E-GEOD-45594 - A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves (Botrytis cinerea infection).

Status
Released on 23 April 2013, last updated on 3 June 2014
Organism
Arabidopsis thaliana
Samples (32)
Array (1)
Protocols (8)
Description
A network model has been generated that describes the immediate gene expression cascade surrounding three similar but distinct NAC transcription factors that have roles to play in leaf senescence and in many stress responses in Arabidopsis. ANAC019, ANAC055 and ANAC072 belong to the same clade of NAC domain genes and have overlapping expression patterns. A combination of promoter DNA/protein interactions identified using yeast 1 hybrid analysis and modeling using gene expression time course data has been used to predict the regulatory network upstream of these genes. Similarities and divergence in regulation during a variety of stress responses are predicted by different combinations of upstream transcription factors binding and also by the modeling. Mutant analysis with potential upstream genes was used to test and confirm some of the predicted interactions.. Gene expression measurements in mutants of ANAC019 and ANAC055 at different times during leaf senescence have shown a distinctly different role for each of these genes. To assess mutant response to Botrytis cinerea infection, Col-0, myb2 and myb108 leaves were inoculated with 4-6 (depending on leaf size) evenly spaced 10μl droplets of B. cinerea spores. Infected leaves were harvested to provide 4 biological replicates. Samples for the comparison between myb108 and Col-0 were harvested at 26 and 30 hpi. Samples for the comparison between myb2 knockout line and Col-0 or myb2 knockout line and Col-0 were harvested at 26 and 30 hpi or 24 and 30 hpi respectively. Analysis of expression differences between Col-0 and myb2 and Col-0 and myb108 under each condition, using dye swaps, was performed using the R Bioconductor package limmaGUI (Wettenhall and Smyth, 2004).
Experiment type
transcription profiling by array 
Contacts
Jonathan David Moore <jonathan.moore@warwick.ac.uk>, Alison Jackson, Andrew Mead, Christopher A Penfold, Claire Hill, David L Wild, Emily Breeze, Emma Cooke, Findlay Bewicke-Copley, Jim Beynon, Jonathan D Moore, Katherine Denby, Laura Bowden, Peijun Zhang, Richard Hickman, Sascha Ott, Vicky Buchanan-Wollaston
Citation
A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves. Hickman R, Hill C, Penfold CA, Breeze E, Bowden L, Moore JD, Zhang P, Jackson A, Cooke E, Bewicke-Copley F, Mead A, Beynon J, Wild DL, Denby KJ, Ott S, Buchanan-Wollaston V. , Europe PMC 23578292
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-45594.idf.txt
Sample and data relationshipE-GEOD-45594.sdrf.txt
Raw data (1)E-GEOD-45594.raw.1.zip
Processed data (1)E-GEOD-45594.processed.1.zip
Array designA-GEOD-16132.adf.txt
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