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

Autor: Krishnan J; Stowers Institute for Medical Research, Kansas City, MO, USA., Seidel CW; Stowers Institute for Medical Research, Kansas City, MO, USA., Zhang N; Stowers Institute for Medical Research, Kansas City, MO, USA., Singh NP; Stowers Institute for Medical Research, Kansas City, MO, USA., VanCampen J; Stowers Institute for Medical Research, Kansas City, MO, USA.; Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA., Peuß R; Stowers Institute for Medical Research, Kansas City, MO, USA.; Institute for Evolution and Biodiversity, University of Münster, Münster, Germany., Xiong S; Stowers Institute for Medical Research, Kansas City, MO, USA., Kenzior A; Stowers Institute for Medical Research, Kansas City, MO, USA., Li H; Stowers Institute for Medical Research, Kansas City, MO, USA., Conaway JW; Stowers Institute for Medical Research, Kansas City, MO, USA., Rohner N; Stowers Institute for Medical Research, Kansas City, MO, USA. nro@stowers.org.; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA. nro@stowers.org.
Jazyk: angličtina
Zdroj: Nature genetics [Nat Genet] 2022 May; Vol. 54 (5), pp. 684-693. Date of Electronic Publication: 2022 May 12.
DOI: 10.1038/s41588-022-01049-4
Abstrakt: 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.
(© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)
Databáze: MEDLINE
Externí odkaz: