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Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis

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Pages 3475-3487 | Received 01 Jul 2015, Accepted 07 Sep 2015, Published online: 13 Nov 2015

References

  • Galhardo RS, Hastings PJ, Rosenberg SM. Mutation as a stress response and the regulation of evolvability. Crit Rev Biochem Mol Biol 2007; 42:399-435; PMID:17917874; http://dx.doi.org/10.1080/10409230701648502
  • Carrasco P, Querol A, del Olmo M. Analysis of the stress resistance of commercial wine yeast strains. Arch Microbiol 2001; 175:450-7; PMID:11491086; http://dx.doi.org/10.1007/s002030100289
  • Zuzuarregui A, Carrasco P, Palacios A, Julien A, del Olmo M. Analysis of the expression of some stress induced genes in several commercial wine yeast strains at the beginning of vinification. J Appl Microbiol 2005; 98:299-307; PMID:15659184; http://dx.doi.org/10.1111/j.1365-2672.2004.02463.x
  • Brosnan MP, Donnelly D, James TC, Bond U. The stress response is repressed during fermentation in brewery strains of yeast. J Appl Microbiol 2000; 88:746-55; PMID:10792534; http://dx.doi.org/10.1046/j.1365-2672.2000.01006.x
  • Attfield PV. Stress tolerance: the key to effective strains of industrial baker's yeast. Nat Biotechnol 1997; 15:1351-7; PMID:9415886; http://dx.doi.org/10.1038/nbt1297-1351
  • Ambrona J, Vinagre A, Ramirez M. Rapid asymmetrical evolution of Saccharomyces cerevisiae wine yeasts. Yeast 2005; 22:1299-306; PMID:16358308; http://dx.doi.org/10.1002/yea.1331
  • Bakalinsky AT, Snow R. The chromosomal constitution of wine strains of Saccharomyces cerevisiae. Yeast 1990; 6:367-82; PMID:2220073; http://dx.doi.org/10.1002/yea.320060503
  • Mortimer RK. Evolution and variation of the yeast (Saccharomyces) genome. Genome Res 2000; 10:403-9; PMID:10779481; http://dx.doi.org/10.1101/gr.10.4.403
  • Kodama Y, Kielland-Brandt MC, Hansen J. Lager brewing yeast Comparative Genomics: Springer Berlin Heidelberg, 2006:145-64
  • Salmon JM. Enological fermentation kinetics of an isogenic ploidy series derived form an industrial Saccharomyces cerevisiae strain. J Ferment Bioeng 1997; 83:253-60; http://dx.doi.org/10.1016/S0922-338X(97)80988-9
  • Romano GH, Harari Y, Yehuda T, Podhorzer A, Rubinstein L, Shamir R, Gottlieb A, Silberberg Y, Pe'er D, Ruppin E, et al. Environmental stresses disrupt telomere length homeostasis. PLoS Genet 2013; 9:e1003721; PMID:24039592; http://dx.doi.org/10.1371/journal.pgen.1003721
  • James TC, Usher J, Campbell S, Bond U. Lager yeasts possess dynamic genomes that undergo rearrangements and gene amplification in response to stress. Curr Genet 2008; 53:139-52; PMID:18183398; http://dx.doi.org/10.1007/s00294-007-0172-8
  • Biemont C, Vieira C. Genetics: junk DNA as an evolutionary force. Nature 2006; 443:521-4; PMID:17024082; http://dx.doi.org/10.1038/443521a
  • Kobayashi T. A new role of the rDNA and nucleolus in the nucleus–rDNA instability maintains genome integrity. Bioessays 2008; 30:267-72; PMID:18293366; http://dx.doi.org/10.1002/bies.20723
  • Lewinska A, Miedziak B, Kulak K, Molon M, Wnuk M. Links between nucleolar activity, rDNA stability, aneuploidy and chronological aging in the yeast Saccharomyces cerevisiae. Biogerontology 2014; 15:289-316; PMID:24711086; http://dx.doi.org/10.1007/s10522-014-9499-y
  • Olson MO. Sensing cellular stress: another new function for the nucleolus? Sci STKE 2004; 2004:pe10; PMID:15026578
  • Grummt I. The nucleolus-guardian of cellular homeostasis and genome integrity. Chromosoma 2013; 122:487-97; PMID:24022641; http://dx.doi.org/10.1007/s00412-013-0430-0
  • Mayer C, Bierhoff H, Grummt I. The nucleolus as a stress sensor: JNK2 inactivates the transcription factor TIF-IA and down-regulates rRNA synthesis. Genes Dev 2005; 19:933-41; PMID:15805466; http://dx.doi.org/10.1101/gad.333205
  • Rubbi CP, Milner J. Disruption of the nucleolus mediates stabilization of p53 in response to DNA damage and other stresses. EMBO J 2003; 22:6068-77; PMID:14609953; http://dx.doi.org/10.1093/emboj/cdg579
  • Mayer C, Zhao J, Yuan X, Grummt I. mTOR-dependent activation of the transcription factor TIF-IA links rRNA synthesis to nutrient availability. Genes Dev 2004; 18:423-34; PMID:15004009; http://dx.doi.org/10.1101/gad.285504
