Comprehensive Analysis of Long Noncoding RNA Modified by m6A Methylation in Oxidative and Glycolytic Skeletal Muscles

Abstract

N6-methyladenosine (m6A) is the most common modification in eukaryotic RNAs. Accumulating evidence shows m6A methylation plays vital roles in various biological processes, including muscle and fat differentiation. However, there is a lack of research on lncRNAs’ m6A 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 m6A-methylation patterns of lncRNAs via MeRIP-seq. We found that most lncRNAs have one m6A peak, and the m6A peaks were preferentially enriched in the last exon of the lncRNAs. Interestingly, we found that lncRNAs’ m6A 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 m6A-modified lncRNAs (dme-lncRNAs). Through QTL enrichment analysis of dme-lncRNAs and PPI analysis for their cis-genes, we finally identified seven key m6A-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 m6A modifications on lncRNAs in oxidative and glycolytic skeletal muscles and provided new targets for the study of pig muscle-fiber-type conversion.

Transcriptome-Wide Study of mRNAs and lncRNAs Modified by m6A RNA Methylation in the Longissimus Dorsi Muscle Development of Cattle-Yak

“…Thus, we reassembled the transcripts of all samples using MeRIP-seq and RNA-seq data and stream neural network algorithms in this study. Our study was the first evidence to identify the m 6 A-methylated lncRNAs dynamic alteration during Longissimus dorsi muscle development in cattle-yak, which results were consistent with the results of m 6 A-lncRNA in mice [ 40 ] and pigs [ 39 ]. Moreover, gene expression levels can be regulated by m 6 A modification, for example, METTL14 knockdown can enhance the expression level of XIST through decreasing the m 6 A modification of XIST , and m 6 A-methylated XIST can also be recognized by YTHDF2 to mediate XIST degradation [ 72 ].…”

“…In addition to the ubiquitous m 6 A modifications on mRNAs, m 6 A modifications on lncRNAs have also attracted more and more attention from researchers. Recent studies have revealed the promotion of m 6 A modification on lncRNA in the muscle development and muscle fiber type conversion [ 14 , 39 , 70 , 71 ], and some researchers reported the dynamic changes of m 6 A-methylated lncRNAs during skeletal muscle formation in mouse C2C12 myoblast cell line [ 40 ]. However, there was still no report about the m 6 A methylation characteristics of lncRNAs in the muscle development stage of cattle-yak.…”

“…Although m 6 A-modified lncRNAs have gradually attracted the attention of researchers, the distribution characteristic and biological function of m 6 A in ncRNAs and regulatory elements are still unclear. Wang et al described a m 6 A methylation profile of lncRNAs in porcine oxidized and glycolytic skeletal muscle, identifying seven m 6 A-modified lncRNAs that may play key roles in muscle fiber conversion [ 39 ]. In mouse C2C12 muscle cell lines, the methylation level of lncRNAs was positively correlated with the abundance of lncRNAs transcripts, and the m 6 A-modified lncRNA map was plotted at different growth periods [ 40 ].…”

Comprehensive analysis of pre-mRNA alternative splicing regulated by m6A methylation in pig oxidative and glycolytic skeletal muscles

“…Our previous study revealed the difference in phenotypic traits in SOL and EDL and evidenced that SOL and EDL are typical oxidative and glycolytic muscle tissues, respectively [ 31 ]. In the present study, the transcriptomes of EDL and SOL muscles were examined to reveal the landscape of AS changes across oxidative and glycolytic muscles.…”

“…Our previous study reported m6A methylome profiling of lncRNA in pig extensor digitorum longus (EDL) and soleus (SOL) muscles [ 31 ]. In the present study, we further integrated RNA-seq and methylated RNA immunoprecipitation sequencing (MeRIP-seq) for the comprehensive analysis of AS events and m6A methylation pattern.…”