Predicting Gene Function from Uncontrolled Expression Variation among Individual Wild-Type Arabidopsis Plants

Bhosale, Rahul; Jewell, Jeremy B.; Hollunder, Jens; Koo, Abraham J.K.; Vuylsteke, Marnik; Michoel, Tom; Hilson, Pierre; Goossens, Alain; Howe, Gregg A.; Browse, John; Maere, Steven

Abstract

Gene expression profiling studies are usually performed on pooled samples grown under tightly controlled experimental conditions to suppress variability among individuals and increase experimental reproducibility. In addition, to mask unwanted residual effects, the samples are often subjected to relatively harsh treatments that are unrealistic in a natural context. Here, we show that expression variations among individual wild-type Arabidopsis thaliana plants grown under the same macroscopic growth conditions contain as much information on the underlying gene network structure as expression profiles of pooled plant samples under controlled experimental perturbations. We advocate the use of subtle uncontrolled variations in gene expression between individuals to uncover functional links between genes and unravel regulatory influences. As a case study, we use this approach to identify ILL6 as a new regulatory component of the jasmonate response pathway.

Citation

Bhosale, R., Jewell, J. B., Hollunder, J., Koo, A. J., Vuylsteke, M., Michoel, T., Hilson, P., Goossens, A., Howe, G. A., Browse, J., & Maere, S. (2013). Predicting Gene Function from Uncontrolled Expression Variation among Individual Wild-Type Arabidopsis Plants. Plant Cell, 25(8), 2865-2877. https://doi.org/10.1105/tpc.113.112268

• Journal Article Type: Article
• Acceptance Date: Jul 18, 2013
• Online Publication Date: Aug 13, 2013
• Publication Date: 2013-08
• Deposit Date: Aug 22, 2019
• Journal: The Plant Cell
• Print ISSN: 1040-4651
• Electronic ISSN: 1532-298X
• Publisher: American Society of Plant Biologists
• Peer Reviewed: Peer Reviewed
• Volume: 25
• Issue: 8
• Pages: 2865-2877
• DOI: https://doi.org/10.1105/tpc.113.112268
• Keywords: Plant Science; Cell Biology
• Public URL: https://nottingham-repository.worktribe.com/output/2470994
• Publisher URL: http://www.plantcell.org/content/25/8/2865