Environmental adaptation in house mice: genetic and non-genetic effects on gene expression
Authors: Mallory A. Ballinger 1; Katya L. Mack 2; Sylvia M. Durkin 1; Michael W. Nachman 1
Affiliations: 1) University of California, Berkeley; 2) Stanford University
Keywords: Other (Gene regulatory evolution)
A major goal in evolution biology is to identify the gene regulatory mechanisms underlying adaptive evolution. However, it is well known that gene regulation is highly plastic and dependent on the environment. Nevertheless, the genetic and non-genetic effects of gene regulation are rarely considered together in the context of adaptive evolution. Specifically, relatively little is known about the contributions of cis- and trans-regulation to gene expression plasticity. House mice (Mus musculus domesticus) provide an excellent opportunity to study the gene regulatory mechanisms of plasticity as they have recently expanded into a wide range of novel environments. Here, using RNA-seq data collected from liver and brown adipose tissue, we studied gene expression in mice reared in warm and cold environments in parents adapted to warm and cold environments and in their F1 hybrids. We identified strong patterns of expression divergence across environments, largely attributable to cis-regulatory changes. Patterns of expression plasticity were largely attributable to trans-effects as trans-effects showed greater sensitivity to temperature change. Finally, we identified genes for which there were significant effects of temperature on regulatory divergence, with genes exhibiting cis-by-environment and trans-by-environment effects. Among these genes, we identified two candidates - Scd1 and Cdh13 - that show patterns of adaptive plasticity and are regulated by cis-by-environment effects. These two genes play important roles in adiposity and thermoregulation. Overall, these findings demonstrate the utility of allele-specific expression to identify regulatory mechanisms associated with plasticity and highlight the role the environment plays in adaptive gene regulation in house mice.