Cited by 420DNA Repair MechanismsFungal and yeast genetics researchBacterial Genetics and Biotechnology

The DOI matches its Crossref record; 34 of the 36 references it cites were found in a registry or an index.

Global response of Saccharomyces cerevisiae to an alkylating agent

Open access

Jelinsky, Scott A., Samson, Leona D.·1999·Proceedings of the National Academy of Sciences

Open this paper in CoChat — free account

Abstract

DNA chip technology enables simultaneous examination of how ≈6,200 Saccharomyces cerevisiae gene transcript levels, representing the entire genome, respond to environmental change. By using chips bearing oligonucleotide arrays, we show that, after exposure to the alkylating agent methyl methanesulfonate, ≈325 gene transcript levels are increased and ≈76 are decreased. Of the 21 genes that already were known to be induced by a DNA-damaging agent, 18 can be scored as inducible in this data set, and surprisingly, most of the newly identified inducible genes are induced even more strongly than these 18. We examined 42 responsive and 8 nonresponsive ORFs by conventional Northern blotting, and 48 of these 50 ORFs responded as they did by DNA chip analysis, with magnitudes displaying a correlation coefficient of 0.79. Responsive genes fall into several expected and many unexpected categories. Evidence for the induction of a program to eliminate and replace alkylated proteins is presented.

Integrity signals

Registry

Crossref · 10.1073/pnas.96.4.1486

Cites

34 of 34 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

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?

Molecular cloning: A laboratory manual
Deininger, P. L. (1990) · Analytical Biochemistry · doi:10.1016/0003-2697(90)90595-z · Cited by 84,684
DNA Repair and Mutagenesis
Friedberg, E. C., Walker, G. C., Siede, W., Wood, R. D., Schultz, R. A., & Ellenberger, T. (2005) · doi:10.1128/9781555816704 · Cited by 5,683
Expression monitoring by hybridization to high-density oligonucleotide arrays
Lockhart, D. J., Dong, H., Byrne, M. C., Follettie, M. T., Gallo, M. V., Chee, M. S., Mittmann, M., Wang, C., Kobayashi, M., Norton, H., et al. (1996) · Nature Biotechnology · doi:10.1038/nbt1296-1675 · Cited by 2,841
DNA repair and mutagenesis
Bootsma, D., & Hoeijmakers, J. H. J. (1996) · Trends in Genetics · doi:10.1016/0168-9525(96)81408-9 · Cited by 2,285
A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle
Cho, R. J., Campbell, M. J., Winzeler, E. A., Steinmetz, L. M., Conway, A. R., Wodicka, L. M., Wolfsberg, T. G., Gabrielian, A. E., Landsman, D., Lockhart, D. J., et al. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80114-8 · Cited by 2,024
A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae
Schmitt, M. E., Brown, T. A., & Trumpower, B. L. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.10.3091 · Cited by 1,344
SGD: Saccharomyces Genome Database
Cherry, J. M. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.73 · Cited by 1,145
Genome-wide expression monitoring in Saccharomyces cerevisiae
Wodicka, L. M., Dong, H., Mittmann, M., Ho, M.-H., & Lockhart, D. J. (1997) · Nature Biotechnology · doi:10.1038/nbt1297-1359 · Cited by 973
Characterization of the Yeast Transcriptome
Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, R. J., Basrai, M. A., Bassett, D. E., Hieter, P., Vogelstein, B., & Kinzler, K. W. (1997) · Cell · doi:10.1016/s0092-8674(00)81845-0 · Cited by 973
DNA damage-inducible transcripts in mammalian cells.
Fornace, A. J., Alamo, I., & Hollander, M. C. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.23.8800 · Cited by 624

Flagged first, then by citations

Show all 36 references

2 of the 36 references couldn’t be matched to a known paper.

Research works printed but not linked: 5

P Herrlich, C Blattner, A Knebel, K Bender, H J Rahmsdorf Biol Chem 378, 1217–1229 (1997).
10.1128/mcb.13.7.4242-4250.1993 · DOI
J B Bachant, S J Elledge DNA Repair in Prokaryotes and Lower Eukaryotes, DNA Damage and Repair, eds J A Nickoloff, M F Hoekstra (Humana, Totowa, NJ) 1 (1998).
W Xiao, K K Singh, B Chen, L Samson Mol Cell Biol 13, 7213–7221 (1993).
J E Landers, S L Cassel, D L George Cancer Res 57, 3562–3568 (1997).

