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

Abstract

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 N6-methyladenosine (m6A) plays important roles in various biological processes, making it essential to profile m6A modification on a transcriptome-wide scale in developing muscle. Patterns of m6A methylation in lncRNAs in developing muscle have not been uncovered. Here, we reveal differentially expressed lncRNAs and report temporal m6A 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 m6A-lncRNAs harbor the consensus m6A motif “DRACH” along lncRNA transcripts. Interestingly, we found that m6A methylation levels of lncRNAs are positively correlated with the transcript abundance of lncRNAs. Overexpression or knockdown of m6A methyltransferase METTL3 alters the expression levels of these lncRNAs. Furthermore, we highlight that the function of m6A genic lncRNAs might correlate to their nearby mRNAs. Our work reveals a fundamental expression reference of m6A-mediated epitranscriptomic modifications in lncRNAs that are temporally expressed in developing muscle.

Novel insights into the interaction between N6‐methyladenosine methylation and noncoding RNAs in musculoskeletal disorders

“…The lncRNA Brip1os and m6A methyltransferase METTL3 are downregulated, whereas Brip1os near the mRNA Tbx2 is upregulated. METTL3 regulates skeletal muscle development by the METTL3/Brip1os/Tbx2 axis 171 . These studies showed that METTL3 regulates muscle‐specific ncRNAs via the post‐transcriptional level, playing an important role in skeletal muscle differentiation and development.…”

“…169,170 New evidence indicated that muscle-specific ncRNAs are regulated by m6A RNA modification at the post-transcriptional level. 30,171 ) repressing the expression level of miRNAs. 30 Overall, these studies revealed crosstalk between m6A and ncRNA during skeletal muscle differentiation and development, providing new insights into ncRNA m6A modification in skeletal muscle and MSD (Figure 3B and Table 1).…”

“…The functional regulation of ncRNA and m6A methylation in skeletal muscle development, differentiation and maintenance of muscle homoeostasis has been reported widely 169,170 . New evidence indicated that muscle‐specific ncRNAs are regulated by m6A RNA modification at the post‐transcriptional level 30,171 . Diao et al found that pri‐miRNA sequences are significantly enriched in conserved m6A modification motifs.…”

“… 169 , 170 New evidence indicated that muscle‐specific ncRNAs are regulated by m6A RNA modification at the post‐transcriptional level. 30 , 171 Diao et al found that pri‐miRNA sequences are significantly enriched in conserved m6A modification motifs. The m6A writer METTL3 is overexpressed in muscle injury and regeneration mouse model, whereas muscle‐specific miRNAs miR‐1a, miR‐133a, miR‐133b and miR‐206 are downregulated.…”

Regulatory role of RNA N6-methyladenosine modifications during skeletal muscle development

“…Recent studies have found that during myogenesis, m 6 A methylation levels of lncRNA are positively correlated with the transcriptional abundance of lncRNA, and m 6 A methylation modifies lncRNA to positively or negatively regulate its adjacent mRNA. Functional verification showed that METTL3-mediated m 6 A-lncRNA Brip1os is involved in muscle differentiation by negatively regulating the expression of Tbx2 mRNA (Xie et al, 2021b), revealing a novel mechanism of post-transcriptional regulation during skeletal muscle development.…”