Super-Enhancer-Associated Gene 3-Hydroxybutyrate Dehydrogenase 1 Increases Intramuscular Fat Deposition of Yaks (<i>Bos grunniens</i>)

Intramuscular fat (IMF) is a pivotal determinant of meat quality in yaks (<i>Bos grunniens</i>). While nutritional factors are well-documented, the epigenetic landscape, particularly the transcriptional architecture governed by super-enhancers (SEs), remains largely unexplored in the context of IMF deposition. To investigate SE-associated genes, Chromatin immunoprecipitation sequencing (ChIP-seq) assays using H3K27ac antibodies and RNA-sequencing (RNA-Seq) were conducted on <i>longissimus dorsi</i> (LD) muscle tissues with high and low IMF contents. Integrated multi-omics analysis identified 82 enhancer-associated genes exhibiting significant upregulation in high-IMF samples, with 63 loci characterized as SE-associated. In particular, H3K27ac signal distribution analysis indicated that SEs were distributed across functional regions such as promoters, gene bodies, exons, and introns. Among these SE-related genes, 3-hydroxybutyrate dehydrogenase 1 (<i>BDH1</i>) was further investigated to understand its function and regulatory mechanisms. To address this, overexpression or knockdown experiments were conducted, followed by CCK-8, EdU, Bodipy functional assays, and Real-time quantitative PCR (RT-qPCR) analysis. Functional experiments revealed that <i>BDH1</i> acts as a key positive regulator of yak preadipocyte differentiation and is a prime SE-associated candidate regulatory gene. Furthermore, dual-luciferase reporter assays were performed to identify its SE region, revealing that the activity of 4 enhancer regions was significantly upregulated. Collectively, these findings implicate SE-associated genes in IMF deposition in yaks, provide a valuable resource for future research, and underscore the functional relevance of <i>BDH1</i> in this process.