Comparative chromatin accessibility and transcriptome analyses identify key energy metabolism genes for hypoxia adaptation in embryos of Tibetan chickens

Tibetan chickens have evolved a unique energy metabolism that enables them to survive in high-altitude environments characterized by hypoxia. However, the genetic basis of this trait remains unclear. In this study, eggs from Tibetan and Leghorn chickens were incubated in hypoxic conditions (13 % O₂). After 16 days, RNA-seq was performed on 23 liver tissues from 13 Tibetan and 10 Leghorn chicken embryos. Six ATAC-seq datasets were also generated from three Tibetan and three Leghorn chickens, respectively. Differential expression analysis revealed that 2,421 genes were down-regulated and 1,785 genes were up-regulated in the livers of Tibetan chicken embryos. A total of 414 significant differentially accessible regions (DARs) were identified between the two breeds. Of these, 400 were upregulated and 14 were downregulated in Tibetan chickens. Combined analysis of ATAC-seq and RNA-seq data revealed that 102 of the upregulated genes were associated with the gain of DARs in Tibetan chickens. However, no down-regulated genes were found to overlap with the loss of DARs in Tibetan chickens. Several genes, including ACLY, OGDH, PDHB, ECI1, ACAT2, HMGCL, DECR2, and EPHX2, were identified as potentially contributing to hypoxic adaptation in Tibetan chickens during the embryonic stage. These genes carry upregulated peaks and are involved in the TCA cycle and fatty acid degradation. In particular, several transcription factors (TFs), belonging to the kruppel-like factor (KLF), peroxisome proliferator-activated receptors (PPAR) and hepatocyte nuclear factor (HNF) families, which are involved in lipid metabolism and energy homeostasis, were identified in the gain peaks of Tibetan chickens. These results highlight the vital role of enhancing the liver's capacity to supply energy in the hypoxic adaptation of Tibetan chickens. Overall, our results provide new insights into the epigenetic modifications and transcriptional regulation of this adaptation, suggesting avenues for future research into the hypoxic adaptation of highland animals.