Genome-wide identification and analysis of circular RNAs differentially expressed in the longissimus dorsi between Kazakh cattle and Xinjiang brown cattle

• Published in: PeerJ (San Francisco, CA) CA), 2020-03, Vol.8, p.e8646-e8646
• Main Authors: Yan, Xiang-Min, Zhang, Zhe, Meng, Yu, Li, Hong-Bo, Gao, Liang, Luo, Dan, Jiang, Hao, Gao, Yan, Yuan, Bao, Zhang, Jia-Bao
• Format: Article
• Language: English
• Subjects: Analysis; Beef cattle; Binding sites; Bioinformatics; Cattle; Cell Biology; CircRNA; Gene regulation; Genes; Genetics; Genomes; Genomics; Insulin; Kazakh cattle; Kinases; Longissimus muscle; Meat; MicroRNA; MicroRNAs; miRNA; Quality control; RNA; Software; Transcription; Transcription (Genetics); Xinjiang brown cattle
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.8646

Xinjiang brown cattle have better meat quality than Kazakh cattle. Circular RNAs (circRNAs) are a type of RNA that can participate in the regulation of gene transcription. Whether circRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed circRNAs regulate muscle formation and differentiation are still unknown. In this study, we established two RNA-seq libraries, each of which consisted of three samples. A total of 5,177 circRNAs were identified in longissimus dorsi samples from Kazakh cattle and Xinjiang brown cattle using the Illumina platform, 46 of which were differentially expressed. Fifty-five Gene Ontology terms were significantly enriched, and 12 Kyoto Encyclopedia of Genes and Genomes pathways were identified for the differentially expressed genes. Muscle biological processes were associated with the origin genes of the differentially expressed circRNAs. In addition, we randomly selected six overexpressed circRNAs and compared their levels in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle using RT-qPCR. Furthermore, we predicted 66 interactions among 65 circRNAs and 14 miRNAs using miRanda and established a coexpression network. A few microRNAs known for their involvement in myoblast regulation, such as miR-133b and miR-664a, were identified in this network. Notably, bta_circ_03789_1 and bta_circ_05453_1 are potential miRNA sponges that may regulate insulin-like growth factor 1 receptor expression. These findings provide an important reference for prospective investigations of the role of circRNA in longissimus muscle growth and development. This study provides a theoretical basis for targeting circRNAs to improve beef quality and taste.