Construction of circRNA-related ceRNA networks in longissimus dorsi muscle of Queshan Black and Large White pigs

• Published in: Molecular genetics and genomics : MGG 2022, Vol.297 (1), p.101-112
• Main Authors: Qi, Kunlong, Liu, Yingke, Li, Chenlei, Li, Xinjian, Li, Xiuling, Wang, Kejun, Qiao, Ruimin, Han, Xuelei
• Format: Article
• Language: English
• Subjects: Animal Genetics and Genomics; Animals; Back Muscles - metabolism; Binding, Competitive; Biochemistry; Biomedical and Life Sciences; Cell differentiation; Cell proliferation; Circular RNA; Computational Biology - methods; Exons; Gene Expression Regulation; Gene regulation; Gene Regulatory Networks; Hogs; Human Genetics; Life Sciences; Meat; Meat quality; Microbial Genetics and Genomics; miRNA; Molecular modelling; Muscle contraction; Muscle, Skeletal - metabolism; Musculoskeletal system; Myoblasts; Original Article; Plant Genetics and Genomics; Pork; Pork Meat; RNA, Circular - genetics; RNA, Long Noncoding - genetics; RNA, Small Interfering - genetics; RNA, Small Interfering - metabolism; RNA-Seq; Signal transduction; Skeletal muscle; Species Specificity; Swine - genetics; Swine - metabolism; Transcriptome; Transcriptomes; Wnt protein
• ISSN: 1617-4615; 1617-4623
• DOI: 10.1007/s00438-021-01836-4

Circular RNA (circRNA) is a class of non-coding RNA (ncRNA) that plays an important regulatory role in various biological processes of the organisms and has a major function in muscle growth and development. However, its molecular mechanisms of how it regulates pork quality remain unclear at present. In this study, we compared the longissimus dorsi (LD) muscle expression profiles of Queshan Black (QS) and Large White (LW) pigs to explore the role of circRNAs in meat quality using transcriptome sequencing. A total of 62 differentially expressed circRNAs (DECs), including 46 up- and 16 down-regulated, 39 differentially expressed miRNAs (DEmiRNAs), including 21 up- and 18 down-regulated and 404 differentially expressed mRNAs (DEMs), including 174 up- and 230 down-regulated were identified, and most circRNAs were composed of exons. Our results indicated that the DEC parent genes and DEMs were enriched in the positive regulation of fast-twitch skeletal muscle fiber contraction, relaxation of skeletal muscle, regulation of myoblast proliferation, AMPK signaling pathway, Wnt and Jak-STAT signaling pathway. Furthermore, circSETBP1/ssc-miR-149/ PIK3CD and circGUCY2C/ssc-miR-425-3p/ CFL1 were selected by constructing the competitive endogenous RNA (ceRNA) regulatory network, circSETBP1, circGUCY2C, PIK3CD and CFL1 had low expression level in QS, while ssc-miR-149 and ssc-miR-425-3p had higher expression level than LW, our analysis revealed that circSETBP1, circGUCY2C, ssc-miR-149, ssc-miR-425-3p, PIK3CD and CFL1 were associated with lipid regulation, cell proliferation and differentiation, so the two ceRNAs regulatory networks may play an important role in regulating intramuscular fat (IMF) deposition, thereby affecting pork quality. In conclusion, we described the gene regulation by the circRNA–miRNA–mRNA ceRNA networks by comparing QS and LW pigs LD muscle transcriptome, and the two new circRNA-associated ceRNA regulatory networks that could help to elucidate the formation mechanism of pork quality. The results provide a theoretical basis for further understanding the genetic mechanism of meat quality formation.