Sorted by citations

The DNA damage response: putting checkpoints in perspective
Zhou, B.-B. S., & Elledge, S. J. (2000) · Nature · doi:10.1038/35044005 · Cited by 3,213
“First, in yeast and mammals, a large number of genes involved in DNA repair are transcriptionally induced in response to DNA damage in a DNA damage response pathway dependent manner, suggesting that many facets of repair are enhance”
Background
Transcriptional Regulatory Networks in Saccharomyces cerevisiae
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) · Science · doi:10.1126/science.1075090 · Cited by 2,956
Coordinated plant defense responses in Arabidopsis revealed by microarray analysis
Schenk, P. M., Kazan, K., Wilson, I. W., Anderson, J. P., Richmond, T., Somerville, S. C., & Manners, J. M. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.21.11655 · Cited by 1,370
Remodeling of Yeast Genome Expression in Response to Environmental Changes
Causton, H. C., Ren, B., Koh, S. S., Harbison, C. T., Kanin, E. I., Jennings, E. G., Lee, T. I., True, H. L., Lander, E. S., & Young, R. A. (2001) · Molecular Biology of the Cell · doi:10.1091/mbc.12.2.323 · Cited by 1,382
“A transient reduction in the synthesis of ribosomal protein mRNAs would permit energy and other resources to be diverted toward the synthesis and use of molecular chaperones, along with other mechanisms involved in surviving a change in the environment (Jelinsky and Samson, 1999).”
BackgroundMethodInfluential
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
Transcriptional Profiling Shows that Gcn4p Is a Master Regulator of Gene Expression during Amino Acid Starvation in Yeast
Natarajan, K., Meyer, M. R., Jackson, B. M., Slade, D., Roberts, C., Hinnebusch, A. G., & Marton, M. J. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.13.4347-4368.2001 · Cited by 749
“Stimulated by the previous finding that many amino acid biosynthetic genes were induced by MMS (48), we discovered that MMS induces GCN4 translation dependent on Gcn2p.”
BackgroundMethodInfluential
Relating Whole-Genome Expression Data with Protein-Protein InteractionsPreprint
Jansen, R., Greenbaum, D. S., & Gerstein, M. (2002) · Genome Research · doi:10.1101/gr.205602 · Cited by 657
“…a comprehensive reference set, which we merged and scaled together from a variety of Affymetrix GeneChip and SAGE data sets (Velculescu 1997; Holstege 1998; Roth et al. 1998; Jelinsky and Samson 1999) into a single representative data source (scaling details on our website; Greenbaum et al. 2001).”
BackgroundMethod
Recruitment of the INO80 Complex by H2A Phosphorylation Links ATP-Dependent Chromatin Remodeling with DNA Double-Strand Break Repair
van Attikum, H., Fritsch, O., Höhn, B., & Gasser, S. M. (2004) · Cell · doi:10.1016/j.cell.2004.11.033 · Cited by 609
“…cells, while nine connection with either the DNA repair machinery or the fail to be repressed in the ino80 mutant (Supplemental damage response (Jelinsky and Samson, 1999). can be detected as early as 1 hr after HO induction, reaching a maximum at 4 hr after the switch to galactose NHEJ, they…”
Background
Identification of additional genes belonging to the LexA regulon in Escherichia coli
de Henestrosa, A. R. F., Ogi, T., Aoyagi, S., Chafin, D. R., Hayes, J. J., Ohmori, H., & Woodgate, R. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01826.x · Cited by 566
“The precise number of proteins induced as part of the global SOS response is presently unknown, but it is likely to be considerable given the unexpected number of damageinducible genes recently reported in Saccharomyces cerevisiae (Jelinsky and Samson, 1999).”
Background
Surviving the Breakup: The DNA Damage Checkpoint
Harrison, J. C., & Haber, J. E. (2006) · Annual Review of Genetics · doi:10.1146/annurev.genet.40.051206.105231 · Cited by 565
“transcriptionally responsive genes (51, 65).”
Genomic Expression Responses to DNA-damaging Agents and the Regulatory Role of the Yeast ATR Homolog Mec1p
Gasch, A. P., Huang, M., Metzner, S., Botstein, D., Elledge, S. J., & Brown, P. O. (2001) · Molecular Biology of the Cell · doi:10.1091/mbc.12.10.2987 · Cited by 542
“The results of hierarchical clustering revealed that both MMS and ionizing radiation triggered rapid and extensive changes in the genomic expression program in wild-type cells (Figure 1), as has been previously observed (Jelinsky and Samson, 1999; Jelinsky et al., 2000).”
Result
RESPONSE Re: Markers of DNA Repair and Susceptibility to Cancer in Humans: an Epidemiologic Review
Berwick, M. (2000) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/92.18.1537 · Cited by 545
Proteasomal Proteomics: Identification of Nucleotide-sensitive Proteasome-interacting Proteins by Mass Spectrometric Analysis of Affinity-purified Proteasomes
Verma, R., Chen, S., Feldman, R. M. R., Schieltz, D. M., Yates, J. R., Dohmen, R. J., & Deshaies, R. J. (2000) · Molecular Biology of the Cell · doi:10.1091/mbc.11.10.3425 · Cited by 540
“The expression of Ubp6 is increased 5-fold upon treatment of cells with DNA-damaging reagents (Jelinsky and Samson, 1999).”
Background
Genome-Wide Transcriptional Profiling of the Escherichia coli Responses to Superoxide Stress and Sodium Salicylate
