TY - JOUR T1 - Genetic and environmental perturbations drive modular transcriptome responses JF - bioRxiv DO - 10.1101/517235 SP - 517235 AU - Stephanie Mark AU - Joerg Weiss AU - Eesha Sharma AU - Ting Liu AU - Wei Wang AU - Julie M. Claycomb AU - Asher D. Cutter Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/01/10/517235.abstract N2 - Background Transcriptome profiling for distinct environmental and genetic perturbations permits genomic characterization of gene expression modularity, and the robustness of that modularity in the face of extrinsic and genetically intrinsic changes. We quantified the transcriptome responses for distinct temperature-adapted genotypes of the nematode Caenorhabditis briggsae when exposed to chronic temperature stress.Results We found that 56% of the 8795 differentially-expressed genes show genotype-specific changes in expression in response to temperature (genotype-by-environment interactions, GxE). Most genotype-specific responses occur under heat stress, indicating that cold versus heat stress responses involve distinct genomic architectures. The 22 co-expression modules that we identified differ in their enrichment of genes with genetic versus environmental versus interaction effects, as well as their genomic spatial distributions, functional attributes, and rates of molecular evolution at the sequence level. Modules enriched for genes with simple effects of either genotype or temperature alone on profiles of differential expression tend to evolve especially rapidly.Conclusions These results illustrate how the form of transcriptome modularity, in terms of response to environmental and genetic perturbation, ramifies to distinctive profiles of evolutionary change. Chromosome-scale patterning of nucleotide differences predominates as the source of genetic differences among expression profiles rather than cis-acting regulatory alleles, and natural selection regimes are largely decoupled between coding sequences and non-coding flanking sequences that contain regulatory elements. ER -