Spatiotemporal Regulation of Circular RNA Expression During Ningxiang Pig Skeletal Muscle, Subcutaneous Fat, and Liver Development

Abstract

Background: In recent years, thousands of different circular RNA (circRNAs) have been discovered by comparative analysis of different pig breeds. However, very few studies have been conducted on the spatiotemporal expression pattern of circRNA during organ development which is crucial for functional and evolutionary analysis.Results: Here, we systematically analyzed circRNAs associated with fatty acid metabolism in the three main organs (muscle, fat and liver) for four growth time points (30d, 90d, 150d and 210d after birth) of Ningxiang pigs, a famous native pig breeds in China, known for its excellent meat quality. We identified 61,683 circRNAs and analyzed their molecular characteristics, potential functions, and interaction with miRNA. The circRNAs showed striking spatiotemporal specificity in the form of dynamic expression. At 90d, the number and complexity of differentially expressed circRNAs in the liver is the most obvious. We used STEM (Short Time Series Expression Miner) to perform time series analysis on differentially expressed circRNAs, and found that there are multiple model spectra that are significantly enriched with time changes in all the three organs. All the significantly changed circRNAs, miRNAs and mRNAs obtained from STEM analysis of each tissue were used to confirm that the circRNA and mRNA have a targeting relationship with miRNA. It is worth noting that we screened out 2384 (fat), 2672 (muscle) and 9187 (liver) circRNAs-miRNA-mRNA network pairs related to developmental time changes. Finally, we used fluorescence in situ hybridization（FISH）to show the dynamic subcellular localization of circRNA during development.Conclusion: To a certain extent, these data indicate that circRNA is highly abundant in muscle, fat and liver, and is dynamically expressed in a spatiotemporal manner. These results suggest that circRNAs play an important role in fat metabolism of Ningxiang pigs. Our findings also provide new ideas and perspectives for the study of Ningxiang pigs' lipid metabolism regulation pathway and meat quality traits.