Pomposiello, P. J., Bennik, M. H. J., & Demple, B. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.13.3890-3902.2001 · Cited by 487
“coli (4, 37, 44), Bacillus subtilis (14), Caulobacter crescentus (25), and Saccharomyces cerevisiae (15, 23).”
Background
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
“), drug treatments (methyl methanesulfonate treatmen”
The use and analysis of microarray data
Butte, A. J. (2002) · Nature Reviews Drug Discovery · doi:10.1038/nrd961 · Cited by 482
“, compared microarray measurements with NORTHERN BLOTS”
Result
Expression Profiling in the Muscular Dystrophies
Chen, Y., Zhao, P., Borup, R., & Hoffman, E. P. (2000) · The Journal of Cell Biology · doi:10.1083/jcb.151.6.1321 · Cited by 485
“Whereas expression profiling is widely felt to provide the parallel data generation needed to understand many complex biological processes, previous reports of expression profiling have been limited to physiological responses of microorganisms to environmental change and the subclassification of human cancers (Alon et…”
The genomics of yeast responses to environmental stress and starvation
Gasch, A. P., & Werner‐Washburne, M. (2002) · Functional & Integrative Genomics · doi:10.1007/s10142-002-0058-2 · Cited by 448
“Cells exposed to MMS induce the expression of a number of genes specific to DNA damage, but they also trigger expression changes in genes involved in protein folding and degradation, oxidative stress defense, amino acid metabolism, and aerobic processes ( Jelinsky and Samson 1999; Jelinsky et al. 2000; Gasch et al. 20…”
BackgroundInfluential
Integrated Analysis of Transcriptomic and Proteomic Data
Haider, S., & Pal, R. (2013) · Current Genomics · doi:10.2174/1389202911314020003 · Cited by 446
The Transcriptional Response of Yeast to Saline Stress
Posas, F., Chambers, J. R., Heyman, J. A., Hoeffler, J. P., de Nadal, E., & Ariño, J. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m910016199 · Cited by 423
Functional Specificity among Ribosomal Proteins Regulates Gene Expression
Komili, S., Farny, N. G., Roth, F. P., & Silver, P. A. (2007) · Cell · doi:10.1016/j.cell.2007.08.037 · Cited by 398
“…= very long, À1 = slightly short, À2 = short, À3 = very short g (Ni and Snyder, 2001) h (Jorgensen et al., 2002) i (Enyenihi and Saunders, 2003) j (Jelinsky and Samson, 1999) k (Bonangelino et al., 2002) l (Zewail et al., 2003) m (Parsons et al., 2004) n (Page et al., 2003) o (Askree et al.,…”
Background
Toxicology and genetic toxicology in the new era of “toxicogenomics”: impact of “-omics” technologies
Aardema, M. J., & MacGregor, J. T. (2002) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/s0027-5107(01)00292-5 · Cited by 396
“Exposure to alkylating agents was found to induce genes involved in DNA repair that were co-regulated with genes involved with eliminating and replacing alkylated proteins [33,34].”
Background
Gcn4p, a Master Regulator of Gene Expression, Is Controlled at Multiple Levels by Diverse Signals of Starvation and Stress
Hinnebusch, A. G., & Natarajan, K. (2002) · Eukaryotic Cell · doi:10.1128/ec.01.1.22-32.2002 · Cited by 383
“1), the induction of amino acid biosynthetic genes by MMS is probably mediated by Gcn4p.”
BackgroundInfluential
Mechanisms and Regulation of Mitotic Recombination in Saccharomyces cerevisiae
Symington, L. S., Rothstein, R. J., & Lisby, M. (2014) · Genetics · doi:10.1534/genetics.114.166140 · Cited by 375
“DNA damage-induced genes with relevance to mitotic recombination are the ribonucleotide reductase genes RNR1–4, which are required for reduction of ribonucleotides to their corresponding 29-deoxyribonucleotides (dNTPs) necessary for DNA synthesis during recombination, the DNA damage checkpoint genes RAD53 and MEC1, wh…”
Background
Trm9-Catalyzed tRNA Modifications Link Translation to the DNA Damage Response
Begley, U., Dyavaiah, M., Patil, A., Rooney, J. P., DiRenzo, D. M., Young, C. M., Conklin, D. S., Zitomer, R. S., & Begley, T. J. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.09.021 · Cited by 333
“cerevisiae transcripts are regulated in a dose- and time-dependent manner after methyl methanesulfonate (MMS) exposure (Gasch et al., 2000, 2001; Gasch and Werner-Washburne, 2002; Jelinsky and Samson, 1999; Jelinsky et al., 2000; Workman et al., 2006).”
Background
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
“cerevisiae’s ;6,200 genes were responsive to MMS exposure; ;300 genes were induced by 4- to 250-fold, and ;100 genes were repressed by 3- to 18-fold (17).”
BackgroundMethodInfluentialSelf-citation
Genes required for ionizing radiation resistance in yeast
Bennett, C. B., Lewis, L. K., Karthikeyan, G., Lobachev, K. S., Jin, Y. H., Sterling, J. F., Snipe, J. R., & Resnick, M. A. (2001) · Nature Genetics · doi:10.1038/ng778 · Cited by 328
“In this regard, it is notable that among the approximately 50 new mutants that were sensitive to MMS as well as γ-rays, only three ( DHH1 , UBC13 and ERG3 ) correspond to genes that show large changes in expression after MMS exposure of haploid yeas”
Background
Elucidating mechanisms of drug-induced toxicity
Liebler, D. C., & Guengerich, F. P. (2005) · Nature Reviews Drug Discovery · doi:10.1038/nrd1720 · Cited by 330
