Author response: A novel enhancer near the Pitx1 gene influences development and evolution of pelvic appendages in vertebrates

Thompson, Abbey C; Capellini, Terence D.; Guenther, Catherine; Chan, Yingguang Frank; Infante, Carlos R.; Menke, Douglas B.; Kingsley, David M.

doi:10.7554/elife.38555.023

2018

DOI: 10.7554/elife.38555.023

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Author response: A novel enhancer near the Pitx1 gene influences development and evolution of pelvic appendages in vertebrates

Abbey C Thompson

Terence D. Capellini

Catherine Guenther

et al.

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2020

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

Krishnan

Seidel

Zhang

et al. 2020

Preprint

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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.

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

Krishnan

Seidel

Zhang

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

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Author response: A novel enhancer near the Pitx1 gene influences development and evolution of pelvic appendages in vertebrates

Cited by 1 publication

References 0 publications

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

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

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