Spatiotemporal Regulation of Circular RNA Expression during Liver Development of Chinese Indigenous Ningxiang Pigs

Background: There have been many studies on the relationship between circRNAs and fat deposition. Although the liver is a central organ for fat metabolism, there are few reports on the relationship between circRNAs in the liver and fat deposition. Methods: In this study, we systematically analyzed circular RNAs in the liver of Ningxiang pigs, at four time points after birth (30 days, 90 days, 150 days and 210 days). Results: A total of 3705 circRNAs were coexpressed in four time periods were found, and KEGG analysis showed that the significantly upregulated pathways were mainly enriched in lipid metabolism and amino acid metabolism, while significantly downregulated pathways were mainly related to signal transduction, such as ECM–receptor interaction, MAPK signaling pathway, etc. Short time-series expression miner (STEM) analysis showed multiple model spectra that were significantly enriched over time in the liver. By constructing a competing endogenous RNA (ceRNA) regulatory network, 9187 pairs of networks related to the change in development time were screened. Conclusions: The expression profiles of circRNAs in Ningxiang pig liver were revealed at different development periods, and it was determined that there is differential coexpression. Through enrichment analysis of these circRNAs, it was revealed that host genes were involved in metabolism-related signaling pathways and fatty acid anabolism. Through STEM analysis, many circRNAs involved in fat metabolism, transport, and deposition pathways were screened, and the first circRNA–miRNA–mRNA regulation network map in Ningxiang pig liver was constructed. The highly expressed circRNAs related to fat deposition were verified and were consistent with RNA-Seq results.