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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.<\/jats:p>","DOI":"10.3390\/ani14131972","type":"journal-article","created":{"date-parts":[[2024,7,3]],"date-time":"2024-07-03T11:35:57Z","timestamp":1720006557000},"page":"1972","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["The Whole Genome DNA Methylation Signatures of Hindlimb Muscles in Chinese Alligators during Hibernation and Active Periods"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1176-8387","authenticated-orcid":false,"given":"Jihui","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Food Science and Biology Engineering, Wuhu Institute of Technology, Wuhu 241000, China"},{"name":"College of Life Sciences, Anhui Normal University, Wuhu 241000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaobing","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Anhui Normal University, Wuhu 241000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,7,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"101202","DOI":"10.1016\/j.isci.2020.101202","article-title":"A Unique Energy-Saving Strategy during Hibernation Revealed by Multi-Omics Analysis in the Chinese Alligator","volume":"23","author":"Lin","year":"2020","journal-title":"iScience"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1071\/ZO18005","article-title":"Insights into the seasonal adaptive mechanisms of Chinese alligators (Alligator sinensis) from transcriptomic analyses","volume":"66","author":"Sun","year":"2018","journal-title":"Aust. 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