title: The ROS Wheel: Refining ROS Transcriptional Footprints.
abstract: 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.
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.).
authors.forename: Patrick
authors.identifier: 0000-0003-4667-2294
authors.initials: P
authors.lastname: Willems
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.).
authors.forename: Amna
authors.identifier: 0000-0001-9959-1362
authors.initials: A
authors.lastname: Mhamdi
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.).
authors.forename: Simon
authors.identifier: 0000-0001-8322-0428
authors.initials: S
authors.lastname: Stael
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.).
authors.forename: Veronique
authors.identifier: 0000-0003-4762-6580
authors.initials: V
authors.lastname: Storme
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.).
authors.forename: Pavel
authors.identifier: 0000-0003-2737-0493
authors.initials: P
authors.lastname: Kerchev
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.).
authors.forename: Graham
authors.initials: G
authors.lastname: Noctor
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.).
authors.forename: Kris
authors.identifier: 0000-0002-4237-0283
authors.initials: K
authors.lastname: Gevaert
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (P.W., A.M., S.S., V.S., P.K., F.V.B.);Medical Biotechnology Center, VIB, 9000 Ghent, Belgium (P.W., S.S., K.G.);Department of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W., S.S., K.G.);Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (A.M., G.N.); andUnité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (A.M., G.N.) frank.vanbreusegem@psb.ugent.be.
authors.forename: Frank
authors.identifier: 0000-0002-3147-0860
authors.initials: F
authors.lastname: Van Breusegem
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D008954:Models, Biological; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D010084:Oxidation-Reduction; D018384:Oxidative Stress / Q000235:genetics*; D017382:Reactive Oxygen Species / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D029681:Arabidopsis Proteins; D017382:Reactive Oxygen Species