Integrative analysis of CUT&Tag-seq and RNA-seq reveals widespread H3K27ac upregulation associated with the activation of muscle-growth-related transcriptional programs in broiler breast muscle.

Broilers have developed pronounced features of metabolizable energy intake and rapid growth during long-term selection, yet whether their epigenetic landscape has undergone systematic alterations remains unclear. In this study, using transcriptome and H3K27ac CUT&Tag data from White-feathered broilers and Wenchang chickens, we found that intensive selection profoundly remodeled the genome-wide H3K27ac landscape in broiler breast muscle. At equal body weight, broilers exhibited higher feed consumption and metabolizable energy intake than Wenchang chickens, suggesting a superior capacity to utilize energy for muscle synthesis. PCA of H3K27ac CUT&Tag data from 7-day-old breast muscle revealed a clear separation between the two breeds, with broilers showing globally elevated H3K27ac levels; the number of upregulated peaks was 16.37-fold higher than downregulated peaks. Genes near differential peaks were enriched in muscle growth signaling pathways such as mTOR, MAPK, and TGF-β, and showed significant enrichment of MEF2B and SIX1 binding motifs. Transcriptome analysis further indicated that lipid metabolism and muscle development pathways were activated in broilers, whereas cell-cycle and DNA-repair pathways were downregulated, suggesting energy metabolism is biased toward protein synthesis. Among differential H3K27ac regions, 459 genes were differentially expressed, and 82.1% showed consistent directions of H3K27ac and mRNA changes, indicating that elevated H3K27ac substantially promotes transcriptional activation of muscle-related genes. Broilers also exhibited significantly higher acetyl-CoA concentrations in breast muscle (1.46-fold), while acetyltransferase and deacetylase expression remained unchanged, implying that the elevated histone acetylation is primarily driven by increased substrate (acetyl-CoA). Together, these results suggest a potential mechanism where enhanced metabolizable energy intake and metabolism in broilers leads to acetyl-CoA accumulation, which may in turn promote H3K27ac deposition and activate muscle-growth pathways for efficient energy-to-muscle conversion. This study reveals widespread H3K27ac upregulation associated with the activation of muscle-growth-related transcriptional programs in broiler breast muscle, suggests a potential regulatory axis linking metabolism, epigenetics, transcription, and muscle growth, and highlights that epigenetic modifications can undergo coordinated shifts during animal breeding, providing new insights into the mechanisms underlying genetic improvement (Fig. 1).