The role of NUDT3 in skeletal myogenesis and the association of its genetic variants with carcass traits in pigs

Skeletal muscle underpins human locomotion and metabolic homeostasis, while pork is an important source of dietary protein. Genome-wide association studies revealed that NUDT3 (Nudix-type hydrolase 3) was strongly associated with lean mass in human (Homo sapiens) and pigs (Sus scrofa), whereas the roles of NUDT3 on skeletal muscle development and growth remain unclear. This study showed that reduced NUDT3 by siRNA in vitro significantly arrested the cell cycle, indicated by an elevated ratio of cells at the G1 stage and decreased EdU+ cells in porcine muscle satellite cells (PMSCs). Besides, knockdown of NUDT3 significantly inhibited myogenic differentiation, and NUDT3 overexpression yielded the opposite effects. In vivo, enforced expression of NUDT3 in Tibialis anterior (TA) of mice (Mus musculus) significantly increased the population of Pax7+ and eMyHC+ cells upon cardiotoxin-induced injury, thus facilitating regenerative myogenesis. Mechanistically, RNA-seq revealed that NUDT3 significantly repressed NF-κB signaling activity in a Nudix motif-dependent way, thus accelerating skeletal myogenesis. Furthermore, eight SNPs significantly associated with NUDT3 expression in porcine muscles have been identified through co-localization of GWAS and eQTL signals, four of which were located in the conserved E6 and E7 enhancers of NUDT3, as indicated by HiCuT (H3K27ac) and CRISPRi system. In particular, rs327612517 in E7, significantly associated with loin muscle area and loin muscle depth (PigBiobank), significantly affected the E7 enhancer activity, as suggested by dual-luciferase reporter assay and EMSA. Collectively, our findings have established NUDT3 as a novel and positive modulator of skeletal myogenesis and demonstrated rs327612517 as a candidate SNP in improvement of lean yield in pigs.