“Studies in Saccharomyces cerevisiae with model alkylating agents and arsenic revealed distinct transcriptome-profile change”
Background
Glutathione, Altruistic Metabolite in Fungi
Pócsi, I., Prade, R. A., & Penninckx, M. J. (2004) · Advances in microbial physiology/Advances in Microbial Physiology · doi:10.1016/s0065-2911(04)49001-8 · Cited by 311
“cerevisiae exposed to methyl methanesulfonate showed induction (>4 fold) of 325 transcripts (Jelinsky and Samson, 1999) with 28.”
Background
A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage
Chang, M., Bellaoui, M., Boone, C. M., & Brown, G. W. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.262669299 · Cited by 301
Monitoring gene expression using DNA microarrays
Harrington, C. A., Rosenow, C., & Retief, J. (2000) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(00)00091-6 · Cited by 289
What is Bioinformatics? A Proposed Definition and Overview of the Field
Luscombe, N. M., Greenbaum, D., & Gerstein, M. (2001) · Methods of Information in Medicine · doi:10.1055/s-0038-1634431 · Cited by 453
“Much of the effort has so far focused on the yeast [19-24] and human genomes [25, 26].”
Background
A Systems Approach to Mapping DNA Damage Response Pathways
Workman, C. T., Mak, H. C., McCuine, S., Tagne, J., Agarwal, M., Ozier, O. W., Begley, T. J., Samson, L. D., & Ideker, T. (2006) · Science · doi:10.1126/science.1122088 · Cited by 272
Self-citation
Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents
Birrell, G. W., Brown, J. A. L., Wu, H. I., Giaever, G. N., Chu, A. M., Davis, R. W., & Brown, J. M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.132275199 · Cited by 255
In Vitro Assembly and Recognition of Lys-63 Polyubiquitin Chains
Hofmann, R. M., & Pickart, C. M. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m103378200 · Cited by 253
Distinct Physiological Functions of Thiol Peroxidase Isoenzymes in Saccharomyces cerevisiae
Park, S. G., Cha, M., Jeong, W., & Kim, I.-H. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.8.5723 · Cited by 244
Protein Damage by Reactive Electrophiles: Targets and Consequences
Liebler, D. C. (2007) · Chemical Research in Toxicology · doi:10.1021/tx700235t · Cited by 235
An overview on glutathione in versus non-conventional yeasts
Penninckx, M. J. (2002) · FEMS Yeast Research · doi:10.1016/s1567-1356(02)00081-8 · Cited by 235
“methanesulfonate (MMS) has shown that the transcripts of 325 ORFs were induced over four-fold by the reagent [65].”
Background
Over 1000 genes are involved in the DNA damage response of Escherichia coli
Khil, P. P., & Camerini‐Otero, R. D. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02878.x · Cited by 234
“An analysis of the response to DNA damage in other organisms on a genomic scale, such as human (Amundson et al., 1999) and yeast (Jelinsky and Samson, 1999; Jelinsky et al., 2000), has also revealed a complicated and elaborate picture of gene expression changes after genotoxic stress.”
BackgroundInfluential
Partitioning the transcriptional program induced by rapamycin among the effectors of the Tor proteins
Shamji, A. F., Kuruvilla, F. G., & Schreiber, S. L. (2000) · Current Biology · doi:10.1016/s0960-9822(00)00866-6 · Cited by 234
Genome-wide expression analyses: Metabolic adaptation of to high sugar stress
Erasmus, D. J., VANDERMERWE, G., & VANVUUREN, H. (2003) · FEMS Yeast Research · doi:10.1016/s1567-1356(02)00203-9 · Cited by 232
“Methods for poly(A)þ RNA puri¢cation, ampli¢cation and labelling, and cRNA fragmentation have been described previously [46].”
Method
Non-traditional platinum compounds for improved accumulation, oral bioavailability, and tumor targeting
Lovejoy, K. S., & Lippard, S. J. (2009) · Dalton Transactions · doi:10.1039/b913896j · Cited by 230
Gene Expression Profile of Campylobacter jejuni in Response to Growth Temperature Variation
Stintzi, A. P. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.6.2009-2016.2003 · Cited by 230
“In several gene expression studies with Saccharomyces cerevisiae, it has been observed that the expression level of ribosomal genes is similarly affected by various environmental stresses (13, 16).”
Background
Transcript Expression in Saccharomyces cerevisiae at High Salinity
Yale, J., & Bohnert, H. J. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m008209200 · Cited by 226
DNA bending and a flip‐out mechanism for base excision by the helix–hairpin–helix DNA glycosylase, Escherichia coli AlkA
Hollis, T., Ichikawa, Y., & Ellenberger, T. (2000) · The EMBO Journal · doi:10.1093/emboj/19.4.758 · Cited by 222
“, 1995), causing widespread cellular responses (Jelinsky and Samson, 1999), including the activation of cell cycle checkpoints and/or programmed cell death (Engelward et al.”
Background
A question of size: the eukaryotic proteome and the problems in defining it
Harrison, P. M. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.5.1083 · Cited by 224
Genome-Wide Expression Patterns in Saccharomyces cerevisiae : Comparison of Drug Treatments and Genetic Alterations Affecting Biosynthesis of Ergosterol
Bammert, G. F., & Fostel, J. M. (2000) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.44.5.1255-1265.2000 · Cited by 213
