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| Status |
Public on Dec 07, 2013 |
| Title |
Measurement of temperature affects on Arabidopsis transcription and decay rates |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by array
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| Summary |
The goal of this study is to measure Arabidopsis mRNA transcription and mRNA decay rates genome wide at two temperatures, and thus to calculate the temperature coefficient of both processes. Sensing and response to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes to transcription or decay rates and whether passive or active temperature regulation is involved. Results Using a base analogue labelling method we directly measured the temperature coefficient (Q10) of mRNA synthesis and degradation rates of the Arabidopsis transcriptome. We show that for most genes transcript levels are buffered against passive increases in transcription rates by balancing passive increases in the rate of decay. Strikingly, for temperature-responsive transcripts, increasing temperature raises transcript abundance primarily by promoting faster transcription relative to decay and not vice versa, suggesting a global transcriptional mechanism process exists for the activethat controls of mRNA abundance by temperature/
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| Overall design |
The design of this expreiment is thus: at time zero (dawn) 3 biological replicate samples were harvested, and then the base analogue 4-thiouracil (4SU) was added to three remaining biological replicate samples. At time T these were harvested and the latter biotinylated and separated into 4SU-containing (labelled) and 4SU non-containing (unlabelled) fractions by passage through a streptavidin column. Total RNA for both timepoints was hybridisaed on the chips, as were the separated fractions from time T, giving 12 chips in total. This design was repeated at a second temperature, giving 24 hybridisations. The two tempertaures were 27C and 17C and time T was 1 hour after dawn at 27C and two hours after dawn at 17C.
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| Contributor(s) |
Penfield S, Sidaway-Lee K |
| Citation(s) |
24580780 |
| Submission date |
Dec 06, 2013 |
| Last update date |
Aug 15, 2018 |
| Contact name |
Steven Penfield |
| Organization name |
University or Exeter
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| Department |
Biosciences
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| Street address |
Stocker Raod
|
| City |
Exeter |
| ZIP/Postal code |
EX44QD |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL198 |
[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array |
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| Samples (24)
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| Relations |
| Affiliated with |
GSE69995 |
| BioProject |
PRJNA230792 |
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