Identification of Candidate Circular RNAs Underlying Intramuscular Fat Content in the Donkey

Abstract

Intramuscular fat (IMF) content is a crucial indicator of meat quality. Circular RNAs (circRNAs) are a large class of endogenous RNAs that are involved in many physiological processes. However, the expression and function of circRNA in IMF in the donkey remains unresolved. Here we performed an expression profiling of circRNAs in the donkey longissimus dorsi muscle and identified 12,727 candidate circRNAs. Among these, 70% were derived from the exons of protein genes. Furthermore, a total of 127 differentially expressed (DE) circRNAs were identified in high (H) and low (L) IMF content groups, including 63 upregulated and 64 downregulated circRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the host genes of the DE circRNAs showed that the host genes were enriched in lipid metabolism related GO terms (e.g., fatty acid beta-oxidation using acyl-CoA dehydrogenase and MLL3/4 complex), and signaling pathways (e.g., TGF-beta and lysine degradation signaling pathway). Further analyses indicated that 127 DE circRNAs were predicted to potentially interact with miRNAs, leading to the construction of circRNA-miRNA regulatory network. Multiple circRNAs can potentially function as sponges of miRNAs that regulate the differentiation of adipocytes. Our results provide valuable expression profile information for circRNA in the donkey and new insight into the regulatory mechanisms of circRNAs in the regulation of IMF content.

Dynamic Expression and Regulatory Network of Circular RNA for Abdominal Preadipocytes Differentiation in Chicken (Gallus gallus)

“…Previous studies have demonstrated that circRNAs play crucial roles in lipid metabolism, including hepatocellular triglyceride accumulation and lipid peroxidation in humans ( Guo et al, 2017 ; Guo et al, 2018 ), adipocyte proliferation and differentiation in mammals and cattle ( Arcinas et al, 2019 ; Jiang et al, 2020 ), IMF deposition in yaks and donkeys ( Li et al, 2020a ; Wang H. et al, 2020 ), hepatic lipid biosynthesis in pigs ( Huang et al, 2018 ), and subcutaneous fat deposition in pigs and Chinese buffalo ( Li A. et al, 2018 ; Huang et al, 2019 ). Here, the parental genes of all identified circRNAs were mainly enriched in molecular binding, enzymatic activity, and development-related GO terms, indicating that chicken adipogenesis is a complex process that incorporates numerous events.…”

“…With regard to livestock and poultry, some circRNAs have also been identified by high throughput sequencing and confirmed to participate in regulating their important biological process, such as embryos development ( Veno et al, 2015 ), formation of skeletal muscle fiber ( Li et al, 2020b ), hepatic lipid metabolism ( Huang et al, 2018 ), and adipogenic differentiation ( Li A. et al, 2018 ) in pig; muscle growth and development ( Wei et al, 2017 ; Li et al, 2018b ; Li et al, 2018c ; Liu et al, 2020 ; Shen et al, 2020 ; Yue et al, 2020 ; Elnour et al, 2021 ), testis development ( Gao et al, 2018 ), adipogenesis ( Jiang et al, 2020 ) and milk fat content ( Chen et al, 2021 ) in cattle; fat deposition in buffalo and yak ( Huang et al, 2019 ; Wang H. et al, 2020 ); intramuscular fat (IMF) content denoting a crucial indicator of meat quality in donkey ( Li et al, 2020a ); follicular development ( Shen et al, 2019 ), Marek’s tumourigenesis ( Wang L. et al, 2020 ) as well as muscle growth development ( Ouyang et al, 2018a ; Ouyang et al, 2018b ) in chicken. And it has yet indicated some functional circRNAs related to lipid metabolism, for instance, circFUT10 could promote bovine preadipocyte proliferation but inhibit adipocyte differentiation ( Jiang et al, 2020 ); circRNA_26852 and circRNA_11897, might get involved in porcine adipocyte differentiation and lipid metabolism ( Li A. et al, 2018 ); circ11103 could increase the triglyceride levels in bovine mammary epithelial cells and the contents of unsaturated fatty acids ( Chen et al, 2021 ); additionally, 19:45387150|45389986 and 21:6969877|69753491, were deemed as potential modulators of buffalo back subcutaneous adipose deposition ( Huang et al, 2019 ).…”

Identification and Characterization of Circular RNAs in Association With the Deposition of Intramuscular Fat in Aohan Fine-Wool Sheep

“…Many studies have recently shown that circRNAs play an important role in IMF. Li et al found that circRNAs influenced IMF in Donkeys ( Li et al, 2020 ). Studies have also found that circRNA inhibits the differentiation of preadipocytes ( Shen et al, 2021 ).…”

DataSheet1.ZIP

“…Previous studies have demonstrated that circRNAs play crucial roles in lipid metabolism, including hepatocellular triglyceride accumulation and lipid peroxidation in humans (Guo et al, 2017;Guo et al, 2018), adipocyte proliferation and differentiation in mammals and cattle (Arcinas et al, 2019;Jiang et al, 2020), IMF deposition in yaks and donkeys (Li et al, 2020a;Wang H. et al, 2020), hepatic lipid biosynthesis in pigs (Huang et al, 2018), and subcutaneous fat deposition in pigs and Chinese buffalo (Li A. et al, 2018;Huang et al, 2019). Here, the parental genes of all identified circRNAs were mainly enriched in molecular binding, enzymatic activity, and development-related GO terms, indicating that chicken adipogenesis is a complex process that incorporates numerous events.…”

“…With regard to livestock and poultry, some circRNAs have also been identified by high throughput sequencing and confirmed to participate in regulating their important biological process, such as embryos development (Veno et al, 2015), formation of skeletal muscle fiber (Li et al, 2020b), hepatic lipid metabolism (Huang et al, 2018), and adipogenic differentiation (Li A. et al, 2018) in pig; muscle growth and development (Wei et al, 2017;Li et al, 2018b;Li et al, 2018c;Liu et al, 2020;Shen et al, 2020;Yue et al, 2020;Elnour et al, 2021), testis development (Gao et al, 2018), adipogenesis (Jiang et al, 2020) and milk fat content (Chen et al, 2021) in cattle; fat deposition in buffalo and yak (Huang et al, 2019;Wang H. et al, 2020); intramuscular fat (IMF) content denoting a crucial indicator of meat quality in donkey (Li et al, 2020a); follicular development (Shen et al, 2019), Marek's tumourigenesis (Wang L. et al, 2020) as well as muscle growth development (Ouyang et al, 2018a;Ouyang et al, 2018b) in chicken. And it has yet indicated some functional circRNAs related to lipid metabolism, for instance, circFUT10 could promote bovine preadipocyte proliferation but inhibit adipocyte differentiation (Jiang et al, 2020); circRNA_26852 and circRNA_11897, might get involved in porcine adipocyte differentiation and lipid metabolism (Li A. et al, 2018); circ11103 could increase the triglyceride levels in bovine mammary epithelial cells and the contents of unsaturated fatty acids (Chen et al, 2021); additionally, 19:45387150|45389986 and 21:6969877|69753491, were deemed as potential modulators of buffalo back subcutaneous adipose deposition (Huang et al, 2019).…”