Comprehensive characterization of lncRNA N6-methyladenosine modification dynamics throughout bovine skeletal muscle development

Abstract

N6-methyladenosine (m6A) methylation is a key epigenetic modification that can modulate gene expression and strongly affect mammalian developmental processes. However, the genome-wide methylation of long non-coding RNAs (lncRNAs) and its implications for the development of skeletal muscle remain poorly understood. Bovine skeletal muscle samples from five developmental stages were analyzed in this study to establish lncRNA methylome and transcriptomic maps. Globally, 59.67% of lncRNAs in skeletal muscle with m6A modifications, and this percentage decreased progressively during development. lncRNA expression levels were positively associated with the number of m6A peaks, with lncRNAs possessing 3 or more peaks showing significantly higher expression levels than those with 1 or 2 peaks. Specific lncRNAs involved in skeletal muscle development were identified through two analytical approaches. The first approach employed weighted gene co-expression network analysis (WGCNA) of transcriptomic data to identify correlations between annotated lncRNAs and growth-related traits, resulting in 21 candidate hub lncRNAs. The intersection of these 21 hub lncRNAs with 151 differentially methylated lncRNAs (DM-lncRNAs) identified 10 shared candidate lncRNAs. The second approach integrated MeRIP-seq and RNA-seq data to identify 36 lncRNAs that were both differentially m6A modified and differentially expressed (dme-lncRNAs). GO and KEGG enrichment analyses of cis-target genes associated with these dme-lncRNAs identified eight candidate lncRNAs. Combining the results from the two approaches identified 16 key m6A-modified lncRNAs likely involved in skeletal muscle development. These findings highlight the regulatory and functional significance of dynamic lncRNA methylation in skeletal muscle development.