Identification of circRNAs related to adipose and skeletal muscle growth and development in the pig

Skeletal muscle development and adipose tissue deposition are central determinants of growth performance, carcass composition, and metabolic health in pigs. Understanding the regulatory networks that govern these processes is essential for improving livestock productivity and meat quality. Circular RNAs (circRNAs), a class of covalently closed non-coding RNAs, that exhibit high stability, tissue- and stage-specific expression and have been reported to exert regulatory functions in mammals such as humans and mice, as well as in other model organisms. However, their roles in porcine muscle growth and fat deposition, and their evolutionary conservation, remain poorly understood. This thesis integrates large-scale transcriptomic profiling and functional assays to characterise circRNA expression patterns, regulatory functions, and genetic associations with fat deposition and muscle development in pigs and mice. In subcutaneous adipose tissue, circRNA expression was profiled in Landrace (lean-type) and Songliao Black (obese-type) pigs with contrasting backfat thickness. A total of 883 circRNAs were identified, of which 26 were differentially expressed circRNAs (DECs) between breeds and a further 11 DECs between high- and low-backfat groups. Predicted circRN-miRNA-mRNA interaction networks highlighted sus_CCL3L1_0001 and sus-intergenic_001702 as candidates associated with adipogenesis. The target genes of these circRNAs were enriched in fatty acid biosynthesis, adipose metabolism, and Wnt/TGF-β signalling pathways, supporting their potential regulatory roles in adipose tissue development and energy homeostasis. Expanding beyond targeted adipose tissue analysis, 3,700 porcine RNA-seq datasets spanning 23 tissues, multiple breeds and developmental stages were integrated to construct a comprehensive circRNA expression atlas comprising 150,963 high-confidence circRNAs. Analysis of 246 deeply sequenced samples from adipose, skeletal muscle, liver, hypothalamus, and pituitary tissues across Meishan, Wuzhishan, Tibetan, and Yorkshire pigs identified 5,239 tissue-specific circRNAs, including 316 adipose-specific candidates. Notably, circOXR1 displayed transient postnatal activation in Meishan pigs and was shown to modulate adipocyte differentiation and lipid accumulation, whereas circME1 was consistently upregulated in Meishan relative to Yorkshire pigs, highlighting its potential role in breed-specific regulation of adipose metabolism. Time-series transcriptome profiling across 27 developmental stages in Tongcheng (obese-type) and Landrace (lean-type) pigs identified circUBE3A as a central regulator of skeletal muscle development. CircUBE3A was validated to promote myoblast proliferation while suppressing differentiation, underscoring its potential role in breed-specific muscle growth patterns. A comparison of porcine (D0, D60, D160) and murine (D0, D20, D60) skeletal muscle transcriptomes identified 156 conserved circRNAs, many of which exhibit dynamic, stage-specific expression and enrichment in muscle-related signalling pathways, including apelin, glucagon, and cGMP-PKG pathways. Among them, circAGAP1 in pigs and its murine ortholog circAgap1 were both predicted to regulate GADD45GIP1/Gadd45gip1 through distinct sets of microRNAs (miRNAs), indicating conserved regulatory output achieved via species-specific competing endogenous RNA (ceRNA) interactions.