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

Krishnan, Jaya; Seidel, Chris W.; Zhang, Ning; Singh, Narendra P.; VanCampen, Jake; Peuß, Robert; Xiong, Shaolei; Kenzior, Alexander; Li, Hua; Conaway, Joan W.; Rohner, Nicolas

Forschungsartikel (Zeitschrift) | Peer reviewed

Zusammenfassung

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.

Details zur Publikation

FachzeitschriftNature Genetics (Nat Genet)
Jahrgang / Bandnr. / Volume54
Seitenbereich684-693
StatusVeröffentlicht
Veröffentlichungsjahr2022 (12.05.2022)
Sprache, in der die Publikation verfasst istEnglisch
DOI10.1038/s41588-022-01049-4
Link zum Volltexthttps://www.nature.com/articles/s41588-022-01049-4
StichwörterAnimal Physiology; Epigenomics; Gene regulation

Autor*innen der Universität Münster

Peuß, Robert
Arbeitsgruppe Evolutionsökologie der Tiere (Prof. Kurtz)