Transcriptional regulation in stress recovery of Caenorhabditis elegans

C. elegans serves as an important model for integrative analysis of stress response. Analyzing the transcriptional regulation of stress response and subsequent recovery provides insight into the mechanisms of fitness optimization. Although C. elegans stress responses are well studied, the recovery from stress is poorly understood. We investigated the transcriptional response over the course of a heat-shock experiment in fully sequenced recombinant inbred lines (RILs). This allowed us to identify regulatory loci for stress recovery. The RILs, derived from a cross between N2 and CB4856, were exposed to heat-shock after which they were allowed to recover. In both environments, and in a control environment (no heat stress), genome-wide expression levels were measured. We then performed expression quantitative trait loci (eQTL) mapping across these three environments to identify regulatory loci that contribute to the recovery response. Across all RILs the largest difference in gene expression was found between control and heat-shock. Recovering populations showed patterns of gene expression that were in-between the control and heat-shock. Some RILs had a more control-like gene expression phenotype while other RILs were more heat-shock-like, thus allowing for mapping of loci regulating genetic variation in recovery. We found that genetic variation in gene expression was largely independent of the environment. More specifically, approximately 50% of the eQTL were similar in location and effect over the three environments; therefore did not display interaction with the environment. Only 1% of the genes with an eQTL in all environments displayed environment-specific interaction. The remainder of the eQTL with an environment-specific interaction were specifically detected in one environment. In conclusion, the combination of natural variation and gene expression over the course of a stress response allows for mapping loci underlying regulation in this response. The genes with an eQTL displaying environment interaction are specific for one environment. Incorporation of environment interactions facilitates specifying groups of related eQTL and thereby allows for detailed eQTL network analysis.