Identification of long noncoding RNAs involved in muscle differentiation

Abstract

Long noncoding RNAs (lncRNAs) are a large class of regulatory RNAs with diverse roles in cellular processes. Thousands of lncRNAs have been discovered; however, their roles in the regulation of muscle differentiation are unclear because no comprehensive analysis of lncRNAs during this process has been performed. In the present study, by combining diverse RNA sequencing datasets obtained from public database, we discovered lncRNAs that could behave as regulators in the differentiation of smooth or skeletal muscle cells. These analyses confirmed the roles of previously reported lncRNAs in this process. Moreover, we discovered dozens of novel lncRNAs whose expression patterns suggested their possible involvement in the phenotypic switch of vascular smooth muscle cells. The comparison of lncRNA expression change suggested that many lncRNAs have common roles during the differentiation of smooth and skeletal muscles, while some lncRNAs may have opposite roles in this process. The expression change of lncRNAs was highly correlated with that of their neighboring genes, suggesting that they may function as cis-acting lncRNAs. Furthermore, within the lncRNA sequences, there were binding sites for miRNAs with expression levels inversely correlated with the expression of corresponding lncRNAs during differentiation, suggesting a possible role of these lncRNAs as competing endogenous RNAs. The lncRNAs identified in this study will be a useful resource for future studies of gene regulation during muscle differentiation.

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

“…Nevertheless, recent functional studies in mammals have found that lncRNAs serve as critical regulators in various biological processes by regulating gene expression at the epigenetic, transcription, and postttranscription levels. LncRNAs are widely involved in various important physiological and pathological processes, such as, cell differentiation, morphogenesis, gown, development and death, immunity responses, oncogenesis and cancer [4][5][6].…”

Identification of Long Noncoding RNAs Involved in Differentiation and Survival of Vascular Smooth Muscle Cells

“…Our previous study demonstrated that the expression of some lncRNAs may have a correlation between smooth and skeletal muscles. 21 Interestingly, our findings showed that NR2F1-AS1 , MSC-AS1 , MBNL1-AS1 , FOXC2-AS1 , and CTD-2207P18.2 are highly enriched in skeletal myoblasts as well as in vascular cells compared to other cell types, suggesting that they may have a role in skeletal muscle as well as smooth muscle ( Figures S3 and S4 ).…”

“…To select lncRNAs involved in the VSMC phenotype changes, we used a previously reported model for VSMC differentiation. 21 Most studies have used serum deprivation or growth factors such as TGF-β1 and PDGF to differentiate VSMCs. 8 , 9 , 22 Using a differentiation medium (DM) with reduced serum, we differentiated synthetic VSMCs to contractile VSMCs that are characterized by increased expression of differentiation markers such as ACTA2 , TAGLN , and CNN1 .…”

“…We selected 116 lncRNAs that were differentially expressed during VSMC differentiation based on several criteria (see Materials and Methods ). Finally, seven candidate lncRNAs ( NR2F1-AS1 , FUT8-AS1 , FOXC2-AS1 , CTD-2207P18.2 , MSC-AS1 , GAS6-AS2 , and MBNL1-AS1 ) were selected by combining our previously reported data on muscle differentiation-related lncRNAs 21 with the current RNA-seq results ( Figure 1 B). During the VSMC differentiation, the expression of NR2F1-AS1 , FUT8-AS1 , FOXC2-AS1 , and CTD-2207P18.2 was decreased, whereas the expression of MSC-AS1 , GAS6-AS2 , and MBNL1-AS1 was increased ( Figure 1 C).…”

“…Because we found that NR2F1-AS1 regulates the contractility of VSMCs by controlling the contraction markers ( Figures 3 and 4 ), it is expected that NR2F1-AS1 could operate through other mechanism, including as a miRNA sponge, as suggested in our previous study ( Figure S9 , right panel). 21 …”