E-MTAB-504 - Transcription profiling by array and ChIP of fission yeast to understand the contributions of transcription and mRNA turnover to gene expression dynamics in response to oxidative stress

Status
Last updated on 21 May 2012, released on 1 July 2013
Organism
Schizosaccharomyces pombe
Samples (36)
Array (1)
Protocols (2)
Description
The cooperation of transcriptional and post-transcriptional controls to shape gene regulation is poorly understood. Here we show that a combination of two simple and non-invasive genomic techniques, coupled with kinetic mathematical modelling, afford insight into the multi-layered regulation of gene expression dynamics in response to oxidative stress in the fission yeast Schizosaccharomyces pombe. This study reveals a dominant role of transcriptional control in response to stress, and it points to the first minutes after stress induction as a critical time when control of mRNA turnover can support transcriptional control for rapid gene regulation. In addition, we uncover specialized gene expression strategies such as simultaneous transcriptional repression and mRNA destabilization for genes encoding ribosomal proteins, delayed mRNA destabilization with varying contribution of transcription for the ribosome biogenesis regulon, dominant roles of mRNA stabilisation for genes participating in protein degradation, and adjustment of mRNA turnover during stress adaptation. We also show that genes regulated independently of the Atf1p transcription factor are mainly controlled by mRNA turnover during oxidative stress.

An additional file containing normalized data is available on the FTP site for this experiment.
Experiment types
transcription profiling by array, ChIP-chip by array, co-expression, growth condition, replicate
Contacts
Citation
Contributions of transcription and mRNA turnover to gene expression dynamics of fission yeast in response to oxidative stress. "Samuel Marguerat, Katherine Lawler, Alvis Brazma, Jürg Bähler".
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-MTAB-504.idf.txt
Sample and data relationshipE-MTAB-504.sdrf.txt
Raw data (1)E-MTAB-504.raw.1.zip
Array designA-MEXP-585.adf.txt
Links