From A Role for Checkpoint Kinase-Dependent Rad26 Phosphorylation in Transcription-Coupled DNA Repair in Saccharomyces cerevisiae (2010) · cites this paper as [15]
Many of the DNA-damage-upregulated genes are regulated by Mec1, indicating involvement of the DNA damage checkpoint in the DNA damage-related transcriptional response.
“Many of these genes are regulated by Mec1, indicating an involvement of the DNA damage checkpoint in the DNA damage-related transcriptional response (15).”
From A Role for Checkpoint Kinase-Dependent Rad26 Phosphorylation in Transcription-Coupled DNA Repair in Saccharomyces cerevisiae (2010) · cites this paper as [15]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 12,617 · see citing works
Self-citation
Exploring the metabolic and genetic control of gene expression on a genomic scale.
Derisi, J., Iyer, V., & Brown, P. (1997) · Science · doi:10.1126/science.278.5338.680 · Cited by 4,832 · see citing works
Self-citation
Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes
Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D., & Brown, P. O. (2000) · Molecular Biology of the Cell · doi:10.1091/mbc.11.12.4241 · Cited by 4,815 · see citing works
Self-citation
Comprehensive Identification of Cell Cycle–regulated Genes of the YeastSaccharomyces cerevisiaeby Microarray Hybridization
Spellman, P. T., Sherlock, G. J., Zhang, M. Q., Iyer, V. R., Anders, K. R., Eisen, M. B., Brown, P. O., Botstein, D., & Futcher, B. (1998) · Molecular Biology of the Cell · doi:10.1091/mbc.9.12.3273 · Cited by 4,724 · see citing works
Self-citation
Checkpoints: Controls That Ensure the Order of Cell Cycle Events
Hartwell, L. H., & Weinert, T. A. (1989) · Science · doi:10.1126/science.2683079 · Cited by 3,053 · see citing works
Cell Cycle Checkpoints: Preventing an Identity Crisis
Elledge, S. J. (1996) · Science · doi:10.1126/science.274.5293.1664 · Cited by 2,047 · see citing works
Self-citation
DNA Damage Produced by Ionizing Radiation in Mammalian Cells: Identities, Mechanisms of Formation, and Reparability
Ward, J. F. (1988) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(08)60611-x · Cited by 1,499 · see citing works
Genome-wide analysis of DNA copy-number changes using cDNA microarrays
Pollack, J. R., Perou, C. M., Alizadeh, A. A., Eisen, M. B., Pergamenschikov, A., Williams, C. F., Jeffrey, S. S., Botstein, D., & Brown, P. O. (1999) · Nature Genetics · doi:10.1038/12640 · Cited by 1,416 · see citing works
Self-citation
Linkage of ATM to Cell Cycle Regulation by the Chk2 Protein Kinase
Matsuoka, S. (1998) · Science · doi:10.1126/science.282.5395.1893 · Cited by 1,322 · see citing works
Conservation of the Chk1 Checkpoint Pathway in Mammals: Linkage of DNA Damage to Cdk Regulation Through Cdc25
Sanchez, Y., Wong, C., Thoma, R. S., Richman, R., Wu, Z., Piwnica-Worms, H., & Elledge, S. J. (1997) · Science · doi:10.1126/science.277.5331.1497 · Cited by 1,320 · see citing works
Self-citation
The RAD9 Gene Controls the Cell Cycle Response to DNA Damage in Saccharomyces cerevisiae
Weinert, T. A., & Hartwell, L. H. (1988) · Science · doi:10.1126/science.3291120 · Cited by 1,171 · see citing works
A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization.Preprint
Shalon, D., Smith, S. J., & Brown, P. O. (1996) · Genome Research · doi:10.1101/gr.6.7.639 · Cited by 1,122 · see citing works
Self-citation
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
Iyer, V. R., Horak, C. E., Scafe, C., Botstein, D., Snyder, M. P., & Brown, P. O. (2001) · Nature · doi:10.1038/35054095 · Cited by 1,084 · see citing works
Self-citation
Oxidative stress and the molecular biology of antioxidant defenses.
Scandalios, J. G. (1997) · Cited by 1,037 · see citing works
Mitotic checkpoint genes in budding yeast and the dependence of mitosis on DNA replication and repair.Preprint
Weinert, T. A., Kiser, G. L., & Hartwell, L. H. (1994) · Genes & Development · doi:10.1101/gad.8.6.652 · Cited by 750 · see citing works
A checkpoint regulates the rate of progression through S phase in S. cerevisiae in Response to DNA damage
Paulovich, A. G., & Hartwell, L. H. (1995) · Cell · doi:10.1016/0092-8674(95)90481-6 · Cited by 588 · see citing works
Regulation of RAD53 by the ATM -Like Kinases MEC1 and TEL1 in Yeast Cell Cycle Checkpoint Pathways
Sanchez, Y., Desany, B. A., Jones, W. J., Liu, Q., Wang, B., & Elledge, S. J. (1996) · Science · doi:10.1126/science.271.5247.357 · Cited by 585 · see citing works
