Identification of circRNA-associated ceRNA networks using longissimus thoracis of pigs of different breeds and growth stages

Abstract

Background Long-term artificial selection for growth rate and lean meat rate has eventually led to meat quality deterioration. Muscle fiber type is a key factor that markedly affects meat quality. circRNAs have been reported to participate in diverse biological activities, including myofiber growth and development; thus, we herein compared porcine circRNA transcriptome between oxidative and glycolytic muscle tissues. Results Longissimus thoracis muscle tissues were obtained from Lantang and Landrace pigs at birth (LT1D and LW1D, respectively) and 90 postnatal days (LT90D and LW90D, respectively). Hematoxylin and eosin staining and quantitative real-time PCR revealed that all structural traits of the muscle showed large variations between different breeds and growth stages. In total, 329 known miRNAs and 42,081 transcript candidates were identified; 6,962 differentially expressed transcripts were found to play a key role in myogenesis by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. In addition, 3,352 circRNAs were identified using five predicting algorithms, and 104 circRNA candidates were differentially expressed. Integrated analysis of differentially expressed miRNAs, mRNAs, and circRNAs led to the identification of 777, 855, and 22 convincing ceRNA interactions in LT1D vs. LT90D, LW1D vs. LW90D, and LT90D vs. LW90D, respectively. Finally, we identified a circRNA candidate circKANSL1L, which showed high homology between mice and pigs, and it was found to inhibit the proliferation of C2C12 cells but promote their differentiation. Conclusions We identified genome-wide circRNAs in 0- and 90-day-old Lantang and Landrace pigs by RNA-seq and found that circRNAs were abundant, differentially expressed, and associated with myogenesis. Our results should serve as a reference for future studies on pork quality.

Expression profile and bioinformatics analysis of circRNA and its associated ceRNA networks in longissimus dorsi from Lufeng cattle and Leiqiong cattle

“…Among the factors, circRNA as a ncRNA has received considerable attention for its wide range of regulatory functions. circRNAs are dynamically expressed and abundant in muscle tissue of many species, including humans, cattle, goat, pig, chicken, and mice [ 9 ]. Although the functions of circRNAs remain largely unexplored, they can serve as miRNA sponges and further contribute to mRNA stability or protein production [ 34 ].…”

“…Beef myofibers can affect the traits to a certain extent, such as tenderness, color, and pH drop of beef [ 8 ]. Thus, among the factors that can affect meat quality, myofiber is the strongest [ 9 , 10 ]. However, the growth and development of muscle fibers include ontogeny at different embryonic stages, as well as hypertrophy and transformation at postnatal stages [ 9 , 11 ].…”

“…Thus, among the factors that can affect meat quality, myofiber is the strongest [ 9 , 10 ]. However, the growth and development of muscle fibers include ontogeny at different embryonic stages, as well as hypertrophy and transformation at postnatal stages [ 9 , 11 ]. In addition, the process of myogenesis is a complex biological process regulated by multiple factors, such as myogenic regulatory factors [ 12 ], signaling pathways [ 13 ], noncoding RNAs (ncRNAs) [ 14 ], and genes.…”

CircRNA Identification and CircRNA–miRNA–mRNA Network in Cynoglossus semilaevis Sexual Size Dimorphism

“…Chinese tongue soles have a female heterogametic (WZ female, ZZ male) sex chromosome system and show obviously female-biased SSD [ 15 ]. As an important regulator for gene expression [ 53 ], circRNAs have been identified to be implicated in myogenesis, skeletal muscle and fat tissue growth, follicle development, and sperm motility [ 54 , 55 , 56 , 57 ]. Herein, we identified the different expression abundances of circRNAs in males, females, and pseudo males to examine the potential roles of circRNAs in C. semilaevis SSD.…”

Integrated analysis of circRNA, lncRNA, miRNA and mRNA to reveal the ceRNA regulatory network of postnatal skeletal muscle development in Ningxiang pig

“…Landrace pigs 1 and 90 days after birth by high-throughput sequencing (Zhuang et al, 2022). Li et al reported the expression of circRNA in skeletal muscle of Mashen pig and Yorkshire pig in three stages after birth, and explored the molecular mechanism of muscle development (Li M. et al, 2021).…”