“cerevisiae genome, Affymetrix DNA microarrays have emerged as a powerful tool for examining the simultaneous expression pattern of more than 6,000 yeast genes (10, 14, 21, 33, 52).”
Background
Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis
Gao, H., Wang, Y., Liu, X., Yan, T., Wu, L., Alm, E. J., Arkin, A. P., Thompson, D. K., & Zhou, J. Z. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.22.7796-7803.2004 · Cited by 203
“jejuni, it has been observed that the expression level of ribosomal genes is similarly affected by heat stress, as well as alkylating agents (9, 19, 33).”
Background
Metabolic surprises in Saccharomyces cerevisiae during adaptation to saline conditions: questions, some answers and a model
Blomberg, A. (2000) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2000.tb08864.x · Cited by 198
Aft2p, a Novel Iron-regulated Transcription Activator That Modulates, with Aft1p, Intracellular Iron Use and Resistance to Oxidative Stress in Yeast
Blaiseau, P.-L., Lesuisse, E., & Camadro, J. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m104987200 · Cited by 193
Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts
Greenbaum, D. S., Jansen, R., & Gerstein, M. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.4.585 · Cited by 183
A transmembrane ubiquitin ligase required to sort membrane proteins into multivesicular bodies
Reggiori, F., & Pelham, H. R. B. (2002) · Nature Cell Biology · doi:10.1038/ncb743 · Cited by 179
“7-fold by alkylating agents, which damage both proteins and DN”
Background
Comprehensive Expression Analysis of Time-dependent Genetic Responses in Yeast Cells to Low Temperature
Sahara, T., Goda, T., & Ohgiya, S. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m209258200 · Cited by 176
Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis
Cavalieri, D., Townsend, J. P., & Hartl, D. L. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.210395297 · Cited by 174
Ribosome quality control antagonizes the activation of the integrated stress response on colliding ribosomes
Yan, L. L., & Zaher, H. S. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.11.033 · Cited by 176
“As expected (Jelinsky and Samson, 1999), the addition of MMS was found to have profound effects on gene expression.”
Background
Characterization of a Six-Subunit Holo-Elongator Complex Required for the Regulated Expression of a Group of Genes in Saccharomyces cerevisiae
Krogan, N. J., & Greenblatt, J. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.23.8203-8212.2001 · Cited by 170
“A similar subset of genes has recently been reported to be coinduced under unfavorable conditions, such as growth in the presence of the agent alkylating methyl methanesulfonate (13) or deletion of the gene encoding the Gcn4 transcriptional activator (17).”
Background
Integrating stress-response and cell-cycle checkpoint pathways
Pearce, A. K., & Humphrey, T. C. (2001) · Trends in Cell Biology · doi:10.1016/s0962-8924(01)02119-5 · Cited by 167
A quantitative estimation of the global translational activity in logarithmically growing yeast cells
von der Haar, T. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-87 · Cited by 169
“[20], Holland [21], Jelinsky and Samson [22] and Roth et al.”
Background
Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping.
Begley, T. J., Rosenbach, A., Ideker, T., & Samson, L. D. (2002) · PubMed · Cited by 162
Self-citation
Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models
Jansen, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg306 · Cited by 161
UBC13, a DNA-damage-inducible gene, is a member of the error-free postreplication repair pathway in Saccharomyces cerevisiae
Brusky, J., Zhu, Y. B., & Xiao, W. (2000) · Current Genetics · doi:10.1007/s002940050515 · Cited by 155
“a recent report on the global response of yeast cells to DNA-alkylation damage (Jelinsky and Samson 1999), and provides a kinetic evaluation of UBC13 inducibility.”
Background
Ybp1 Is Required for the Hydrogen Peroxide-induced Oxidation of the Yap1 Transcription Factor
Veal, E. A., Ross, S. J., Malakasi, P., Peacock, E., & Morgan, B. A. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m303542200 · Cited by 156
General Statistics of Stochastic Process of Gene Expression in Eukaryotic Cells
Kuznetsov, V. A., Knott, G. D., & Bonner, R. F. (2002) · Genetics · doi:10.1093/genetics/161.3.1321 · Cited by 151
Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins
Jansen, R. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.6.1481 · Cited by 149
Role of the non‐respiratory pathways in the utilization of molecular oxygen by Saccharomyces cerevisiae
Rosenfeld, E., & Beauvoit, B. (2003) · Yeast · doi:10.1002/yea.1026 · Cited by 149
“Non-respiratory cytochromes and other haemoproteins Cytochrome c peroxidase (CCP1) Mitochondrial intermembrane space [156] Catalase A (CTA1) Peroxisome [171] Catalase T (CTT1) Cytosol, vacuole [171] Cytochrome b5 (CYB5) Endoplasmic reticulum [81] Acyl-CoA desaturase (OLE1) Endoplasmic reticulum [138] Inositol-phosphor…”
Background
The apurinic/apyrimidinic endonuclease activity of Ape1/Ref-1 contributes to human glioma cell resistance to alkylating agents and is elevated by oxidative stress.
Silber, J. R., Bobola, M. S., Blank, A., Schoeler, K. D., Haroldson, P. D., Huynh, M. B., & Kolstoe, D. D. (2002) · PubMed · Cited by 146