Self-citation
Control of the DNA damage checkpoint by Chk1 and Rad53 protein kinases through distinct mechanisms
Sanchez, Y., Bachant, J., Wang, H., Hu, F., Liu, D., Tetzlaff, M., & Elledge, S. J. (1999) · Science · doi:10.1126/science.286.5442.1166 · Cited by 536 · see citing works
Self-citation
The complete sequence of the coding region of the ATM gene reveals similarity to cell cycle regulators in different species
Savitsky, K., Sfez, S., Tagle, D. A., Ziv, Y., Sartiel, A., Collins, F. S., Shiloh, Y., & Rotman, G. (1995) · Human Molecular Genetics · doi:10.1093/hmg/4.11.2025 · Cited by 535 · see citing works
Overexpression of a kinase‐inactive ATR protein causes sensitivity to DNA‐damaging agents and defects in cell cycle checkpoints
Cliby, W. A., Roberts, C. J., Cimprich, K. A., Stringer, C. M., Lamb, J. R., Schreiber, S. L., & Friend, S. H. (1998) · The EMBO Journal · doi:10.1093/emboj/17.1.159 · Cited by 534 · see citing works
The DNA Replication and Damage Checkpoint Pathways Induce Transcription by Inhibition of the Crt1 Repressor
Huang, M., Zhou, Z., & Elledge, S. J. (1998) · Cell · doi:10.1016/s0092-8674(00)81601-3 · Cited by 499 · see citing works
Self-citation
The SAD1/RAD53 protein kinase controls multiple checkpoints and DNA damage-induced transcription in yeast.Preprint
Allen, J. B., Zhou, Z. Y., Siede, W., Friedberg, E. C., & Elledge, S. J. (1994) · Genes & Development · doi:10.1101/gad.8.20.2401 · Cited by 497 · see citing works
Self-citation
Widespread aneuploidy revealed by DNA microarray expression profiling
Hughes, T. R., Roberts, C. J., Dai, H. A., Jones, A. R., Meyer, M. R., Slade, D., Burchard, J., Dow, S., Ward, T. R., Kidd, M. J., et al. (2000) · Nature Genetics · doi:10.1038/77116 · Cited by 482 · see citing works
Recovery from DNA replicational stress is the essential function of the S-phase checkpoint pathwayPreprint
Desany, B. A., Alcasabas, A. A., Bachant, J. B., & Elledge, S. J. (1998) · Genes & Development · doi:10.1101/gad.12.18.2956 · Cited by 448 · see citing works
Self-citation
Regulation of yAP‐1 nuclear localization in response to oxidative stress
Kuge, S., Jones, N., & Nomoto, A. (1997) · The EMBO Journal · doi:10.1093/emboj/16.7.1710 · Cited by 445 · see citing works
Biochemistry of DNA Lesions
Ward, J. F. (1985) · Radiation Research · doi:10.2307/3576637 · Cited by 441 · see citing works
Global response of Saccharomyces cerevisiae to an alkylating agent
Jelinsky, S. A., & Samson, L. D. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.4.1486 · Cited by 419 · see citing works
Regulation of gene expression by oxygen in Saccharomyces cerevisiae
Zitomer, R. S., & Lowry, C. V. (1992) · Microbiological Reviews · doi:10.1128/mr.56.1.1-11.1992 · Cited by 413 · see citing works
TEL1, a gene involved in controlling telomere length in S. cerevisiae, is homologous to the human ataxia telangiectasia gene
Greenwell, P. W., Kronmal, S., Porter, S. E., Gassenhuber, J., Obermaier, B., & Petes, T. D. (1995) · Cell · doi:10.1016/0092-8674(95)90479-4 · Cited by 379 · see citing works
TEL1, an S. cerevisiae homolog of the human gene mutated in ataxia telangiectasia, is functionally related to the yeast checkpoint gene, MEC1
Morrow, D. M., Tagle, D. A., Shiloh, Y., Collins, F. S., & Hieter, P. (1995) · Cell · doi:10.1016/0092-8674(95)90480-8 · Cited by 370 · see citing works
The Schizosaccharomyces pombe rad3 checkpoint gene.
Bentley, N. J., Holtzman, D. A., Flaggs, G., Keegan, K. S., DeMaggio, A. J., Ford, J. C., Hoekstra, M. F., & Carr, A. M. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb01054.x · Cited by 369 · see citing works
Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth
Zhu, G., Spellman, P. T., Volpe, T., Brown, P. O., Botstein, D., Davis, T. N., & Futcher, B. (2000) · Nature · doi:10.1038/35017581 · Cited by 362 · see citing works
Self-citation
The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors
Hofmann, K. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)89072-6 · Cited by 349 · see citing works
DUN1 encodes a protein kinase that controls the DNA damage response in yeast
Zhou, Z. Y., & Elledge, S. J. (1993) · Cell · doi:10.1016/0092-8674(93)90321-g · Cited by 346 · see citing works
Self-citation
Regulatory Networks Revealed by Transcriptional Profiling of Damaged Saccharomyces cerevisiae Cells: Rpn4 Links Base Excision Repair with Proteasomes