  • Lewinska A, Wnuk M, Grzelak A, Bartosz G. Nucleolus as an oxidative stress sensor in the yeast Saccharomyces cerevisiae. Redox Rep 2010; 15:87-96; PMID:20500990; http://dx.doi.org/10.1179/174329210X12650506623366
  • Kobayashi T. Strategies to maintain the stability of the ribosomal RNA gene repeats–collaboration of recombination, cohesion, and condensation. Genes Genet Syst 2006; 81:155-61; PMID:16905869; http://dx.doi.org/10.1266/ggs.81.155
  • Defossez PA, Prusty R, Kaeberlein M, Lin SJ, Ferrigno P, Silver PA, Keil RL, Guarente L. Elimination of replication block protein Fob1 extends the life span of yeast mother cells. Mol Cell 1999; 3:447-55; PMID:10230397; http://dx.doi.org/10.1016/S1097-2765(00)80472-4
  • Kaeberlein M, McVey M, Guarente L. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev 1999; 13:2570-80; PMID:10521401; http://dx.doi.org/10.1101/gad.13.19.2570
  • de Beus E, Brockenbrough JS, Hong B, Aris JP. Yeast NOP2 encodes an essential nucleolar protein with homology to a human proliferation marker. J Cell Biol 1994; 127:1799-813; PMID:7806561; http://dx.doi.org/10.1083/jcb.127.6.1799
  • Hediger F, Dubrana K, Gasser SM. Myosin-like proteins 1 and 2 are not required for silencing or telomere anchoring, but act in the Tel1 pathway of telomere length control. J Struct Biol 2002; 140:79-91; PMID:12490156; http://dx.doi.org/10.1016/S1047-8477(02)00533-6
  • Chattopadhyay MK, Tabor CW, Tabor H. Spermidine but not spermine is essential for hypusine biosynthesis and growth in Saccharomyces cerevisiae: spermine is converted to spermidine in vivo by the FMS1-amine oxidase. Proc Natl Acad Sci U S A 2003; 100:13869-74; PMID:14617780; http://dx.doi.org/10.1073/pnas.1835918100
  • Silva GM, Finley D, Vogel C. K63 polyubiquitination is a new modulator of the oxidative stress response. Nat Struct Mol Biol 2015; 22:116-23; PMID:25622294; http://dx.doi.org/10.1038/nsmb.2955
  • Mortimer RK, Romano P, Suzzi G, Polsinelli M. Genome renewal: a new phenomenon revealed from a genetic study of 43 strains of Saccharomyces cerevisiae derived from natural fermentation of grape musts. Yeast 1994; 10:1543-52; PMID:7725789; http://dx.doi.org/10.1002/yea.320101203
  • Lewinska A, Miedziak B, Wnuk M. Assessment of yeast chromosome XII instability: single chromosome comet assay. Fungal Genet Biol 2014; 63:9-16; PMID:24333410; http://dx.doi.org/10.1016/j.fgb.2013.12.003
  • Krol K, Brozda I, Skoneczny M, Bretne M, Skoneczna A. A genomic screen revealing the importance of vesicular trafficking pathways in genome maintenance and protection against genotoxic stress in diploid Saccharomyces cerevisiae cells. PLoS One 2015; 10:e0120702; PMID:25756177; http://dx.doi.org/10.1371/journal.pone.0120702
  • Dworak N, Wnuk M, Zebrowski J, Bartosz G, Lewinska A. Genotoxic and mutagenic activity of diamond nanoparticles in human peripheral lymphocytes in vitro. Carbon 2014; 68:763-76; http://dx.doi.org/10.1016/j.carbon.2013.11.067
  • Andrews S. FastQC: a quality control tool for high throughput sequence data. http://wwwbioinformaticsbabrahamacuk/projects/fastqc 2010
  • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25:1754-60; PMID:19451168; http://dx.doi.org/10.1093/bioinformatics/btp324
  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25:2078-9; PMID:19505943; http://dx.doi.org/10.1093/bioinformatics/btp352
  • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010; 26:841-2; PMID:20110278; http://dx.doi.org/10.1093/bioinformatics/btq033
  • Garisson E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv 2012:1207.3907 [q-bio.GN]. Available at http://arxiv.org/abs/1207.3907
  • Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 2012; 6:80-92; PMID:22728672; http://dx.doi.org/10.4161/fly.19695
  • McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 2010; 26:2069-70; PMID:20562413; http://dx.doi.org/10.1093/bioinformatics/btq330
  • Mi H, Muruganujan A, Casagrande JT, Thomas PD. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc 2013; 8:1551-66; PMID:23868073; http://dx.doi.org/10.1038/nprot.2013.092
  • Wnuk M, Miedziak B, Kulak K, Panek A, Golec E, Deregowska A, Adamczyk J, Lewinska A. Single-cell analysis of aneuploidy events using yeast whole chromosome painting probes (WCPPs). J Microbiol Methods 2015; 111:40-9; PMID:25639739; http://dx.doi.org/10.1016/j.mimet.2015.01.022

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