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Proper development of mammalian skeletal muscle relies on precise gene expression regulation. Our previous studies revealed that muscle development is regulated by both mRNA and long non-coding RNAs (lncRNAs). Accumulating evidence has demonstrated that N 6 -methyladenosine (m 6 A) plays important roles in various biological processes, making it essential to profile m 6 A modification on a transcriptome-wide scale in developing muscle. Patterns of m 6 A methylation in lncRNAs in developing muscle have not been uncovered. Here, we reveal differentially expressed lncRNAs and report temporal m 6 A methylation patterns in lncRNAs expressed in mouse myoblasts and myotubes by RNA-seq and methylated RNA immunoprecipitation (MeRIP) sequencing. Many lncRNAs exhibit temporal differential expression, and m 6 A-lncRNAs harbor the consensus m 6 A motif “DRACH” along lncRNA transcripts. Interestingly, we found that m 6 A methylation levels of lncRNAs are positively correlated with the transcript abundance of lncRNAs. Overexpression or knockdown of m 6 A methyltransferase METTL3 alters the expression levels of these lncRNAs. Furthermore, we highlight that the function of m 6 A genic lncRNAs might correlate to their nearby mRNAs. Our work reveals a fundamental expression reference of m 6 A-mediated epitranscriptomic modifications in lncRNAs that are temporally expressed in developing muscle.

Characterization of Long Non-coding RNAs Modified by m6A RNA Methylation in Skeletal Myogenesis