DNA methylation-mediated regulation of hypoxia-responsive genes facilitates high-altitude adaptation in Tibetan chickens

The Tibetan chicken (Gallus gallus domesticus), a native breed inhabiting the Qinghai-Tibet Plateau, has developed remarkable tolerance to chronic hypoxia. However, the molecular and epigenetic mechanisms underlying its high-altitude adaptation remain unclear. In this study, we integrated genome, transcriptome, and DNA methylome data from Tibetan chickens (TC) and three low-altitude breeds. Principal component analysis revealed clear genetic, epigenetic, and transcriptional divergence between TC and lowland chickens. Cardiac enzyme assays showed significantly higher activities of LDH, SDH, SOD, CAT, and GSH-Px in TC (p < 0.05), indicating enhanced oxidative metabolism and antioxidant defense under hypoxia. Transcriptomic analysis identified 2,532 common differentially expressed genes (co-DEGs), with upregulated genes enriched in oxidative phosphorylation, fatty acid metabolism, and hypoxia response pathways. Integration with methylome data demonstrated a significant negative correlation between promoter methylation and gene expression. Among 144 genes showing promoter hypomethylation coupled with transcriptional activation, five key genes-PDK4, BNIP3L, ATG3, SLC7A5, and OMA1-were identified as central regulators of hypoxia adaptation, participating in metabolic reprogramming, mitochondrial homeostasis, and autophagy. Our findings reveal that promoter hypomethylation acts as a major epigenetic mechanism mediating transcriptional activation of hypoxia-responsive genes in Tibetan chickens. The coordinated regulation of energy metabolism, antioxidant defense, and mitochondrial quality control contributes to their physiological resilience in high-altitude environments. This study provides novel insights into the molecular and epigenetic basis of high-altitude adaptation in avian species and offers valuable references for hypoxia-resistance breeding in poultry.