Ploidy influences cellular responses to gross chromosomal rearrangements in saccharomyces cerevisiae

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Jung, Paul P ^a   Fritsch, Emilie S ^b   Blugeon, Corinne ^c   Souciet, Jean Luc ^a   Potier, Serge ^a   Lemoine, Sophie ^c   Schacherer, Joseph ^a   de Montigny, Jacky ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c PSL RESEARCH UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CITRIC ACID; PROTEASOME; RNA; ADENOSINE TRIPHOSPHATE; FUNGAL PROTEIN; TRANSCRIPTOME;

ANEUPLOIDY; ARTICLE; CELL STRUCTURE; CHROMOSOME DELETION; CHROMOSOME DUPLICATION; CHROMOSOME REARRANGEMENT; CHROMOSOME TRANSLOCATION; CITRIC ACID CYCLE; DIPLOIDY; DOWN REGULATION; ENERGY METABOLISM; GENE EXPRESSION; GENE OVEREXPRESSION; GROWTH RATE; HAPLOIDY; NONHUMAN; PROTEIN SYNTHESIS; RIBOSOME; RNA PROCESSING; SACCHAROMYCES CEREVISIAE; STOICHIOMETRY; STRAIN DIFFERENCE; BIOSYNTHESIS; CHROMOSOME; CHROMOSOME ABERRATION; CYTOLOGY; GENETICS; METABOLISM; PLOIDY; UPREGULATION;

SACCHAROMYCES CEREVISIAE;

ADENOSINE TRIPHOSPHATE; CHROMOSOME ABERRATIONS; CHROMOSOMES, FUNGAL; DIPLOIDY; FUNGAL PROTEINS; PLOIDIES; SACCHAROMYCES CEREVISIAE; TRANSCRIPTOME; UP-REGULATION;

EID: 79959625944     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-331     Document Type: Article

References (43)

