Relating perturbation magnitude to temporal gene expression in biological systems.
BACKGROUND
Most transcriptional activity is a result of environmental variability. This cause (environment) and effect (gene expression) relationship is essential to survival in any changing environment. The specific relationship between environmental perturbation and gene expression - and stability of the response - has yet to be measured in detail. We describe a method to quantitatively relate perturbation magnitude to response at the level of gene expression. We test our method using Saccharomyces cerevisiae as a model organism and osmotic stress as an environmental stress.


RESULTS
Patterns of gene expression were measured in response to increasing sodium chloride concentrations (0, 0.5, 0.7, 1.0, and 1.2 M) for sixty genes impacted by osmotic shock. Expression of these genes was quantified over five time points using reverse transcriptase real-time polymerase chain reaction. Magnitudes of cumulative response for specific pathways, and the set of all genes, were obtained by combining the temporal response envelopes for genes exhibiting significant changes in expression with time. A linear relationship between perturbation magnitude and response was observed for the range of concentrations studied.


CONCLUSIONS
This study develops a quantitative approach to describe the stability of gene response and pathways to environmental perturbation and illustrates the utility of this approach. The approach should be applicable to quantitatively evaluate the response of organisms via the magnitude of response and stability of the transcriptome to environmental change.
Callister
Stephen J
SJ
Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA. stephen.callister@pnl.gov
Parnell
J Jacob
JJ
Pfrender
Michael E
ME
Hashsham
Syed A
SA