Integrated analysis of miRNA-mediated ceRNA networks in ovine skeletal muscle development

Abstract

Background: The embryo stage is a key period for sheep skeletal muscle growth and development. Proliferation, differentiation, and hypertrophy of fibers affect muscle growth potential directly. Analyzing transcriptome data is of great significance for revealing important time nodes of fetus muscle development and screening related regulation factors. Muscle development is a complex biological process, including a intricate network of multiple factor interactions. Among them, non-coding RNA, especially miRNA-mediated regulation, plays a fine regulatory role. The purpose of this study was to investigate the important genes and transcripts involved in the genetic mechanism of embryos skeletal muscle development in late pregnancy. Results: Herein we did a small RNA sequencing(RNA-Seq) of embryo at 85 days (D85N), 105 days (D105N) and 135 days(D135N), then performed bioinformatic analysis in order to identify the miRNA-mediated co-expression networks. Our findings identified 505 DE-miRNAs. Integrating the current miRNA data and the previously obtained lncRNA data, multiple networks were constructed, including miRNA-mRNA, miRNA-target gene(TG)-pathway, lncRNA-miRNA-mRNA, and miRNA-TG-transcription factor (TF) network. The results showed that the miRNA-mRNA network and lncRNA-miRNA-mRNA network identified three important lncRNAs (MSTRG.3533, MSTRG.4324, and MSTRG.1470) and three miRNAs(miR-493-3p, miR-3959-3p and miR-410-5p). The four genes ( TEAD1 , ZBTB34 , GSK3B, and POGLUT1 ) and three transcription factors (C / EBPbeta, TFIID, and PR B) play a key regulatory role in the miRNA-TG-TF network. Notably, a similar trend of gene expression was reported by RT-qPCR for RNA-seq data. Conclusions: This study identified three miRNAs, three lncRNAs, four genes, and three transcription factors, and revealed their crucial role in fetal fibrogenesis and lipid metabolism. It also shows that D105N is a pivotal turning point from myotube differentiation to fiber hypertrophy. These findings provide valuable references for network interaction patterns, which helps to evaluate the biological significance of skeletal muscle in the late development stage.

Genome‐wide association studies of preweaning growth and in vivo carcass composition traits in Esme sheep

“…However, its evident role in MAPK signalling pathway nominates the gene as a promising candidate among others (Kucharska et al., 2009). Moreover, the roles of TEAD1 , which is also associated with WW and ADG, in the regulation of growth and development of mammalians by mediating Hippo signalling pathway and specifically on skeletal muscle physiology, hypertrophy, regeneration and embryonic muscle fibre differentiation were well‐established in various species including mice, poultry, pigs and sheep (Joshi et al., 2017; Qiu et al., 2011; Shi et al., 2020). On the other hand, especially those significant SNPs related to SMOX , PTPRT and RALYL genes were each intron variants lying within the genes themselves.…”

Study of microRNA Expression Profile in Different Regions of Ram Epididymis

“…Recent studies have reported that miR-3959-3p plays a major role in foetal fibrogenesis and lipid metabolism (Tianpei Shi et al 2020). miR-487a-3p has been reported to be related to human diseases, including in human Type 1 diabetes (Zurawek et al, 2018), prostate cancer (Wang et al, 2020), pancreatic cancer (Zhou et al, 2020) and kidney cancer (Huang et al, 2019); however, little is known about its role in the reproductive process.…”

Identification of Key Genes and Biological Pathways Associated with Skeletal Muscle Maturation and Hypertrophy in Bos taurus, Ovis aries, and Sus scrofa

“…The fundamental mechanism underlying livestock growth is the accumulation of muscle and adipose tissue [ 2 ]. Being the largest tissue in the body, skeletal muscle represents one of the most important complexes of biologically active tissues in mammals [ 3 ]. Elucidating the mechanism(s) of muscle growth and the intrinsic properties of the muscle may provide information that allows improvements in the quality of meat in production [ 4 ].…”

“…Analysis of transcriptomic data is a tool of great importance that allows identification of the key differentially expressed genes (DEGs) at each time point of the fetal and postnatal muscle development and to investigate the associated regulatory factors [ 3 ]. A complex gene network regulates the quality of meat and carcass [ 10 ].…”