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Series GSE12221 Query DataSets for GSE12221
Status Public on Oct 01, 2008
Title Decay profiles of Saccharomyces cerevisiae mRNAs following oxidative stress and DNA damage
Platform organisms Schizosaccharomyces pombe; Saccharomyces cerevisiae
Sample organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Summary We subjected yeast to two stresses, oxidative stress, which under current settings induces a fast and transient response in mRNA abundance, and DNA damage, which triggers a slow enduring response. Using microarrays, we performed a transcriptional arrest experiment to measure genome-wide mRNA decay profiles under each condition. Genome-wide decay kinetics in each condition were compared to decay experiments that were performed in a reference condition (only transcription inhibition without an additional stress) to quantify changes in mRNA stability in each condition. We found condition-specific changes in mRNA decay rates and coordination between mRNA production and degradation. In the transient response, most induced genes were surprisingly destabilized, while repressed genes were somewhat stabilized, exhibiting counteraction between production and degradation. This strategy can reconcile high steady-state level with short response time among induced genes. In contrast, the stress that induces the slow response displays the more expected behavior, whereby most induced genes are stabilized, and repressed genes destabilized. Our results show genome-wide interplay between mRNA production and degradation, and that alternative modes of such interplay determine the kinetics of the transcriptome in response to stress.

Keywords: Four separate time courses
 
Overall design We used Affymetrix microarrays to measure the decay profiles of all genes following transcription inhibition in four separate experiments. In two reference experiments, only transcription inhibtion was applied. In two other experiments, an additional stress was applied prior to transcription inhibition: oxidative stress (0.3mM hydrogen peroxide) or DNA damage (0.1% methyl methanesulfonate).
 
Contributor(s) Shalem O, Dahan O, Levo M, Martinez MR, Furman I, Segal E, Pilpel Y
Citation(s) 18854817
Submission date Jul 23, 2008
Last update date Feb 21, 2017
Contact name Ophir Shalem
E-mail(s) ophir.shalem@weizmann.ac.il
Organization name Weizmann Inst.
Street address Hertzel
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platforms (1)
GPL2529 [Yeast_2] Affymetrix Yeast Genome 2.0 Array
Samples (37)
GSM307229 oxidative stress decay profile, t=0
GSM307230 oxidative stress decay profile, t=0, replicate
GSM307231 oxidative stress decay profile, t=5min
This SubSeries is part of SuperSeries:
GSE12222 Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
Relations
BioProject PRJNA113855

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE12221_RAW.tar 37.6 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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