Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish

Cis-regulatory changes are key drivers of adaptative evolution. However, their contribution to the metabolic adaptation of organisms is not well understood. Here, we used a unique vertebrate model, Astyanax mexicanus-different morphotypes of which survive in nutrient-rich surface and nutrient-deprived cave waters-to uncover gene regulatory networks underlying metabolic adaptation. We performed genome-wide epigenetic profiling in the liver tissues of Astyanax and found that many of the identified cis-regulatory elements (CREs) have genetically diverged and have differential chromatin features between surface and cave morphotypes, while retaining remarkably similar regulatory signatures between independently derived cave populations. One such CRE in the hpdb gene harbors a genomic deletion in cavefish that abolishes IRF2 repressor binding and derepresses enhancer activity in reporter assays. Selection of this mutation in multiple independent cave populations supports its importance in cave adaptation, and provides novel molecular insights into the evolutionary trade-off between loss of pigmentation and adaptation to food-deprived caves. Genome-wide epigenomic profiling of liver tissue from one surface and two independent cave populations of Astyanax mexicanus sheds light on regulatory changes underlying metabolic adaptations to the nutrient-deprived cave environment.

Automated summary

Cis-regulatory changes have been found to contribute to the metabolic adaptation in different morphotypes of Astyanax mexicanus, with genetically diverged and differentially regulated elements identified between surface and cave populations. This study sheds light on the molecular mechanisms underlying metabolic adaptations to nutrient-deprived cave environments.