BIOASSAY OF CADMIUM USING A DNA MICROARRAY: GENOME-WIDE EXPRESSION PATTERNS OF SACCHAROMYCES CEREVISIAE RESPONSE TO CADMIUM
Momose, Y., & Iwahashi, H. (2001) · Environmental Toxicology and Chemistry · doi:10.1002/etc.5620201030 · Cited by 145
Microarray technology — enhanced versatility, persistent challenge
Epstein, C. B. (2000) · Current Opinion in Biotechnology · doi:10.1016/s0958-1669(99)00065-8 · Cited by 139
SUMO-2 Orchestrates Chromatin Modifiers in Response to DNA Damage
Hendriks, I. A., Treffers, L. W., Vries, M. V., Olsen, J. V., & Vertegaal, A. C. O. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.02.033 · Cited by 136
“Moreover, genes involved in the DDR are upregulated in response to MMS [33].”
Background
What is bioinformatics? An introduction and overview
Luscombe, N. M., Greenbaum, D. S., & Gerstein, M. (2001) · Yearbook of Medical Informatics · doi:10.1055/s-0038-1638103 · Cited by 142
“For yeast, the Young [10], Church [47] and Samson datasets [48] use the GeneChip method, while the Stanford cell cycle [49], diauxic shift [50] and deletion mutant datasets [51] use the microarray.”
Method
SSU1 mediates sulphite efflux in Saccharomyces cerevisiae
Park, H., & Bakalinsky, A. T. (2000) · Yeast · doi:10.1002/1097-0061(200007)16:10 · Cited by 134
Plant functional genomics
Holtorf, H., Guitton, M.-C., & Ralf Reski, A. (2002) · Die Naturwissenschaften · doi:10.1007/s00114-002-0321-3 · Cited by 133
“…microarrays which contain all 6,200 predicted ORFs have been used to record mRNA profiles under conditions such as cell-cycle progression, diauxic shift, sporulation, alkylating treatment, and starvation (Chu et al. 1998; Spellman et al. 1998; Brown and Botstein 1999; Jelinsky and Samson 1999).”
Method
Two redox centers within Yap1 for H2O2 and thiol-reactive chemicals signaling
Azevedo, D., Tacnet, F., Delaunay, A., Rodrigues‐Pousada, C., & Tolédano, M. B. (2003) · Free Radical Biology and Medicine · doi:10.1016/s0891-5849(03)00434-9 · Cited by 136
Unique Gene Expression Patterns in Liver and Kidney Associated with Exposure to Chemical Toxicants
Bartosiewicz, M. J., Jenkins, D., Penn, S. G., Emery, J., & Buckpitt, A. R. (2001) · Journal of Pharmacology and Experimental Therapeutics · doi:10.1016/s0022-3565(24)29613-0 · Cited by 133
Regulation of ribosome biogenesis within the nucleolus
Leary, D. J., & Huang, S. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)03143-x · Cited by 132
TATA Binding Protein-Associated CK2 Transduces DNA Damage Signals to the RNA Polymerase III Transcriptional Machinery
Ghavidel, A., & Schultz, M. C. (2001) · Cell · doi:10.1016/s0092-8674(01)00473-1 · Cited by 131
Use of Transcriptomics in Understanding Mechanisms of Drug-Induced Toxicity
Cui, Y., & Paules, R. S. (2010) · Pharmacogenomics · doi:10.2217/pgs.10.37 · Cited by 130
“One of the pioneer toxicogenomic studies examined the transcription profile of Saccharomyces cerevisiae upon exposure to the alkylating agent methyl methanesulfonate using Affymetrix (CA, USA) GeneChip® oligonucleotide arrays representing the whole yeast genome [10].”
Background
Microarrays for microbiologists
Lucchini, S., Thompson, A., & Hinton, J. C. D. (2001) · Microbiology · doi:10.1099/00221287-147-6-1403 · Cited by 130
“…cDNA glass slides Wilson et al. (1999) Effect of amino acid biosynthesis inhibitor sulfometuron methyl Sacch. cerevisiae cDNA glass slides Jia et al. (2000) Antifungal agents Sacch. cerevisiae HDA Bammert & Fostel (2000) Cellular response to bacterial infection Infection of monocytes…”
Background
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
Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae
Said, M. R., Begley, T. J., Oppenheim, A. V., Lauffenburger, D. A., & Samson, L. D. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0405996101 · Cited by 122
Self-citation
Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl
Jia, M. H., LaRossa, R. A., Lee, J.-M., Rafalski, A. J., DeRose, E. J., Gonye, G., & Xue, Z. (2000) · Physiological Genomics · doi:10.1152/physiolgenomics.2000.3.2.83 · Cited by 125
“These techniques, for the first time, permit analysis of comprehensive expression profile changes in response to environmental challenges, for instance, nutrient availability and presence of inhibitory chemicals (9, 24, 34).”
Background
Transcription, genomes, function
Cho, R. J., & Campbell, M. J. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02065-5 · Cited by 126
Differential global gene expression in red and white skeletal muscle
Campbell, W. G., Gordon, S. E., Carlson, C. J., Pattison, J. S., Hamilton, M. T., & Booth, F. W. (2001) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.2001.280.4.c763 · Cited by 125
“Although the fold change in differential expression determined by Northern analysis and microarray technology has not always been the same (15), the direction of change should, in every case, be the same.”
Background
The environmental stress response: a common yeast response to diverse environmental stresses
Gasch, A. P. (2007) · Springer eBooks · doi:10.1007/3-540-45611-2_2 · Cited by 125
