Advanced search
1 file | 3.34 MB Add to list

The ROS wheel: refining ROS transcriptional footprints

Patrick Willems (UGent) , Amna M'Hamdi (UGent) , Simon Stael (UGent) , Veronique Storme (UGent) , Pavel Kerchev (UGent) , Graham Noctor, Kris Gevaert (UGent) and Frank Van Breusegem (UGent)
(2016) PLANT PHYSIOLOGY. 171(3). p.1720-1733
Author
Organization
Project
Biotechnology for a sustainable economy (Bio-Economy)
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.
Keywords
MICROARRAY DATA, OXIDATIVE STRESS, ANTHOCYANIN BIOSYNTHESIS, STRESS RESPONSES, GENE-EXPRESSION, OZONE-INDUCED CHANGES, GENOME-WIDE ANALYSIS, ARABIDOPSIS-THALIANA, UV-B RESPONSE, PROBE LEVEL

Downloads

  • Willems et al. 2016 Plant Physiology 171 1720.pdf
    • full text
    • |
    • open access
    • |
    • PDF
    • |
    • 3.34 MB

Citation

Please use this url to cite or link to this publication:

MLA
Willems, Patrick et al. “The ROS Wheel: Refining ROS Transcriptional Footprints.” PLANT PHYSIOLOGY 171.3 (2016): 1720–1733. Print.
APA
Willems, Patrick, M’Hamdi, A., Stael, S., Storme, V., Kerchev, P., Noctor, G., Gevaert, K., et al. (2016). The ROS wheel: refining ROS transcriptional footprints. PLANT PHYSIOLOGY, 171(3), 1720–1733.
Chicago author-date
Willems, Patrick, Amna M’Hamdi, Simon Stael, Veronique Storme, Pavel Kerchev, Graham Noctor, Kris Gevaert, and Frank Van Breusegem. 2016. “The ROS Wheel: Refining ROS Transcriptional Footprints.” Plant Physiology 171 (3): 1720–1733.
Chicago author-date (all authors)
Willems, Patrick, Amna M’Hamdi, Simon Stael, Veronique Storme, Pavel Kerchev, Graham Noctor, Kris Gevaert, and Frank Van Breusegem. 2016. “The ROS Wheel: Refining ROS Transcriptional Footprints.” Plant Physiology 171 (3): 1720–1733.
Vancouver
1.
Willems P, M’Hamdi A, Stael S, Storme V, Kerchev P, Noctor G, et al. The ROS wheel: refining ROS transcriptional footprints. PLANT PHYSIOLOGY. 2016;171(3):1720–33.
IEEE
[1]
P. Willems et al., “The ROS wheel: refining ROS transcriptional footprints,” PLANT PHYSIOLOGY, vol. 171, no. 3, pp. 1720–1733, 2016.
@article{8113315,
  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.},
  author       = {Willems, Patrick and M'Hamdi, Amna and Stael, Simon and Storme, Veronique and Kerchev, Pavel and Noctor, Graham and Gevaert, Kris and Van Breusegem, Frank},
  issn         = {0032-0889},
  journal      = {PLANT PHYSIOLOGY},
  keywords     = {MICROARRAY DATA,OXIDATIVE STRESS,ANTHOCYANIN BIOSYNTHESIS,STRESS RESPONSES,GENE-EXPRESSION,OZONE-INDUCED CHANGES,GENOME-WIDE ANALYSIS,ARABIDOPSIS-THALIANA,UV-B RESPONSE,PROBE LEVEL},
  language     = {eng},
  number       = {3},
  pages        = {1720--1733},
  title        = {The ROS wheel: refining ROS transcriptional footprints},
  url          = {http://dx.doi.org/10.1104/pp.16.00420},
  volume       = {171},
  year         = {2016},
}

Altmetric
View in Altmetric
Web of Science
Times cited: