Role of super-enhancer-associated miRNAs and histone modifications in intramuscular fat deposition in yak

Intramuscular fat (IMF) content is a crucial factor in determining meat quality, yet yak meat is typically characterized by low IMF levels. The epigenetic mechanisms underlying IMF deposition, particularly the role of super-enhancers (SEs), remain poorly understood. RNA-seq identified 66 differentially expressed (DE) miRNAs and 56 DE pri-miRNAs in yak longissimus dorsi with varying IMF contents. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed 1209 SE-associated pri-miRNA genes and 2709 SE-associated mature miRNA genes with distinct histone modifications. These SEs not only enhance the transcription of miRNA genes but also affect the processing and maturation of primary miRNAs (pri-miRNAs). H3K27ac-marked SEs regulated key miRNAs, including miR-1991, miR-2284b, miR-2284 ac, and miR-2285ay. Enrichment of muscle-specific transcription factors within H3K27ac-enriched regions, including USF1, KLF4, SMAD, and ATF, suggesting their role in regulating miRNA expression and muscle function. Functional studies confirmed that miR-2285ay, a SE-associated miRNA, promotes yak adipocyte differentiation through a series of cell and molecular biology experiments. Dual-luciferase assays demonstrated the regulatory role of SEs in miR-2285ay expression through the enhancer activity of their constituent regions. Our study provides preliminary insights into the epigenetic regulation of intramuscular fat deposition and provides a reference for improving yak beef quality through genetic improvement in the future.