Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants.
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.
Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium.
Rahul
R
Bhosale
Jeremy B
JB
Jewell
Jens
J
Hollunder
Abraham J K
AJ
Koo
Marnik
M
Vuylsteke
Tom
T
Michoel
Pierre
P
Hilson
Alain
A
Goossens
Gregg A
GA
Howe
John
J
Browse
Steven
S
Maere
D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics*; D003517:Cyclopentanes / Q000494:pharmacology; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D053263:Gene Regulatory Networks / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D058977:Molecular Sequence Annotation; D054883:Oxylipins / Q000494:pharmacology; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics; D012984:Software
D003517:Cyclopentanes; D054883:Oxylipins; C011006:jasmonic acid