Comparative DNA methylation reveals epigenetic adaptation to high altitude in snub-nosed monkeys

DNA methylation has been proved to have a crucial role in environmental adaptations. Here, using whole-genome bisulfite sequencing method, we acquired the genome-wide DNA methylation profiles of Yunnan snub-nosed monkeys (Rhinopithecus bieti), which are known as the nonhuman primates that inhabit the highest altitude, and their close relatives, golden snub-nosed monkeys (R. roxellana). Overall, the DNA methylation levels had a trend towards slightly increased in golden snub-nosed monkeys compared with Yunnan snub-nosed monkeys, indicating a relatively more genome region are hypermethylated in the golden snub-nosed monkey. Comparative genomic methylation analysis found that genes associated with different methylated regions were involved in membrane fusion and vesicular formation and trafficking, hemoglobin, cell cycles regulation, and neuron differentiation. This result suggested that the high-altitude-related epigenetic modifications are comprehensive, involving a complete adaptation process from inhibiting single Ca2+ channel protein to multiple proteins collaboratively enhancing vesicular function or inhibiting cell differentiation and proliferation. Further function assays have shown that overexpression or downregulation of candidate genes, such as SNX10, TIMELESS and CACYBP, affects cell viability under stress conditions. Our research indicates that comparing DNA methylation in similar species can provide new candidate genome regions/genes associated with local adaptations, thereby enhancing our understanding of how organisms adapt to their environments.