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

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.

Profiling and Functional Analysis of Circular RNAs in Porcine Fast and Slow Muscles

“…Previous research has shown that circ-QKI and circ-BNC2 are upregulated during in vitro differentiation of control myoblasts, and downregulated in DMD conditions (Legnini et al, 2017). Many circRNAs have important biological functions by acting as microRNA or protein inhibitors ("sponges"), or are themselves translated during muscle development and growth (Legnini et al, 2017;Wei et al, 2017;Ouyang et al, 2018;Hong et al, 2019;Kristensen et al, 2019). CircLMO7, a circular RNA identified in bovine skeletal muscle at two developmental stages, was shown to regulate myoblast differentiation and survival by sponging miR-378a-3p (Wei et al, 2017).…”

Circular RNAs Are Regulators of Diverse Animal Transcriptomes: One Health Perspective

“…While Liang et al (2017) profiled circRNAs in the postnatal pork muscle tissue, Hong et al (2019) analyzed circRNA expression profiles during embryonic skeletal muscle development in Duroc pigs. Their analysis used RNAse R-enriched samples harvested at 33, 65, and 90 days before birth (Hong et al, 2019).…”

“…While Liang et al (2017) profiled circRNAs in the postnatal pork muscle tissue, Hong et al (2019) analyzed circRNA expression profiles during embryonic skeletal muscle development in Duroc pigs. Their analysis used RNAse R-enriched samples harvested at 33, 65, and 90 days before birth (Hong et al, 2019). Significantly fewer circRNAs were found to be expressed on day 90 when compared to the other two time points, an interesting find considering the main muscle fiber development in pigs occur at 33 and 65 days post-coitus, indicating circRNA may have crucial functions in the initiation stage of skeletal muscle development.…”

circ2GO: A Database Linking Circular RNAs to Gene Function

“…At the cellular level, circRNAs are important regulators in many cellular processes, such as cell signaling [ 13 ], embryonic development [ 14 ], cellular senescence [ 15 ], and control of the cell cycle [ 16 ]. They also play critical roles in the occurrence and development of various types of diseases [ 17 ], including cardiovascular diseases (e.g., atherosclerotic vascular disease risk [ 18 , 19 ]), neurological disorders (e.g., Alzheimer’s disease [ 20 , 21 ]), osteoarthritis [ 22 ], diabetes [ 23 ] and, most importantly, in cancer [ 24 , 25 ].…”