Myoblast differentiation is a complex process whereby the mononuclear muscle precursor cells myoblasts express skeletal-muscle-specific genes and fuse with each other to form multinucleated myotubes. The objective of this study was to identify potentially novel mechanisms that mediate myoblast differentiation. We first compared transcriptomes in C2C12 myoblasts before and 6 days after induction of myogenic differentiation by RNA-seq. This analysis identified 11,046 differentially expressed genes, of which 5615 and 5431 genes were upregulated and downregulated, respectively, from before differentiation to differentiation. Functional enrichment analyses revealed that the upregulated genes were associated with skeletal muscle contraction, autophagy, and sarcomeres while the downregulated genes were associated with ribonucleoprotein complex biogenesis, mRNA processing, ribosomes, and other biological processes or cellular components. Western blot analyses showed an increased conversion of LC3-I to LC3-II protein during myoblast differentiation, further demonstrating the upregulation of autophagy during myoblast differentiation. Blocking the autophagic flux in C2C12 cells with chloroquine inhibited the expression of skeletal-muscle-specific genes and the formation of myotubes, confirming a positive role for autophagy in myoblast differentiation and fusion.

Intramuscular fat (IMF), the white adipose tissue deposited between skeletal muscle fibers, is a key determinant of beef quality due to its contribution to

Skeletal muscle undergoes extensive developmental and functional changes during the transition from neonatal to adult stages, but the biological processes and regulatory mechanisms underlying these changes remain incompletely understood. In this study, we integrated RNA-seq and H3K27ac ChIP-seq analyses to characterize transcriptional and epigenomic changes during muscle maturation in neonatal and adult Angus-cross cattle. RNA-seq analysis of longissimus muscle identified 2785 differentially expressed genes (DEGs) between neonatal and adult muscles. Adult muscle showed increased expression of genes associated with muscle maturation, whereas neonatal muscle exhibited higher activity of pathways related to energy metabolism and protein translation. H3K27ac profiling revealed extensive remodeling of active regulatory elements during muscle maturation, including stage-specific enhancers and super-enhancers. Motif enrichment analysis indicated distinct transcription factor networks associated with neonatal- and adult-specific regulatory landscapes. Neonatal muscle-specific enhancers were enriched for motifs of myogenic regulators, including MYOD1, MYOG, SIX family members, and ASCL2, whereas adult muscle-specific enhancers showed increased enrichment of the MEF2 family members. Integration of transcriptomic and epigenomic datasets identified stage-specific enhancers associated with genes involved in neonatal and adult muscle functions. Together, these findings demonstrate that the transition from neonatal to adult muscle is accompanied by coordinated changes in transcriptional programs and enhancer landscapes, providing new insights into the regulatory mechanisms underlying skeletal muscle maturation.

Deciphering the regulatory syntax of the genome is essential to understand the genetic and molecular architecture of complex traits, as most trait-associated variants lie in non-coding regions. Yet, functional annotation of the bovine genome remains limited, hindering our ability to unravel the mechanisms underpinning complex traits of economic and ecological importance in cattle. Here, we present a comprehensive epigenetic atlas comprising 1,138 genome-wide epigenetic profiles, including chromatin accessibility, six histone modifications, CCCTC-binding factor (CTCF) transcription factor binding, DNA methylation, chromatin conformation, and transcriptomes across 53 adult tissues, five fetal tissues, and seven primary cell types. This atlas-level data enables us to annotate around 45% of the genome as putative regulatory elements exhibiting tissue- or cell-specific regulatory activity. Leveraging sequence-to-function deep learning models, we discovered 301 sequence motifs and predicted the functional impact of genetic variants through in silico mutagenesis, thereby facilitating the decoding of the regulatory syntax of the cattle genome and fine-mapping of GWAS loci for 22 complex traits. Cross-species analysis further revealed evolutionarily conserved features of regulatory architecture and provided evolutionary insights into complex traits and diseases in humans. Together, this atlas offers a foundational resource for advancing cattle functional genomics, sustainable breeding, and studies of regulatory evolution.