Comprehensive Analysis of Long Noncoding RNA Modified by m(6)A Methylation in Oxidative and Glycolytic Skeletal Muscles

N(6)-methyladenosine (m(6)A) is the most common modification in eukaryotic RNAs. Accumulating evidence shows m(6)A methylation plays vital roles in various biological processes, including muscle and fat differentiation. However, there is a lack of research on lncRNAs’ m(6)A modification in regulating pig muscle-fiber-type conversion. In this study, we identified novel and differentially expressed lncRNAs in oxidative and glycolytic skeletal muscles through RNA-seq, and further reported the m(6)A-methylation patterns of lncRNAs via MeRIP-seq. We found that most lncRNAs have one m(6)A peak, and the m(6)A peaks were preferentially enriched in the last exon of the lncRNAs. Interestingly, we found that lncRNAs’ m(6)A levels were positively correlated with their expression homeostasis and levels. Furthermore, we performed conjoint analysis of MeRIP-seq and RNA-seq data and obtained 305 differentially expressed and differentially m(6)A-modified lncRNAs (dme-lncRNAs). Through QTL enrichment analysis of dme-lncRNAs and PPI analysis for their cis-genes, we finally identified seven key m(6)A-modified lncRNAs that may play a potential role in muscle-fiber-type conversion. Notably, inhibition of one of the key lncRNAs, MSTRG.14200.1, delayed satellite cell differentiation and stimulated fast-to-slow muscle-fiber conversion. Our study comprehensively analyzed m(6)A modifications on lncRNAs in oxidative and glycolytic skeletal muscles and provided new targets for the study of pig muscle-fiber-type conversion.