1. Lengauer C, Kinzler KW, Vogelstein B. Genetic instabilities in human cancers. Nature 1998, 396:643-649. 10.1038/25292, 9872311.
2. Albertson DG, Collins C, McCormick F, Gray JW. Chromosome aberrations in solid tumors. Nat Genet 2003, 34:369-376. 10.1038/ng1215, 12923544.
3. Weaver BA, Cleveland DW. The aneuploidy paradox in cell growth and tumorigenesis. Cancer Cell 2008, 14:431-433. 10.1016/j.ccr.2008.11.011, 3132552, 19061834.
4. Marx J. Debate surges over the origins of genomic defects in cancer. Science 2002, 297:544-546. 10.1126/science.297.5581.544, 12142522.
5. Babu JR, Jeganathan KB, Baker DJ, Wu X, Kang-Decker N, van Deursen JM. Rae1 is an essential mitotic checkpoint regulator that cooperates with Bub3 to prevent chromosome missegregation. J Cell Biol 2003, 160:341-353. 10.1083/jcb.200211048, 2172680, 12551952.
6. Baker DJ, Jeganathan KB, Cameron JD, Thompson M, Juneja S, Kopecka A, Kumar R, Jenkins RB, de Groen PC, Roche P, van Deursen JM. BubR1 insufficiency causes early onset of aging-associated phenotypes and infertility in mice. Nat Genet 2004, 36:744-749. 10.1038/ng1382, 15208629.
7. Michel LS, Liberal V, Chatterjee A, Kirchwegger R, Pasche B, Gerald W, Dobles M, Sorger PK, Murty VV, Benezra R. MAD2 haplo-insufficiency causes premature anaphase and chromosome instability in mammalian cells. Nature 2001, 409:355-359. 10.1038/35053094, 11201745.
8. Chen C, Kolodner RD. Gross chromosomal rearrangements in Saccharomyces cerevisiae replication and recombination defective mutants. Nat Genet 1999, 23:81-85.
9. Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2002, 99:16144-16149. 10.1073/pnas.242624799, 138579, 12446845.
10. Torres EM, Sokolsky T, Tucker CM, Chan LY, Boselli M, Dunham MJ, Amon A. Effects of aneuploidy on cellular physiology and cell division in haploid yeast. Science 2007, 317:916-924. 10.1126/science.1142210, 17702937.
11. Pavelka N, Rancati G, Zhu J, Bradford WD, Saraf A, Florens L, Sanderson BW, Hattem GL, Li R. Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. Nature 2010, 468:321-325. 10.1038/nature09529, 2978756, 20962780.
12. Nikitin D, Tosato V, Zavec AB, Bruschi CV. Cellular and molecular effects of nonreciprocal chromosome translocations in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2008, 105:9703-9708. 10.1073/pnas.0800464105, 2474487, 18599460.
13. Hughes TR, Roberts CJ, Dai H, Jones AR, Meyer MR, Slade D, Burchard J, Dow S, Ward TR, Kidd MJ, Friend SH, Marton MJ. Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet 2000, 25:333-337. 10.1038/77116, 10888885.
14. Torres EM, Dephoure N, Panneerselvam A, Tucker CM, Whittaker CA, Gygi SP, Dunham MJ, Amon A. Identification of aneuploidy-tolerating mutations. Cell 2010, 143:71-83. 10.1016/j.cell.2010.08.038, 2993244, 20850176.
15. Torres EM, Williams BR, Amon A. Aneuploidy: cells losing their balance. Genetics 2008, 179:737-746. 10.1534/genetics.108.090878, 2429870, 18558649.
16. Veitia RA. Exploring the etiology of haploinsufficiency. Bioessays 2002, 24:175-184. 10.1002/bies.10023, 11835282.
17. Papp B, Pál C, Hurst LD. Dosage sensitivity and the evolution of gene families in yeast. Nature 2003, 424:194-197. 10.1038/nature01771, 12853957.
18. Roelants F, Potier S, Souciet JL, de Montigny J. Reactivation of the ATCase domain of the URA2 gene complex: a positive selection method for Ty insertions and chromosomal rearrangements in Saccharomyces cerevisiae. Mol Gen Genet 1995, 246:767-773. 10.1007/BF00290725, 7898447.
19. Schacherer J, Tourrette Y, Souciet J-L, Potier S, De Montigny J. Recovery of a function involving gene duplication by retroposition in Saccharomyces cerevisiae. Genome Res 2004, 14:1291-1297. 10.1101/gr.2363004, 442144, 15231745.
20. Schacherer J, Tourrette Y, Potier S, Souciet JL, de Montigny J. Spontaneous duplications in diploid Saccharomyces cerevisiae cells. DNA Repair (Amst) 2007, 6:1441-1452.
21. Tourrette Y, Schacherer J, Fritsch E, Potier S, Souciet J-L, de Montigny J. Spontaneous deletions and reciprocal translocations in Saccharomyces cerevisiae: influence of ploidy. Mol Microbiol 2007, 64:382-395. 10.1111/j.1365-2958.2007.05660.x, 17493124.
