Genome-Wide Analysis of Circular RNAs Mediated ceRNA Regulation in Porcine Embryonic Muscle Development.

Linjun Hong,Dewu Liu,Ting Gu,Sixiu Huang,Zheng Xu,Yanjuan He,Zhenfang Wu,Xingwang Wang,Gengyuan Cai,Zicong Li,Jie Yang,Huaqiang Yang,Qun Hu,Chen Zhou,Enqin Zheng

doi:10.3389/fcell.2019.00289

Abstract

Many circular RNAs (circRNAs) have been discovered in various tissues and cell types in pig. However, the temporal expression pattern of circRNAs during porcine embryonic muscle development remains unclear. Here, we present a panorama view of circRNA expression in embryonic muscle development at 33-, 65-, and 90-days post-coitus (dpc) from Duroc pigs. An unbiased analysis reveals that more than 5,000 circRNAs specifically express in embryonic muscle development. The amount and complexity of circRNA expression is most pronounced in skeletal muscle at day 33 of gestation. Our circRNAs annotation analyses show that “hot-spot” genes produce multiple circRNA isoforms and RNA binding protein (RBPs) may regulate the biogenesis of circRNAs. Furthermore, we observed that host genes of differentially expressed circRNA across porcine muscle development are enriched in skeletal muscle function. A competing endogenous RNA (ceRNA) network analysis of circRNAs reveals that circRNAs regulate muscle gene expression by functioning as miRNA sponges. Finally, our experimental validation demonstrated that circTUT7 regulate the expression of HMG20B in a ceRNA mechanism. Our analyses show that circRNAs are dynamically expressed and interacting with muscle genes through ceRNA manner, suggesting their critical functions in embryonic skeletal muscle development.

Highlights

Pork is one of the most important source of meat in the world, which accounts for nearly 40% of all meat consumed and closely related to human health (Wang et al, 2015; Sun et al, 2018)
We found that 5,528 circRNAs is expressed explicitly in our dataset, suggesting RNase R + RNA-seq can provide a comprehensive view of circRNAs during embryonic muscle development (Figure 1B)
We found that a high percentage of circRNAs is expressed on day 33 of gestations, indicating that their crucial functions in the initiation stage of skeletal muscle development (Figure 1C)

Summary

Introduction

Pork is one of the most important source of meat in the world, which accounts for nearly 40% of all meat consumed and closely related to human health (Wang et al, 2015; Sun et al, 2018). Lean meats are favorite amongst people following low-fat diets and low calorie (Sun et al, 2018). Skeletal muscle is the major component of lean meat. The study of the mechanism underlying skeletal muscle development is beneficial to genetic improvement for lean meat quality and quantity. The most critical goal of meat production science is analyzing and understanding of the development of porcine skeletal muscle.

Methods

Results

Conclusion