NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE78856 Query DataSets for GSE78856
Status Public on Mar 03, 2016
Title Genomic instability induced by lowered expression of POL3 in yeast
Organism Saccharomyces cerevisiae
Experiment type Genome variation profiling by genome tiling array
Genome variation profiling by SNP array
Summary DNA replication stress (DRS)-linked genomic instability has emerged as an important factor driving cancer development. To understand the mechanisms of DRS-associated genomic instability and phenotypic evolution, we mapped chromosomal alterations in a yeast strain with lowered expression of the replicative DNA polymerase δ. At a whole-genome level, we identified both hotspots of mitotic recombination and chromosome-specific aneuploidy dependent on decreased levels of DNA polymerase δ. The high rate of chromosome loss is likely a reflection of reduced DNA repair capacity in strains with low levels of DNA polymerase. Most recombinogenic DNA lesions were introduced during S or G2 phase, presumably as a consequence of broken replication forks.
 
Overall design To reduce the expression of gene POL3, a KANMX-GAL1 cassette was inserted before the ORF of this gene in haploid strains JSC54-1 (W303-1A) and JSC20-1 (YJM789), resulting in mutants DZ1 and DZ2 (genotypes of these strains were listed in Table S1 and primers used to for strain construction were in Table S2), respectively. Mating DZ1 and DZ2 and subsequent knockout of MATalpha generated a diploid strain DZ12. We grew single cells of strain DZ12 to colonies on solid low-gal (2% yeast extract, 2% peptone and 3% raffinose, 0.005% galactose) medium and 35 colonies were selected for whole genome SNP-microarray analysis that can examine about 13,000 SNPs located throughout the genome. 6 DZ12-derived colonies (DZHG1-6) from single cycle growth on high-gal medium (0.05% galactose) were also examined. To induce reciprocal crossover events in DZ12, DZ12 cells were incubated in YPD liquid medium for 6 h to deplete polymerase δ and then plated on solid medium to form sectored colonies (S1-S60). These sectored colonies were analyzed with SNP microarray specific for chromosome 4.
 
Contributor(s) Zheng D, Petes T
Citation(s) 27911848
Submission date Mar 02, 2016
Last update date Feb 10, 2017
Contact name Daoqiong Zheng
E-mail(s) zhengdaoqiong@163.com
Phone 86 571 88206636
Organization name College of Life Sciences, Zhejiang University
Department Institute of Microbiology
Street address 866 Yuhangtang Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310058
Country China
 
Platforms (3)
GPL20144 Agilent-027438 Yeast S-Y SNP v1 [Probe Name Version]
GPL21552 Agilent-047217 ch4array_v3 (SPOT_ID version)
GPL21553 Agilent-031671 Chr4 RA V2 027289 (SPOT_ID version)
Samples (109)
GSM2079625 DZ12_lowgal_1 (DZ12-1)
GSM2079626 DZ12_lowgal_2 (DZ12-2)
GSM2079627 DZ12_lowgal_3 (DZ12-3)
Relations
BioProject PRJNA314183

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE78856_RAW.tar 522.0 Mb (http)(custom) TAR (of GPR, TXT)
Processed data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap