There is considerable insight into pathways and genes associated with heat-stress conditions. Most genes involved in stress response have been identified using mutant screens or gene knockdowns. Yet, there is limited understanding of the temporal dynamics of global gene expression in stressful environments. Here, we studied global gene expression profiles during 12 hours of heat stress in the nematode C. elegans. Using a high-resolution time series of increasing stress exposures, we found a distinct shift in gene expression patterns between 3–4 hours into the stress response, separating an initially highly dynamic phase from a later relatively stagnant phase. This turning point in expression dynamics coincided with a phenotypic turning point, as shown by a strong decrease in movement, survival and, progeny count in the days following the stress. Both detectable at transcriptional and phenotypic level, this study pin-points a relatively small time frame during heat stress at which enough damage is accumulated, making it impossible to recover the next few days.

BackgroundThe detrimental effects of a short bout of stress can persist and potentially turn lethal, long after the return to normal conditions. Thermotolerance, which is the capacity of an organism to withstand relatively extreme temperatures, is influenced by the response during stress exposure, as well as the recovery process afterwards. While heat-shock response mechanisms have been studied intensively, predicting thermal tolerance remains a challenge.ResultsHere, we use the nematode Caenorhabditis elegans to measure transcriptional resilience to heat stress and predict thermotolerance. Using principal component analysis in combination with genome-wide gene expression profiles collected in three high-resolution time series during control, heat stress, and recovery conditions, we infer a quantitative scale capturing the extent of stress-induced transcriptome dynamics in a single value. This scale provides a basis for evaluating transcriptome resilience, defined here as the ability to depart from stress-expression dynamics during recovery. Independent replication across multiple highly divergent genotypes reveals that the transcriptional resilience parameter measured after a spike in temperature is quantitatively linked to long-term survival after heat stress.ConclusionOur findings imply that thermotolerance is an intrinsic property that pre-determines long-term outcome of stress and can be predicted by the transcriptional resilience parameter. Inferring the transcriptional resilience parameters of higher organisms could aid in evaluating rehabilitation strategies after stresses such as disease and trauma.

13There is considerable insight into pathways and genes associated with heat-stress conditions. 14 Most genes involved in stress response have been identified using mutant screens or gene 15knockdowns. Yet, there is limited understanding of the temporal dynamics of global gene 16 expression in stressful environments. Here, we studied global gene expression profiles during 12 17 hours of heat stress in the nematode C. elegans. Using a high-resolution time series of increasing 18 stress exposures, we found a distinct shift in gene expression patterns between 3-4 hours into the 19 stress response, separating an initially highly dynamic phase from a later relatively stagnant 20phase. This turning point in expression dynamics coincided with a phenotypic turning point, as 21shown by a strong decrease in movement, survival and, progeny count in the days following the 22 stress. Both detectable at transcriptional and phenotypic level, this study pin-points a relatively 23 small time frame during heat stress at which enough damage is accumulated, making it 24 impossible to recover the next few days. 25 26

20The detrimental effects of a short bout of stress can persist, and potentially turn lethal, long after the return 21 to normal conditions. Thermotolerance, which is the capacity of an organism to withstand relatively extreme 22 temperatures, is influenced by the response during stress exposure, as well as the recovery process 23 afterwards. While heat-shock response mechanisms have been studied intensively, predicting thermal 24 tolerance remains a challenge. Here, we use the nematode Caenorhabditis elegans to measure 25 transcriptional resilience to heat stress and predict thermotolerance. Using high dimensionality reduction 26 techniques in combination with genome-wide gene expression profiles collected in three high resolution 27 time-series during control, heat stress and recovery conditions, we infer a quantitative scale capturing the 28 extent of stress-induced transcriptome dynamics in a single value This scale provides a basis for evaluating 29 transcriptome resilience, defined here as the ability to depart from stress-expression dynamics during 30 recovery. Independent replication across multiple highly divergent genotypes reveals that the transcriptional 31 resilience parameter measured after a spike in temperature is quantitatively linked to long-term survival 32 after heat stress. Our findings imply that thermotolerance is an intrinsic property that pre-determines long 33 term outcome of stress and can be predicted by the transcriptional resilience parameter. Inferring the 34 transcriptional resilience parameters of higher organisms could aid in evaluating rehabilitation strategies 35 after stresses such as disease and trauma. 36

Quantitative genetics seeks to understand the role of allelic variation in trait differences. Introgression lines (ILs) contain a single genetic locus introgressed into another genetic background, and are one of the most powerful quantitative trait locus (QTL) mapping designs. However, albeit useful for QTL discovery, this homogenous background confounds genetic interactions. Here, we created a novel IL population, complementary to a previously created population, which enables identification of genetic interactions in ILs. The novel ILCB4856 panel was made by crossing divergent strains of the model nematode Caenorhabditis elegans (N2 and CB4856). The ILCB4856 panel comprises a population of 145 strains with sequencing confirmed N2 introgressions in a CB4856 background from which a core set of 87 strains covering the entire genome was selected. We present three experiments demonstrating the power of the complementary IL panels. First, we performed QTL mapping identifying new regions associated with lifespan. Second, the existence of opposite-effect loci regulating heat-stress survival is demonstrated. Third, by combining ILN2 and ILCB4856 strains, an interacting expression QTL was uncovered. In conclusion, the complementary IL panels are a unique and ready-to-use resource to identify, resolve, and refine complex trait architectures in C. elegans.