71 / 2026-04-05 13:57:41

Dynamic profiling of the 3D genome for developmental porcine skeletal muscle

Pigs, skeletal muscle, 3D genome, ChIA-PET, growth and development

Skeletal muscle is an important tissue affecting growth rate, carcass composition, meat quality, and economic traits in pigs, yet the dynamic changes in 3D chromatin interaction networks during its development remain poorly understood. In this study, we optimized the ChIA-PET method and constructed H3K27ac ChIA-PET libraries of pig skeletal muscle at eight developmental stages, including E45, E60, E75, E100, D0, D30, D80, and D160, with three biological replicates per stage. Combined with RNA-seq and WGBS data, we systematically characterized the dynamic features of the 3D genome during growth and development of skeletal muscle.

The results demonstrated that the ChIA-PET libraries at all stages maintained stable quality and high reproducibility. The 3D reconstruction, aggregate peak analysis, and contact map consistently indicated that the 3D genome of skeletal muscle gradually shifted from a relatively loose and plastic state during the embryonic stage to a more compact, localized, and stable state after birth, while maintaining a relatively stable overall chromosomal framework. Functional analysis of differential loops showed a gradual transition from early cell proliferation to later muscle structural formation, muscle contraction, and lipid metabolism. Validation at the MYOG locus using 3C-qPCR further confirmed the reliability of the interactions identified by ChIA-PET. Multi-omics analysis demonstrated that RNA-seq, WGBS, and ChIA-PET generally exhibited consistency in sample clustering and developmental stage stratification, while changes in individual pathways showed only weak positive correlations with gene expression alterations.

In summary, we generated a dynamic 3D genome map of porcine developmental skeletal muscle, and revealed a gradual transition of the 3D genome from a loose to an ordered state and from a plastic to a stable state. These findings provided a theoretical basis for understanding the spatial regulatory mechanisms underlying skeletal muscle growth and development and meat quality formation.