Journal
PLANT PHYSIOLOGY
Volume 171, Issue 3, Pages 1720-1733Publisher
OXFORD UNIV PRESS INC
DOI: 10.1104/pp.16.00420
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Funding
- Ghent University Special Research Fund [01J11311]
- Ghent University Multi-disciplinary Research Partnership (Ghent BioEconomy grant) [01MRB510W]
- Interuniversity Attraction Poles Programme [IUAP P7/29]
- Belgian Science Policy Office
- Research Foundation- Flanders [G0D7914N]
- Vlaamse Gemeenschap [Tournesol T2005.18]
- Agence Nationale de la Recherche (project Cynthiol) [ANR12-BSV6-0011]
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In the last decade, microarray studies have delivered extensive inventories of transcriptome-wide changes in messenger RNA levels provoked by various types of oxidative stress in Arabidopsis (Arabidopsis thaliana). Previous cross-study comparisons indicated how different types of reactive oxygen species (ROS) and their subcellular accumulation sites are able to reshape the transcriptome in specific manners. However, these analyses often employed simplistic statistical frameworks that are not compatible with large-scale analyses. Here, we reanalyzed a total of 79 Affymetrix ATH1 microarray studies of redox homeostasis perturbation experiments. To create hierarchy in such a high number of transcriptomic data sets, all transcriptional profiles were clustered on the overlap extent of their differentially expressed transcripts. Subsequently, meta-analysis determined a single magnitude of differential expression across studies and identified common transcriptional footprints per cluster. The resulting transcriptional footprints revealed the regulation of various metabolic pathways and gene families. The RESPIRATORY BURST OXIDASE HOMOLOG F-mediated respiratory burst had a major impact and was a converging point among several studies. Conversely, the timing of the oxidative stress response was a determining factor in shaping different transcriptome footprints. Our study emphasizes the need to interpret transcriptomic data sets in a systematic context, where initial, specific stress triggers can converge to common, aspecific transcriptional changes. We believe that these refined transcriptional footprints provide a valuable resource for assessing the involvement of ROS in biological processes in plants.
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