ArticleNature genetics2022
Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish.
Article in Nature genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 41 citations in OpenAlex.
- Exploring Astyanax mexicanus as a model for unraveling genotype-environment interactions and metabolic adaptations.Lab animal · 2026Review
- Molecular integration of seasonal temperature signals in flowering time control.Nature reviews. Genetics · 2026Review
- Chromatin Accessibility Reveals Adaptive Regulatory Variation in a Keystone Freshwater Fish.Molecular ecology · 2026Article
- Parallel adaptation to geothermally-warmed habitats due to common structural variation and functional developmental pathways.Nature communications · 2026Article
- Evolution of Resistance to Avian Malaria Infection in an Endemic Hawaiian Honeycreeper.Ecology and evolution · 2026Article
- Convergent evolution of albinism in cave animals is driven by shared mechanisms and adaptive advantages.Communications biology · 2026Article
- Cave evolution on repeat: reuse of the same genomic regions across lineages but not across traits inbioRxiv : the preprint server for biology · 2026Article
- INSIG1 parallel substitution drives lipid/sterol metabolic plasticity mediating desert adaptation in ungulates.Communications biology · 2026Article
- Water Parameters and Hydrodynamics in Rivers and Caves HostingEcology and evolution · 2026Article
- Integrative Genomics Refines Tissues, Candidate Genes and Putative Regulatory Links Involved in the Humic Adaptation of Keystone Freshwater Fish.Molecular ecology · 2025Article
- Latitudinal-environmental variations driving the local adaptation ofMarine life science & technology · 2025Article
- Divergent 3D genome organization in livers of cave and surface morphs ofbioRxiv : the preprint server for biology · 2025Article
- Differentially expressed miRNAs offer new perspective into cave adaptation of Astyanax mexicanus.Annals of the New York Academy of Sciences · 2025Article
- Chr23-miR-200s and Dmrt1 Control Sexually Dimorphic Trade-Off Between Reproduction and Growth in Zebrafish.International journal of molecular sciences · 2025Article
- Evolutionary ecophysiology in extreme environments under a global change scenario.Conservation physiology · 2025Article
- Transcriptome analysis reveals the genetic basis underlying the formation and seasonal changes of nuptial pads in Rana chensinensis.BMC genomics · 2024Article
- Genome-wide analysis of histone modifications can contribute to the identification of candidate cis-regulatory regions in the threespine stickleback fish.BMC genomics · 2024Article
- Article
- 3D spheroid culturing of Astyanax mexicanus liver-derived cell lines recapitulates distinct transcriptomic and metabolic states of in vivo tissue environment.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2024Article
- The nature and distribution of putative non-functional alleles suggest only two independent events at the origins of Astyanax mexicanus cavefish populations.BMC ecology and evolution · 2024Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 2 countries.
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Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.