N⁶-Methyladenosine RNA Modification Regulates the Differential Muscle Development in Large White and Ningxiang Pigs

N6-methyladenosine (m⁶A) is the most common modification in eukaryotic RNAs. Growing research indicates that m⁶A methylation is crucial for a multitude of biological processes. However, research on the m⁶A modifications in the regulation of porcine muscle growth is lacking. In this study, we identified differentially expressed genes in the neonatal period of muscle development between Large White (LW) and NingXiang (NX) pigs and further reported m⁶A methylation patterns via MeRIP-seq. We found that m⁶A modification regulates muscle cell development, myofibrils, cell cycle, and phosphatase regulator activity during the neonatal phase of muscle development. Interestingly, differentially expressed genes in LW and NX pigs were mainly enriched in pathways involved in protein synthesis. Furthermore, we performed a conjoint analysis of MeRIP-seq and RNA-seq data and identified 27 differentially expressed and m⁶A-modified genes. Notably, a typical muscle-specific envelope transmembrane protein, WFS1, was differentially regulated by m⁶A modifications in LW and NX pigs. We further revealed that the m⁶A modification accelerated the degradation of WFS1 in a YTHDF2-dependent manner. Noteworthy, we identified a single nucleotide polymorphism (C21551T) within the last exon of WFS1 that resulted in variable m⁶A methylation, contributing to the differing WFS1 expression levels observed in LW and NX pigs. Our study conducted a comprehensive analysis of the m⁶A modification on NX and LW pigs during the neonatal period of muscle development, and elucidated the mechanism by which m⁶A regulates the differential expression of WFS1 in the two breeds.