Genome-wide analysis ofcis-regulatory changes in the metabolic adaptation of cavefish

Abstract

Changes in cis-regulatory elements play important roles in adaptation and phenotypic evolution. However, their contribution to metabolic adaptation of organisms is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, different morphotypes of which survive in nutrient-rich surface and nutrient-deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide epigenetic profiling in the liver tissue of one surface and two independently derived cave populations. We find that many cis-regulatory elements differ in their epigenetic status/chromatin accessibility between surface fish and cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. These differentially accessible regions are associated with genes of key pathways related to lipid metabolism, circadian rhythm and immune system that are known to be altered in cavefish. Using in vitro and in vivo functional testing of the candidate cis-regulatory elements, we find that genetic changes within them cause quantitative expression differences. We characterized one cis-regulatory element in the hpdb gene and found a genomic deletion in cavefish that abolishes binding of the transcriptional repressor IRF2 in vitro and derepresses enhancer activity in reporter assays. Genetic experiments further validated a cis-mediated role of the enhancer and suggest a role of this deletion in the upregulation of hpdb in wild cavefish populations. Selection of this mutation in multiple independent cave populations supports its importance in the adaptation to the cave environment, providing novel molecular insights into the evolutionary trade-off between loss of pigmentation and adaptation to a food-deprived cave environment.

Resilience in a Natural Model of Metabolic Dysfunction Through Changes in Longevity and Ageing-Related Metabolites

“…Finally, cholesteryl esters (Table S6), and cholesterol in some feeding states (Table S2), were less abundant in cave populations. Using a previously published gene expression dataset (33), we investigated factors that might influence levels of cholesteryl esters. Cholesteryl ester transfer protein (CETP), which transports cholesterol in / out of lipoproteins, is down-regulated in both Pachón and Tinaja compared to surface fish (Fig S6), suggesting a potential causal relationship between lower cholesteryl ester levels in cave populations and this important carrier protein.…”

“…Previously published RNA-Seq data (33) of CETP () and HMGCRA/B ( / ) in cave / surface A. mexicanus . Values on the y–axis are gene expression data in terms of counts measured in liver tissue under normal feeding conditions.…”

Liver-derived cell lines from cavefish Astyanax mexicanus as an in vitro model for studying metabolic adaptation

“…Previous studies have shown drastic metabolic differences in the metabolism of surface fish and cavefish (4,5,14). Most of the differences that have been documented affect glucose and fat metabolism pathways.…”

“…Astyanax mexicanus has emerged as a powerful system to understand the genetic and physiological basis of metabolic adaptation to nutrient deprived habitats (2)(3)(4)(5)(6)(7)(8)(9)(10). The species comes in two morphotypes -the surface fish that live in lush, nutrient-rich rivers and the blind cavefish that dwell in dark and nutrient-poor caves in the Sierra de El Abra of northeast Mexico.…”

“…The liver plays an essential role in this process as a key organ for integration of fat and glucose metabolism and thereby, metabolic adaptation. Previous studies from our lab have shown that cavefish have fatty livers and show differential regulation of many key metabolic genes combined with massive differences in chromatin architecture that correlate with gene expression changes (4,8). Liver cell cultures from several organisms are now commercially available including multiple cell lines from human, mouse, zebrafish, rainbow trout, etc.…”