Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle

Myofibers (primary and secondary myofiber) are the basic structure of muscle and the determinant of muscle mass. To explore the skeletal muscle developmental processes from primary myofibers to secondary myofibers, we conducted an integrative 3 D structure of genome and transcriptomic characterization of longissimus dorsi muscle (LDM) of pig from primary myofiber formation stage [embryonic day 35 (E35)] to secondary myofiber formation stage (E80). In the hierarchical genomic structure, we found that 11.43% of genome switched compartment A/B status, 14.53% of topologically associating domains (TADs) are changed intra-domain interactions (D-scores) and 3,166 genes with differential promoter-enhancer interactions (PEIs) and (or) enhancer activity from E35 to E80. The alterations of genome architecture were found to affect expression of genes that play significant roles in neuromuscular junction (NMJ), embryonic morphogenesis, and skeletal muscle development or metabolism, typically NEFL, MuSK, SLN, Mef2D and GCK. Significantly, Sox6 and MATN2 play important roles in the process of primary to secondary myofibers form and increase the RPS and genes expression in it. In brief, we reveal the genomic reorganization from E35 to E80 and construct genome-wide high-resolution interaction maps that provide a resource for studying long-range control of gene expression from E35 to E80.