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Series GSE146791 Query DataSets for GSE146791
Status Public on Jun 16, 2020
Title The environmental stress response causes ribosome loss in aneuploid yeast cells. 
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary Aneuploidy, a condition characterized by whole chromosome gains and losses, is often associated with significant cellular stress and decreased fitness. However, whether and how cells respond to the aneuploid state has remained controversial. In aneuploid budding yeast, two opposing gene expression patterns have been reported: an environmental stress response (ESR) and a “common aneuploidy gene-expression” (CAGE) signature, in which many ESR genes are oppositely regulated. Here, we investigate and bring clarity to this controversy. We show that the CAGE signature is not an aneuploidy-specific gene expression signature but is the result of euploid control cells, but not aneuploid cells, having grown into stationary phase. Because growth into stationary phase is amongst the strongest inducers of the ESR, the ESR in aneuploid cells was masked when stationary phase euploid cells were used for normalization in transcriptomic studies. When exponentially growing euploid cells are used in gene expression comparisons with aneuploid cells, the CAGE signature is no longer evident in aneuploid cells. Instead, aneuploid cells are found to exhibit the ESR. We further show that the ESR causes a selective loss of ribosomes in aneuploid cells, providing an explanation for the decreased cellular density in aneuploid cells. We conclude that aneuploid budding yeast cells mount the ESR, rather than a CAGE signature, in response to aneuploidy-induced cellular stresses that results in selective ribosome loss.
 
Overall design Examination of gene expression signatures in euploid and aneuploid yeast strains under different growth conditions.
 
Contributor(s) Terhorst A, Sandikci A, Keller A, Whittaker CA, Dunham M, Amon A
Citation(s) 32632008
Submission date Mar 11, 2020
Last update date Sep 15, 2020
Contact name Charles Arthur Whittaker
E-mail(s) charliew@mit.edu
Organization name Koch Institute
Street address 77 Mass Ave 76-189
City Cambridge
State/province MA
ZIP/Postal code 02152
Country USA
 
Platforms (1)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (176)
GSM4407039 2N exp1 rep1 [AS_an.exp1.2N.d6016]
GSM4407040 2N exp1 rep2 [AS_an.exp1.2N.d6017]
GSM4407041 2N exp1 rep3 [AS_an.exp1.2N.d6022]
Relations
BioProject PRJNA611978
SRA SRP252398

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE146791_ensembl.sacCer3_plusSpikeIn.gtf.gz 279.5 Kb (ftp)(http) GTF
GSE146791_sacCer3_plusSpikeIn.fa.gz 3.6 Mb (ftp)(http) FA
GSE146791_terhorst_l2tpm.txt.gz 4.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
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