Jelinsky, S. A., Estep, P., Church, G. M., & Samson, L. D. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.21.8157-8167.2000 · Cited by 335 · see citing works
Enzymatic Processing of Radiation-Induced Free Radical Damage in DNA
Wallace, S. S. (1998) · Radiation Research · doi:10.2307/3579809 · Cited by 334 · see citing works
Ribonucleotide reductases: amazing and confusing.
Stubbe, J. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)39357-3 · Cited by 286 · see citing works
cDNA cloning and gene mapping of a candidate human cell cycle checkpoint protein.
Cimprich, K. A., Shin, T. B., Keith, C. T., & Schreiber, S. L. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.7.2850 · Cited by 273 · see citing works
Timing is everything: regulation of mitotic exit and cytokinesis by the MEN and SIN
McCollum, D., & Gould, K. L. (2001) · Trends in Cell Biology · doi:10.1016/s0962-8924(00)01901-2 · Cited by 253 · see citing works
DNA damage and cell cycle regulation of ribonucleotide reductase
Elledge, S. J., Zhou, Z., Allen, J. B., & Navas, T. A. (1993) · BioEssays · doi:10.1002/bies.950150507 · Cited by 242 · see citing works
Self-citation
Protein kinase mutants of human ATR increase sensitivity to UV and ionizing radiation and abrogate cell cycle checkpoint control
Wright, J. A., Keegan, K. S., Herendeen, D. R., Bentley, N. J., Carr, A. M., Hoekstra, M. F., & Concannon, P. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.13.7445 · Cited by 226 · see citing works
The Level of Intracellular Glutathione Is a Key Regulator for the Induction of Stress-Activated Signal Transduction Pathways Including Jun N-Terminal Protein Kinases and p38 Kinase by Alkylating Agents
Wilhelm, D., Bender, K., Knebel, A., & Angel, P. E. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.8.4792 · Cited by 221 · see citing works
An essential gene, ESR1, is required for mitotic growth, DNA repair and meiotic recombination Saccharomyces cerevisiae
Kato, R., & Ogawa, H. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.15.3104 · Cited by 218 · see citing works
Yeast Rad54 Promotes Rad51-dependent Homologous DNA Pairing via ATP Hydrolysis-driven Change in DNA Double Helix Conformation
Petukhova, G. D., Komen, S. V., Vergano, S., Klein, H. L., & Sung, P. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.41.29453 · Cited by 210 · see citing works
The role of the YAP1 and YAP2 genes in the regulation of the adaptive oxidative stress responses of Saccharomyces cerevisiae
Stephen, D. W. S., Rivers, S. L., & Jamieson, D. J. (1995) · Molecular Microbiology · doi:10.1111/j.1365-2958.1995.tb02407.x · Cited by 206 · see citing works
Ribonucleotide reductases: radical enzymes with suicidal tendencies
Stubbe, J., & van der Donk, W. A. (1995) · Chemistry & Biology · doi:10.1016/1074-5521(95)90084-5 · Cited by 202 · see citing works
DNA damage checkpoints update: getting molecular
Weinert, T. A. (1998) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(98)80140-8 · Cited by 192 · see citing works
Differential toxicities of anticancer agents among DNA repair and checkpoint mutants of Saccharomyces cerevisiae.
Simon, J. A., Szankasi, P., Nguyen, D. K., Ludlow, C. L., Dunstan, H. M., Roberts, C. J., Jensen, E. L., Hartwell, L. H., & Friend, S. H. (2000) · PubMed · Cited by 183 · see citing works
Identification of RNR4 , Encoding a Second Essential Small Subunit of Ribonucleotide Reductase in Saccharomyces cerevisiae
Huang, M., & Elledge, S. J. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.10.6105 · Cited by 177 · see citing works
Self-citation
DNA repair protein Rad55 is a terminal substrate of the DNA damage checkpoints
Bashkirov, V. I., King, J. S., Bashkirova, E. V., Schmuckli-Maurer, J., & Heyer, W.-D. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.12.4393-4404.2000 · Cited by 164 · see citing works
DNA damage checkpoint in budding yeast
Longhese, M. P., Foiani, M., Muzi-Falconi, M., Lucchini, G., & Plevani, P. (1998) · The EMBO Journal · doi:10.1093/emboj/17.19.5525 · Cited by 162 · see citing works
Direct Association between the Yeast Rad51 and Rad54 Recombination Proteins
Jiang, H., Xie, Y., Houston, P. L., Stemke‐Hale, K., Mortensen, U. H., Rothstein, R. J., & Kodadek, T. J. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.52.33181 · Cited by 156 · see citing works