22. Welcker AJ, de Montigny J, Potier S, Souciet JL. Involvement of very short DNA tandem repeats and the influence of the RAD52 gene on the occurrence of deletions in Saccharomyces cerevisiae. Genetics 2000, 156:549-557. 1461274, 11014805.
23. Schacherer J, de Montigny J, Welcker A, Souciet JL, Potier S. Duplication processes in Saccharomyces cerevisiae haploid strains. Nucleic Acids Res 2005, 33:6319-6326. 10.1093/nar/gki941, 1277810, 16269823.
24. Cavalieri D, Townsend JP, Hartl DL. Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proc Natl Acad Sci USA 2000, 97:12369-12374. 10.1073/pnas.210395297, 17348, 11035792.
25. Granek JA, Magwene PM. Environmental and genetic determinants of colony morphology in yeast. PLoS Genet 2010, 6:e1000823. 10.1371/journal.pgen.1000823, 2809765, 20107600.
26. Galitski T, Saldanha AJ, Styles CA, Lander ES, Fink GR. Ploidy regulation of gene expression. Science 1999, 285:251-254. 10.1126/science.285.5425.251, 10398601.
27. Rossi B, Noel P, Bruschi CV. Different aneuploidies arise from the same bridge-induced chromosomal translocation event in Saccharomyces cerevisiae. Genetics 2010, 186:775-790. 10.1534/genetics.110.120683, 20805555.
28. Barrales RR, Jimenez J, Ibeas JI. Identification of novel activation mechanisms for FLO11 regulation in Saccharomyces cerevisiae. Genetics 2008, 178:145-156. 10.1534/genetics.107.081315, 2206066, 18202364.
29. Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G. GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 2004, 20:3710-3715. 10.1093/bioinformatics/bth456, 3037731, 15297299.
30. 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, 11:4241-4257. 15070, 11102521.
31. Schüller C, Brewster JL, Alexander MR, Gustin MC, Ruis H. The HOG pathway controls osmotic regulation of transcription via the stress response element (STRE) of the Saccharomyces cerevisiae CTT1 gene. EMBO J 1994, 13:4382-4389. 395365, 7523111.
32. Berry DB, Gasch AP. Stress-activated genomic expression changes serve a preparative role for impending stress in yeast. Mol Biol Cell 2008, 19:4580-4587. 10.1091/mbc.E07-07-0680, 2575158, 18753408.
33. Gasch AP. Comparative genomics of the environmental stress response in ascomycete fungi. Yeast 2007, 24:961-976. 10.1002/yea.1512, 17605132.
34. Boguslawski G, Polazzi JO. Complete nucleotide sequence of a gene conferring polymyxin B resistance on yeast: similarity of the predicted polypeptide to protein kinases. Proc Natl Acad Sci USA 1987, 84:5848-5852. 10.1073/pnas.84.16.5848, 298960, 3039511.
35. Schacherer J, Ruderfer DM, Gresham D, Dolinski K, Botstein D, Kruglyak L. Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS ONE 2007, 2:e322. 10.1371/journal.pone.0000322, 1829191, 17389913.
36. Deutschbauer AM, Davis RW. Quantitative trait loci mapped to single-nucleotide resolution in yeast. Nat Genet 2005, 37:1333-1340. 10.1038/ng1674, 16273108.
37. Fritsch ES, Schacherer J, Bleykasten-Grosshans C, Souciet JL, Potier S, de Montigny J. Influence of genetic background on the occurrence of chromosomal rearrangements in Saccharomyces cerevisiae. BMC Genomics 2009, 10:99. 10.1186/1471-2164-10-99, 2674068, 19267901.
38. Li XC, Schimenti JC, Tye BK. Aneuploidy and improved growth are coincident but not causal in a yeast cancer model. PLoS Biol 2009, 7:e1000161. 10.1371/journal.pbio.1000161, 2708349, 19636358.
39. Williams BR, Amon A. Aneuploidy: cancer's fatal flaw?. Cancer Res 2009, 69:5289-5291. 10.1158/0008-5472.CAN-09-0944, 2917070, 19549887.
40. Barrett T, Edgar R. Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*. Methods Mol Biol 2006, 338:175-190. 1619899, 16888359.
41. Lemoine S, Combes F, Servant N, Le Crom S. Goulphar: rapid access and expertise for standard two-color microarray normalization methods. BMC Bioinformatics 2006, 7:467. 10.1186/1471-2105-7-467, 1626094, 17059595.
42. Saldanha AJ. Java Treeview--extensible visualization of microarray data. Bioinformatics 2004, 20:3246-3248. 10.1093/bioinformatics/bth349, 15180930.
43. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. BioTechniques 2003, 34:374-378.