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

Shu-Juan Xie,Pan-Long Li,Zhi-Gang Zhou,Qi Zhang,Ya-Rui Hou,Wei-Cai Chen,Yan-Wen Peng,Hang Lei,Wen-Jie Chen,Wan-Yi Xu,Li-Ting Diao,Yan-Xia Hu,Zhen-Dong Xiao,Shuang Tao

doi:10.3389/fcell.2021.762669

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.

Highlights

Skeletal muscle plays critical roles in the regulation of wider metabolism as well as driving locomotion (Cong et al, 2020)
RNA dot blotting was performed to investigate the dynamics of m6A RNA modification during myogenesis, and decreased global m6A levels were observed in myotubes that had been differentiated for 4 days (D4) compared to myoblasts (Figure 1A)
Our previously identified changes in gene expression and epigenetic modifications during skeletal muscle development have greatly improved our understanding of the mechanism related to myogenesis, including coding gene and non-coding RNA modifications m6A Modified long non-coding RNAs (lncRNAs) During Myogenesis (Diao et al, 2021a,b), mRNA expression (Tan et al, 2021), miRNA regulation (Xie et al, 2013, 2018), and lncRNA function (Liu et al, 2021)

Summary

Introduction

Skeletal muscle plays critical roles in the regulation of wider metabolism as well as driving locomotion (Cong et al, 2020). Myogenesis, the development of muscle, is a complex biological process regulated by multiple transcription factors and specific signaling pathways (BrysonRichardson and Currie, 2008; Bentzinger et al, 2012). Our previous studies showed that non-coding RNAs, including miRNAs and lncRNAs (long non-coding RNAs), play essential roles in skeletal muscle development (Xie et al, 2018; Liu et al, 2021; Tan et al, 2021). Numerous studies have shown that lncRNAs play a significant role in biological functions, such as epigenetic modification, mRNA transcription, splicing, stability and translation (Lan et al, 2021). LncRNA MALAT1 interacts with miRNAs or mRNAs to regulate skeletal muscle maintenance (Yong et al, 2020; Liu et al, 2021). Several lncRNAs have been reported to shape muscle (Ro et al, 2018; Sweta et al, 2019; Martone et al, 2020), including linc-MD1 (Cesana et al, 2011), lincYY1 (Lu et al, 2013; Zhou et al, 2015), lncRNA Dum (Wang et al, 2015), linc-RAM (Yu et al, 2017; Zhao et al, 2018), muscle-specific lncR-Irm (Sui et al, 2019), lncR-Myoparr (Hitachi et al, 2019), lnc-MyoD (Gong et al, 2015; Lim et al, 2020), and lncMGPF (Lv et al, 2020)

Methods

Results

Conclusion