Rad53-dependent phosphorylation of Swi6 and down-regulation of CLN1 andCLN2 transcription occur in response to DNA damage inSaccharomyces cerevisiaePreprint
Sidorova, J. M., & Breeden, L. L. (1997) · Genes & Development · doi:10.1101/gad.11.22.3032 · Cited by 150 · see citing works
Yap1p Activates Gene Transcription in an Oxidant-Specific Fashion
Coleman, S. T., Epping, E. A., Steggerda, S. M., & Moye-Rowley, S. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.12.8302 · Cited by 144 · see citing works
Multiple pathways for homologous recombination in Saccharomyces cerevisiae.
Rattray, A. J., & Symington, L. S. (1995) · Genetics · doi:10.1093/genetics/139.1.45 · Cited by 141 · see citing works
Regulation of gene expression by oxygen in Saccharomyces cerevisiae.
Zitomer, R. S., & Lowry, C. V. (1992) · Microbiological Reviews · doi:10.1128/mmbr.56.1.1-11.1992 · Cited by 129 · see citing works
A link between metastasis and resistance to apoptosis of variant small cell lung carcinoma
Shtivelman, E. (1997) · Oncogene · doi:10.1038/sj.onc.1201059 · Cited by 119 · see citing works
Biochemistry of DNA Lesions
Ward, J. F. (1985) · Radiation Research Supplement · doi:10.2307/3583517 · Cited by 107 · see citing works
Reconstitution of a MEC1 -Independent Checkpoint in Yeast by Expression of a Novel Human fork head cDNA
Pati, D., Keller, C., Groudine, M. T., & Plon, S. E. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.6.3037 · Cited by 96 · see citing works
TIP30 has an intrinsic kinase activity required for up‐regulation of a subset of apoptotic genes
Xiao, H., Palhan, V. B., Yang, Y., & Roeder, R. G. (2000) · The EMBO Journal · doi:10.1093/emboj/19.5.956 · Cited by 96 · see citing works
Cell Cycle Checkpoints, Genomic Integrity, and CancerPreprint
Hartwell, L. H., Weinert, T. A., Kadyk, L. C., et al. (1994) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1994.059.01.030 · Cited by 95 · see citing works
Control of G2 delay by the RAD9 gene of Saccharomyces cerevisiae
Weinert, T. A., & Hartwell, L. H. (1989) · Journal of Cell Science · doi:10.1242/jcs.1989.supplement_12.12 · Cited by 87 · see citing works
Duplication of ATR inhibits MyoD, induces aneuploidy and eliminates radiation-induced G1 arrest
Smith, L. G., Liu, S. J., Goodrich, L., Jacobson, D. A., Degnin, C., Bentley, N., Carr, A. M., Flaggs, G., Keegan, K. S., Hoekstra, M. F., et al. (1998) · Nature Genetics · doi:10.1038/ng0598-39 · Cited by 86 · see citing works
A cofactor, TIP30, specifically enhances HIV-1 Tatactivated transcription
Xiao, H., Tao, Y., Greenblatt, J., & Roeder, R. G. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.5.2146 · Cited by 76 · see citing works
Arrest, Adaptation, and Recovery following a Chromosome Double-strand Break in Saccharomyces cerevisiaePreprint
Lee, S.-Y., Pellicioli, A., Demeter, J., VAZE, M. P., Gasch, A. P., Malkova, A., Brown, P. O., Botstein, D., Stearns, T., Foiani, M., et al. (2000) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2000.65.303 · Cited by 67 · see citing works
Self-citation
Repair of double-strand breaks in a temperature conditional radiation-sensitive mutant of Saccharomyces cerevisiae
Budd, M. E., & Mortimer, R. (1982) · Mutation Research Letters · doi:10.1016/0165-7992(82)90080-x · Cited by 63 · see citing works
The Product of the DNA Damage-Inducible Gene of Saccharomyces cerevisiae, DIN7, Specifically Functions in Mitochondria
Fikus, M., Mieczkowski, P. A., Koprowski, P., et al. (2000) · Genetics · doi:10.1093/genetics/154.1.73 · Cited by 47 · see citing works
Roles for oxidative stress and poly(ADP-ribosyl)ation in the killing of cultured hepatocytes by methyl methanesulfonate
Mizumoto, K., Glascott, P. A., & Farber, J. L. (1993) · Biochemical Pharmacology · doi:10.1016/0006-2952(93)90587-m · Cited by 46 · see citing works
Mitotic treasures in the nucleolus
Bachant, J. B., & Elledge, S. J. (1999) · Nature · doi:10.1038/19641 · Cited by 45 · see citing works
Self-citation
Characterization of a novel DNA damage-inducible gene of Saccharomyces cerevisiae, DIN7, which is a structural homolog of the RAD2 and RAD27 DNA repair genes
Mieczkowski, P. A., Fikus, M., & Cieśla, Z. (1997) · Molecular and General Genetics MGG · doi:10.1007/s004380050369 · Cited by 27 · see citing works
The Oxygen Paradox: Biochemistry of Active OxygenPreprint
Hauptmann, N., & Cadenas, E. (1997) · Cold Spring Harbor Monograph Archive · doi:10.1101/087969502.34.1 · Cited by 22 · see citing works