“In response to DNA-damaging agents including methylmethane sulfonate and ionizing radiation, wild type cells responded by inducing the expression of a subset of genes specifically enlisted to repair the resulting cellular damage and by initiating the ESR (Jelinsky and Samson 1999; Jelinsky et al. 2000; Gasch et al. 20…”
Background
The Transcriptome of Prematurely Aging Yeast Cells Is Similar to That of Telomerase-deficient Cells
Lesur, I., & Campbell, J. L. (2004) · Molecular Biology of the Cell · doi:10.1091/mbc.e03-10-0742 · Cited by 131
“In addition, comparison of our results with databases generated recently describing transcriptional responses in yeast to various environmental stresses, conditions that extend life span, and to various mutations that lead to chromosome damage or repair was valuable (Jelinsky and Samson, 1999; Gasch et al., 2000, 2001…”
BackgroundResult
Identification of gene expression patterns in superficial and invasive human bladder cancer.
Thykjær, T., Workman, C. T., Kruhøffer, M., Demtröder, K., Wolf, H., Andersen, L. D., Frederiksen, C. M., Knudsen, S., & Orntoft, T. F. (2001) · PubMed · Cited by 119
Parallel and comparative analysis of the proteome and transcriptome of sorbic acid‐stressed Saccharomyces cerevisiae
de Nobel, H., Lawrie, L. C., Brul, S., Klis, F. M., Davis, M. A. F., Alloush, H. M., & Coote, P. J. (2001) · Yeast · doi:10.1002/yea.793 · Cited by 118
Histone Acetyltransferase Inhibitor Anacardic Acid Causes Changes in Global Gene Expression during In Vitro Plasmodium falciparum Development
Cui, L., Miao, J., Furuya, T., Fan, Q., Li, X., Rathod, P. K., Su, X., & Cui, L. (2008) · Eukaryotic Cell · doi:10.1128/ec.00063-08 · Cited by 113
“Our finding also concurs with findings for other organisms such as baker’s yeast, where the extent of transcriptional response was correlated with the concentrations of the chemicals (6, 34).”
BackgroundResult
The role of glutathione transferases in cadmium stress
Adamis, P. D. B., Gomes, D. S., Pinto, M. L. C. C., Panek, A. D., & Eleuthério, E. C. A. (2004) · Toxicology Letters · doi:10.1016/j.toxlet.2004.07.003 · Cited by 110
Global analysis of transcription kinetics during competence development in Streptococcus pneumoniae using high density DNA arrays
Rimini, R., Jansson, B., Feger, G., Roberts, T. C., Francesco, M. D., Gozzi, A., Faggioni, F., Domenici, E., Wallace, D. M., Frandsen, N., et al. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01931.x · Cited by 110
“This quantitative difference might be ascribed to the different kinds of probes used in the array and the Northern-blot hybridizations, respectively, as previously suggested by Jelinsky and Samson (1999) who observed similar discrepancies when performing global gene expression experiments in yeast.”
Method
The utility of DNA microarrays for characterizing genotoxicity.
Newton, R. K., Aardema, M. J., & Aubrecht, J. (2004) · Environmental Health Perspectives · doi:10.1289/ehp.6709 · Cited by 109
Multiple Yap1p-binding Sites Mediate Induction of the Yeast Major Facilitator FLR1 Gene in Response to Drugs, Oxidants, and Alkylating Agents
Nguyên, D.-T., Alarco, A., & Raymond, M. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m008377200 · Cited by 107
Control of 26S proteasome expression by transcription factors regulating multidrug resistance in Saccharomyces cerevisiae
Owsianik, G., Balzi, L., & Ghislain, M. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02823.x · Cited by 106
“In contrast, alkylating agents increase Yap1p transcript levels (Jelinsky and Samson, 1999).”
Background
Toxicogenomics: a pivotal piece in the puzzle of toxicological research
Gatzidou, E. T., Zira, A. N., & Theocharis, S. E. (2007) · Journal of Applied Toxicology · doi:10.1002/jat.1248 · Cited by 105
“For example, a number of chemicals elicit responses by damaging cellular components or DNA itself (Jelinsky and Samson, 1999; Crosby et al., 2000; Jelinsky et al., 2000).”
Background
Dap1p, a Heme-Binding Protein That Regulates the Cytochrome P450 Protein Erg11p/Cyp51p in Saccharomyces cerevisiae
Mallory, J. C., Crudden, G., Johnson, B. L., Mo, C., Pierson, C. A., Bard, M., & Craven, R. J. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.5.1669-1679.2005 · Cited by 104
“MMS triggers a broad transcriptional response in yeast (10, 17), and approximately 100 genes are required for resistance to MMS (3, 4, 5).”
Background
The DNA Damage-Inducible UbL-UbA Protein Ddi1 Participates in Mec1-Mediated Degradation of Ho Endonuclease
Kaplun, L., Tzirkin, R., Bakhrat, A., Shabek, N., Ivantsiv, Y., & Raveh, D. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.13.5355-5362.2005 · Cited by 101
“DNA damage (25, 68); however, no role for Ddi1 in the DDR”
Background
Genomics and proteomics
Cunningham, M. J. (2000) · Journal of Pharmacological and Toxicological Methods · doi:10.1016/s1056-8719(00)00111-8 · Cited by 101
Emerging technologies in yeast genomics
Kumar, A., & Snyder, M. P. (2001) · Nature Reviews Genetics · doi:10.1038/35066084 · Cited by 100
Dihydroxyacetone Kinases in Saccharomyces cerevisiaeAre Involved in Detoxification of Dihydroxyacetone
Molin, M., Norbeck, J., & Blomberg, A. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m203030200 · Cited by 99
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

