# The Whole Genome DNA Methylation Signatures of Hindlimb Muscles in Chinese Alligators during Hibernation and Active Periods

## TL;DR

This study explores how DNA methylation in Chinese alligators' muscles changes during hibernation and active periods, linking it to metabolic processes.

## Contribution

The study provides the first whole-genome DNA methylation maps of Chinese alligator hindlimb muscles during hibernation and active states.

## Key findings

- Differential methylation was found in genes related to lipid, energy, and amino acid metabolism.
- Promoter methylation of genes like ATP5F1C and FBXO28 suggests a role in hibernation adaptation.
- Key pathways like MAPK and GnRH signaling were enriched in differentially methylated genes.

## Abstract

Hibernation is a physiological state for Chinese alligators to cope with cold weather. DNA methylation, an epigenetic factor discovered early and extensively studied, plays a crucial role in regulating gene expression, development, and stress responses. The role of DNA methylation in regulating gene expression related to hibernation in ectotherms remains unclear. Here, genome-wide DNA methylation maps of the hindlimb muscles of Chinese alligators were generated, and differential methylation genes and related metabolic pathways of the hindlimb muscles of Chinese alligators during hibernation and active periods were screened. These differential genes and metabolic pathways are closely related to lipid metabolism, energy metabolism, and amino acid metabolism. The findings suggest that DNA methylation may play a significant role in regulating the adaptive hibernation mechanisms of Chinese alligators. This study is helpful to further understand the molecular basis of hibernation adaptation in Chinese alligators.

Many ectotherms hibernate to increase their chances of survival during harsh winter conditions. The role of DNA methylation in regulating gene expression related to hibernation in ectotherms remains unclear. Here, we employed whole-genome bisulfite sequencing (WGBS) technology to construct a comprehensive genome-wide DNA methylation landscape of the hindlimb muscles in the Chinese alligator during hibernation and active periods. The results indicated that methylation modifications were most abundant at CG sites, identifying 9447 differentially methylated regions (DMRs) and 2329 differentially methylated genes (DMGs). KEGG pathway enrichment analysis of the DMGs revealed significant enrichment in major pathways such as the neurotrophin signaling pathway, the MAPK signaling pathway, the GnRH signaling pathway, the biosynthesis of amino acids, and the regulation of the actin cytoskeleton, which are closely related to lipid metabolism, energy metabolism, and amino acid metabolism. Among these, 412 differentially methylated genes were located in promoter regions, including genes related to energy metabolism such as ATP5F1C, ATP5MD, PDK3, ANGPTL1, and ANGPTL2, and genes related to ubiquitin-proteasome degradation such as FBXO28, FBXO43, KLHL40, and PSMD5. These findings suggest that methylation in promoter regions may play a significant role in regulating the adaptive hibernation mechanisms in the Chinese alligator. This study contributes to a further understanding of the epigenetic mechanisms behind the hibernation of the Chinese alligator.