Flagged first, then by citations

Sorted by citations

Biclustering algorithms for biological data analysis: a survey
Madeira, S. C., & Oliveira, A. L. (2004) · IEEE/ACM Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2004.2 · Cited by 2,049 · see citing works
Global transcriptional responses of fission yeast to environmental stress
Chen, D., Toone, W. M., Mata, J., Lyne, R., Burns, G., Kivinen, K., Brazma, A., Jones, N., & Bähler, J. (2003) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-08-0499 · Cited by 796 · see citing works
Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast
Brauer, M. J., Huttenhower, C., Airoldi, E. M., Rosenstein, R., Matese, J. C., Gresham, D., Boer, V. M., Troyanskaya, O. G., & Botstein, D. (2008) · Molecular Biology of the Cell · doi:10.1091/mbc.e07-08-0779 · Cited by 558 · see citing works
Self-citation
Predictive Behavior Within Microbial Genetic Networks
Tagkopoulos, I., Liu, Y.-C., & Tavazoie, S. (2008) · Science · doi:10.1126/science.1154456 · Cited by 519 · see citing works
Integrating regulatory motif discovery and genome-wide expression analysis
Conlon, E. M., Liu, X. S., Lieb, J. D., & Liu, J. S. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0630591100 · Cited by 343 · see citing works
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B.-J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., et al. (2006) · Journal of Biology · doi:10.1186/jbiol36 · Cited by 326 · see citing works
Self-citation
A dynamic model of proteome changes reveals new roles for transcript alteration in yeast
Lee, M. V., Topper, S. E., Hubler, S. L., Hose, J., Wenger, C. D., Coon, J. J., & Gasch, A. P. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.48 · Cited by 290 · see citing works
Self-citation
Comparative genomics of the environmental stress response in ascomycete fungi
Gasch, A. P. (2007) · Yeast · doi:10.1002/yea.1512 · Cited by 210 · see citing works
Self-citation
Genome-wide expression profiling of the response to polyene, pyrimidine, azole, and echinocandin antifungal agents in Saccharomyces cerevisiae.
Agarwal, A. K., Rogers, P. D., Baerson, S. R., Jacob, M. R., Barker, K. S., Cleary, J. D., Walker, L. A., Nagle, D. G., & Clark, A. M. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m306291200 · Cited by 204 · see citing works
Nicotinamide Clearance by Pnc1 Directly Regulates Sir2-Mediated Silencing and Longevity
Gallo, C. M., Smith, D. L., & Smith, J. S. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.3.1301-1312.2004 · Cited by 193 · see citing works
A gene ontology inferred from molecular networks
Dutkowski, J., Kramer, M., Surma, M. A., Balakrishnan, R., Cherry, J. M., Krogan, N. J., & Ideker, T. (2013) · Nature Biotechnology · doi:10.1038/nbt.2463 · Cited by 184 · see citing works
Epigenetic silencing mediates mitochondria stress-induced longevity
Schroeder, E. A., Raimundo, N., & Shadel, G. S. (2013) · Cell Metabolism · doi:10.1016/j.cmet.2013.04.003 · Cited by 186 · see citing works
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
Moses, A. M., Chiang, D. Y., Pollard, D. A., Iyer, V. N., & Eisen, M. B. (2004) · Genome Biology · doi:10.1186/gb-2004-5-12-r98 · Cited by 153 · see citing works
Subcellular localization of yeast ribonucleotide reductase regulated by the DNA replication and damage checkpoint pathways