Authors: Jelinsky, S. A., & Samson, L. D.
Affiliations: Harvard University (US)
Corresponding author: Samson, Leona D.
ORCID: Jelinsky, Scott A.
Samson, Leona D.
Venue: Proceedings of the National Academy of Sciences
Publisher: National Academy of Sciences
Published: 1999-02-16
Volume: 96
Issue: 4
Pages: 1486-1491
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.96.4.1486
PMC: PMC15489
OpenAlex: W2155675863
Cited by: 419
References: 36
Citations by year: 2026: 4 · 2025: 1 · 2024: 4 · 2023: 4 · 2022: 2 · 2021: 1 · 2020: 5 · 2019: 6 · 2018: 6 · 2017: 4 · 2016: 5 · 2015: 11 · 2014: 10 · 2013: 8 · 2012: 11
FWCI: 17.46
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Proceedings of the National Academy of Sciences (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: National Institutes of Health (5p01hg001323-03)
National Human Genome Research Institute (P01 HG 01323)
National Cancer Institute (CA-55042, CA09078, T32CA009078, R01CA055042)
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: Saccharomyces cerevisiae, methyl methanesulfonate, alkylating agents, DNA damage response, gene expression profiling, transcriptome, DNA repair genes
MeSH terms: Alkylating Agents, DNA Damage, Fungal Proteins, Genes, Fungal, Methyl Methanesulfonate, Saccharomyces cerevisiae, Transcription, Genetic, Open Reading Frames, Genome, Fungal

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

Global response of Saccharomyces cerevisiae to an alkylating agent

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks