Background
In recent years, thousands of different circular RNAs (circRNAs) have been identified through comparative analysis of different pig breeds. However, very few studies have investigated the spatiotemporal expression patterns of circRNA during organ development, which is crucial for functional and evolutionary analysis.
Results
In this study, we systematically analyzed circRNAs associated with fatty acid metabolism in the three main organs (muscle, fat and liver) a tfour growth time points (30 d, 90 d, 150 d and 210 d after birth) for Ningxiang pigs, awell-known native pig breed in China known for its excellent meat quality. We identified 61,683 circRNAs and analyzed their molecular characteristics, potential functions, and interactions with miRNAs. The circRNAs exhibited notable spatiotemporal specificity in the form of dynamic expression. At 90 d, the number and complexity of differentially expressed circRNAs in the liver was the highest.We used STEM (Short Time-series Expression Miner) to perform time series analysis on differentially expressed circRNAs and observed that there were multiple model spectra that were significantly enriched with time changes in all three organs. All the significantly changed circRNAs, miRNAs and mRNAs obtained from STEM analysis of each tissue were utilized to confirm that the circRNA and mRNA have a targeting relationship with miRNA. Notably, we screened 2384 (fat), 2672 (muscle) and 9187 (liver) circRNA-miRNA-mRNA network pairs related to developmental time changes. Finally, we used fluorescence in situ hybridization (FISH) to demonstrate the dynamic subcellular localization of circRNA during development.
Conclusion
These data suggest that circRNA is highly abundant in muscle, fat and liver and is dynamically expressed in a spatiotemporal manner. These results suggest that circRNAs play important roles in fat metabolism in Ningxiang pigs. Our findings also provide new ideas and perspectives for the study of Ningxiang pigs' lipid metabolism regulation pathway and meat quality traits.