Yao, R., Zhang, Z., An, X., Bucci, B., Perlstein, D. L., Stubbe, J., & Huang, M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1131932100 · Cited by 151 · see citing works
Self-citation
DNA replication as a target of the DNA damage checkpoint
Zegerman, P., & Diffley, J. F. X. (2009) · DNA Repair · doi:10.1016/j.dnarep.2009.04.023 · Cited by 128 · see citing works
Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action
Hillenmeyer, M. E., Ericson, E., Davis, R. W., Nislow, C., Koller, D., & Giaever, G. (2010) · Genome Biology · doi:10.1186/gb-2010-11-3-r30 · Cited by 112 · see citing works
“Functional prediction performance was compared using several types of functional yeast assays: co-fitness; a unified protein-protein interaction network [25] derived from two large-scale affinity precipitation studies [26,27]; synthetic lethality [28]; and co-expression over three microarray gene expression studies [2…”
Method
Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe
Schmidt, M. W., Houseman, A., Ivanov, A. R., & Wolf, D. A. (2007) · Molecular Systems Biology · doi:10.1038/msb4100117 · Cited by 114 · see citing works
The genome-wide expression response to telomerase deletion in Saccharomyces cerevisiae
Nautiyal, S., DeRisi, J. L., & Blackburn, E. H. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.142162499 · Cited by 96 · see citing works
Checkpoint mechanisms at the intersection between DNA damage and repair
Lazzaro, F., Giannattasio, M., Puddu, F., Granata, M., Pellicioli, A., Plevani, P., & Muzi-Falconi, M. (2009) · DNA Repair · doi:10.1016/j.dnarep.2009.04.022 · Cited by 94 · see citing works
Perspectives on the DNA damage and replication checkpoint responses in Saccharomyces cerevisiae
Putnam, C. D., Jaehnig, E. J., & Kolodner, R. D. (2009) · DNA Repair · doi:10.1016/j.dnarep.2009.04.021 · Cited by 83 · see citing works
Dynamical Remodeling of the Transcriptome during Short-Term Anaerobiosis in Saccharomyces cerevisiae : Differential Response and Role of Msn2 and/or Msn4 and Other Factors in Galactose and Glucose Media
Lai, L.-C., Kosorukoff, A. L., Burke, P. V., & Kwast, K. E. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.10.4075-4091.2005 · Cited by 84 · see citing works
A Double-Edged Sword: Aneuploidy is a Prevalent Strategy in Fungal Adaptation
Tsai, H.-J., & Nelliat, A. (2019) · Genes · doi:10.3390/genes10100787 · Cited by 60 · see citing works
Transcriptional responses to DNA damage
Silva, E., & Ideker, T. (2019) · DNA repair · doi:10.1016/j.dnarep.2019.05.002 · Cited by 31 · see citing works
“Accordingly, the ESR signal was also strongly detected, though transiently, in irradiated cells [30].”
Influential
A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2in chromosome end protection
Greenall, A., Lei, G., Swan, D. C., James, K., Wang, L., Peters, H., Wipat, A., Wilkinson, D. J., & Lydall, D. (2008) · Genome Biology · doi:10.1186/gb-2008-9-10-r146 · Cited by 23 · see citing works
A Role for Checkpoint Kinase-Dependent Rad26 Phosphorylation in Transcription-Coupled DNA Repair in Saccharomyces cerevisiae
Taschner, M., Harreman, M., Teng, Y., Gill, H., Anindya, R., Maslen, S. L., Skehel, J. M., Waters, R., & Svejstrup, J. Q. (2010) · Molecular and Cellular Biology · doi:10.1128/mcb.00822-09 · Cited by 19 · see citing works

