The DNA-damage signature in Saccharomyces cerevisiae is associated with single-strand breaks in DNA

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Fry, Rebecca C ^a   DeMott, Michael S ^a   Cosgrove, Joseph P ^a,b   Begley, Thomas J ^c   Samson, Leona D ^a   Dedon, Peter C ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

^c STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALICHEAMICIN GAMMA1; ESPERAMICIN A1; ZINOSTATIN;

ARTICLE; BIOGENESIS; CELL CYCLE REGULATION; CELL DEATH; CELLULAR STRESS RESPONSE; CONTROLLED STUDY; DNA BINDING; DNA DAMAGE; DNA REPAIR; DNA STRAND BREAKAGE; GAMMA RADIATION; GENE EXPRESSION; GENETIC TRANSCRIPTION; NONHUMAN; OXIDATIVE STRESS; REGRESSION ANALYSIS; RIBOSOME; SACCHAROMYCES CEREVISIAE; TRANSCRIPTOMICS;

CELL CYCLE PROTEINS; DNA DAMAGE; DNA REPAIR; ENEDIYNES; GAMMA RAYS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; REGRESSION ANALYSIS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC;

SACCHAROMYCES CEREVISIAE;

EID: 33846486840     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-313     Document Type: Article

References (28)

1. Gasch AP Huang M Metzner S Botstein D Elledge SJ Brown PO Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p Mol Biol Cell 2001 12 10 2987-3003 60150 11598186
2. Friedberg EC Walker GC Siede W DNA Repair and Mutagenesis Washington, D.C., ASM Press 1995
3. Wood RD Mitchell M Lindahl T Human DNA repair genes, 2005 Mutat Res 2005 577 1-2 275-283 15922366
4. Wood RD Mitchell M Sgouros J Lindahl T Human DNA repair genes Science 2001 291 5507 1284-1289 10.1126/science.1056154 11181991
5. Begley TJ Rosenbach AS Ideker T Samson LD Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping Mol Cancer Res 2002 1 2 103-112 12496357
6. Begley TJ Rosenbach AS Ideker T Samson LD Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping Mol Cell 2004 16 1 117-125 10.1016/j.molcel.2004.09.005 15469827
7. Hanway D Chin JK Xia G Oshiro G Winzeler EA Romesberg FE Previously uncharacterized genes in the UV- and MMS-induced DNA damage response in yeast Proc Natl Acad Sci U S A 2002 99 16 10605-10610 124988 12149442 10.1073/pnas.152264899
8. Birrell GW Giaever G Chu AM Davis RW Brown JM A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity Proc Natl Acad Sci U S A 2001 98 22 12608-12613 60101 11606770 10.1073/ pnas.231366398
9. Jelinsky SA Estep P Church GM Samson LD Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes Mol Cell Biol 2000 20 21 8157 8167 86425 11027285 10.1128/MCB.20.21.8157-8167.2000
10. Jelinsky SA Samson LD Global response of Saccharomyces cerevisiae to an alkylating agent Proc Natl Acad Sci U S A 1999 96 4 1486 1491 15489 9990050 10.1073/pnas.96.4.1486
11. Dedon PC Goldberg IH Free-radical mechanisms involved in the formation of sequence-dependent bistranded DNA lesions by the antitumor antibiotics bleomycin, neocarzinostatin, and calicheamicin Chemical Research in Toxicology 1992 5 3 311 332 10.1021/tx00027a001 1380322
12. Dedon PC Salzberg AA Xu J Exclusive production of bistranded DNA damage by calicheamicin Biochemistry 1993 32 April 13 3617-3622 10.1021/ bi00065a013 8466904
13. Schaus SE Cavalieri D Myers AG Gene transcription analysis of Saccharomyces cerevisiae exposed to neocarzinostatin protein-chromophore complex reveals evidence of DNA damage, a potential mechanism of resistance, and consequences of prolonged exposure Proc Natl Acad Sci U S A 2001 98 20 11075 11080 58685 11562456 10.1073/pnas.191340698
14. Watanabe CM Supekova L Schultz PG Transcriptional effects of the potent enediyne anti-cancer agent Calicheamicin gamma(I)(1) Chem Biol 2002 9 2 245-251 10.1016/S1074-5521(02)00103-5 11880039
15. Gasch AP Spellman PT Kao CM Carmel-Harel O Eisen MB Storz G Botstein D Brown PO Genomic expression programs in the response of yeast cells to environmental changes Mol Biol Cell 2000 11 12 4241-4257 15070 11102521
16. Elmroth K Nygren J Martensson S Ismail IH Hammarsten O Cleavage of cellular DNA by calicheamicin gamma1 DNA Repair (Amst) 2003 2 4 363-374 10.1016/S1568-7864(02)00235-5 12606118
17. Drak J Iwasawa N Danishefsky S Crothers DM The carbohydrate domain of calicheamicin g1I determines its sequence specificity for DNA cleavage Proc Natl Acad Sci USA 1991 88 7464-7468 52320 1881884 10.1073/ pnas.88.17.7464
18. Walker S Landovitz R Ding WD Ellestad GE Kahne D Cleavage behavior of calicheamicin g1 and calicheamicin T Proc Natl Acad Sci USA 1992 89 May 4608-4612 49132 1584797 10.1073/pnas.89.10.4608
19. Xi Z Mao QK Goldberg IH Mechanistic studies on the base-catalyzed transformation of neocarzinostatin chromophore: Roles of bulged DNA Biochemistry 1999 38 14 4342-4354 10.1021/bi982734i 10194353
20. Boffa LC Bolognesi C Methylating agents: Their target amino acids in nuclear proteins Carcinogenesis 1985 6 9 1399-1401 4028338
21. Irizarry RA Bolstad BM Collin F Cope LM Hobbs B Speed TP Summaries of Affymetrix GeneChip probe level data Nucleic Acids Res 2003 31 4 e15 150247 12582260 10.1093/nar/gng015
22. Jain N Thatte J Braciale T Ley K O'Connell M Lee JK Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays Bioinformatics 2003 19 15 1945-1951 10.1093/ bioinformatics/btg264 14555628
23. Benjamini Y Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 1995 57 289-300
24. Robinson MD Grigull J Mohammad N Hughes TR FunSpec: A web-based cluster interpreter for yeast BMC Bioinformatics 2002 3 35 139976-12431279 10.1186/1471-2105-3-35
25. Fulford J Nikjoo H Goodhead DT O'Neill P Yields of SSB and DSB induced in DNA by Al(K) ultrasoft X-rays and alpha-particles: Comparison of experimental and simulated yields Int J Radiat Biol 2001 77 10 1053-1066 10.1080/09553000110069308 11682010
26. Milligan JR Aguilera JA Paglinawan RA Ward JF Limoli CL DNA strand break yields after post-high LET irradiation incubation with endonuclease-III and evidence for hydroxyl radical clustering Int J Radiat Biol 2001 77 2 155-164 10.1080/09553000010013445 11236922
27. Yu L Golik, J., Harrison, R., and Dedon, P. The deoxyfucose-anthranilate of esperamicin A1 confers intercalative DNA binding and causes a switch in the chemistry of bistranded DNA lesions. Journal of the American Chemical Society 1994 116 9733-9738 10.1021/ja00100a044
28. Dedon PC Goldberg IH Influence of thiol structure on neocarzinostatin activation and expression of DNA damage Biochemistry 1992 31 7 1909-1917 10.1021/bi00122a003 1531615