Genomic Instability and Cancer Risk Associated with Erroneous DNA Repair
Yoshioka, K., Kusumoto‐Matsuo, R., Matsuno, Y., & Ishiai, M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222212254 · Cited by 60 · see citing works
Molecular chaperones in DNA repair mechanisms: Role in genomic instability and proteostasis in cancer
Hasan, A., Rizvi, S. F., Parveen, S., & Mir, S. S. (2022) · Life Sciences · doi:10.1016/j.lfs.2022.120852 · Cited by 9 · see citing works
Nucleotide excision repair in aging & cancer
Melis, J. P. M. (2012) · Leiden Repository (Leiden University)
Constitutively high dNTP concentration inhibits cell cycle progression and the DNA damage checkpoint in yeast Saccharomyces cerevisiae
Chabes, A., & Stillman, B. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610585104 · Cited by 135 · see citing works
Genomic instability and aging
Li, Z., Anugula, S., & Rasmussen, L. J. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-823761-8.00020-3 · Cited by 6 · see citing works

Authors: Gasch, A. P., Huang, M., Metzner, S., Botstein, D., Elledge, S. J., & Brown, P. O.
Affiliations: Lawrence Berkeley National Laboratory (US)
Department of Biochemistry and
Departments of Biochemistry and
Genetics, and
Howard Hughes Medical Institute (US)
Corresponding author: Brown, Patrick O.
ORCID: Gasch, Audrey P.
Huang, Mingxia
Botstein, David
Elledge, Stephen J.
Brown, Patrick O.
Venue: Molecular Biology of the Cell
Publisher: American Society for Cell Biology (ASCB)
Published: 2001-10
Volume: 12
Issue: 10
Pages: 2987-3003
ISSN: 1059-1524 (ISSN-L)
1939-4586
DOI: 10.1091/mbc.12.10.2987
PMC: PMC60150
OpenAlex: W2162735386
Cited by: 542
References: 71
Citations by year: 2026: 1 · 2025: 4 · 2024: 4 · 2023: 8 · 2022: 12 · 2021: 10 · 2020: 12 · 2019: 13 · 2018: 11 · 2017: 12 · 2016: 20 · 2015: 21 · 2014: 21 · 2013: 23 · 2012: 21
FWCI: 11.66
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Molecular Biology of the Cell (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Howard Hughes Medical Institute
Damon Runyon Cancer Research Foundation
National Institutes of Health (5r01hg000983-06)
National Human Genome Research Institute (HG-00983, HG-00450)
National Institute of General Medical Sciences (GM-44664, GM46406, R37GM046406, R37GM044664, R01GM046406, R01GM044664)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords: ATR kinase, DNA damage response, Saccharomyces cerevisiae, gene expression profiling, methyl methanesulfonate, ionizing radiation, Dun1, DNA repair, cell cycle arrest
MeSH terms: DNA Damage, DNA Repair, DNA, Fungal, Fungal Proteins, Methyl Methanesulfonate, Mutation, Protein Kinases, Radiation, Ionizing, Saccharomyces cerevisiae, Signal Transduction, Gene Expression Regulation, Fungal, Protein Serine-Threonine Kinases, Sequence Homology, Cell Cycle Proteins, Oligonucleotide Array Sequence Analysis, Saccharomyces cerevisiae Proteins, Intracellular Signaling Peptides and Proteins

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Genomic Expression Responses to DNA-damaging Agents and the Regulatory Role of the Yeast ATR Homolog Mec1p

Abstract

Integrity signals

Claims the paper makes

Claims other papers make about this one

Self-check

Cites

Cited by

Related

Record

About these checks