CircRNA screening and ceRNA network construction for milk fat metabolism in dairy cows

Abstract

BackgroundMilk fat is one of the main reference elements for evaluating milk quality and is a primary objective trait in dairy cattle breeding. In recent years, circular RNAs (circRNAs) have been found to play crucial roles in many biological processes. However, the function and expression profiles of circRNAs in milk fat synthesis in cows are not completely understood. We performed RNA sequencing to analyze the genome-wide expression of circRNA transcripts in bovine mammary epithelial cells (BMECs) from cows with extreme differences in milk fat percentage. We identified candidate differential circRNAs associated with milk fat metabolism using functional enrichment analysis and constructed a lipid metabolism-related competing endogenous RNA (ceRNA) interactive regulatory network.ResultsA total of 290 circRNAs were significantly differentially expressed (DE-circRNAs) in high milk fat percentage (HMF) cows compared to that in low milk fat percentage (LMF) cows. Of the 290 circRNAs, 142 were significantly upregulated and 148 were significantly downregulated. Enrichment analysis (Gene Ontology and Kyoto Encyclopedia of Genes and Genomes) identified four DE-circRNAs (circ_0001122, circ_0007367, circ_0018269, and circ_0015179) that potentially regulate milk fat metabolism. Among them, circ_0001122, circ_0007367, and circ_0015179 had relatively high expression levels in cow mammary gland tissue compared to other tissues (heart, liver, kidney, uterus, ovaries, and small intestine) of cows. The regulatory networks circ_0001122:miR-12043:LIPG, circ_0007367:miR-331-3p:CIDEA/PML, and circ_0018269:miR-11989:RORC/HPX are potential networks to explore the mechanism of milk fat regulation.ConclusionsThese results reveal the possible role of circRNAs in milk fat metabolism in dairy cows. Several important circRNAs and ceRNAs affecting milk fat synthesis were identified, providing insights into the complex biology of milk fat synthesis as well as a novel theoretical perspective for future research on lactation, milk quality, and breed improvement in dairy cows.

Circ_0003945: an emerging biomarker and therapeutic target for human diseases

“…Its knockdown impeded trophoblast cell proliferation and migration via miR-1244/FOXM1 axis ( 47 ). Interestingly, circ_0003945 was significantly upregulated in cow mammary gland tissue, influencing milk fat metabolism by sponging miR-331-3p ( 48 ). These studies underscore the potential role of circ_0003945 in various diseases beyond tumors.…”

“…Studies have confirmed that circ_0003945 showed resistance to digestion by ribonuclease R (RNase R), whereas the corresponding linear transcript was considerable diminished after RNase R treatment, underscoring the stability of its covalently closed-loop structures ( 42 , 43 ). Circ_0003945 have been associated with a variety of diseases, including various neoplasms and non-malignant conditions such as microcirculatory perfusion ( 44 , 45 ), diabetic retinopathy (DR) ( 35 ), osteoarthritis (OA) ( 46 ), preeclampsia (PE) ( 47 ), and milk fat metabolism ( 48 ). Noteworthy, circ_0003945 was highly overexpressed and linked to poor prognosis, including in glioma ( 49 ), thyroid cancer (TC) ( 36 ), esophageal cancer (EC) ( 50 ), non-small cell lung cancer (NSCLC) ( 51 ), breast cancer (BC) ( 34 ), hepatocellular carcinoma (HCC) ( 52 ), pancreatic cancer ( 53 ), colorectal cancer (CRC) ( 54 ), ovarian cancer (OC) ( 55 ), cervical cancer (CC) ( 56 ), prostate cancer ( 57 ), and osteosarcoma ( 58 ) ( Figure 3 ).…”

Understanding Circular RNAs in Health, Welfare, and Productive Traits of Cattle, Goats, and Sheep

“…Regarding specifically milk fat metabolism, Feng et al (2022) [ 31 ] analyzed circRNA profiles in bovine mammary epithelial cells (BMECs) of cows with a high percentage of milk fat (HMF) and a low percentage of milk fat (LMF) to discern circRNAs associated with milk fat metabolism. The study unveiled a total of 290 DE circRNAs, comprising 142 upregulated and 148 downregulated ones.…”

“…Among the enriched pathways, the PI3K-Akt signaling pathway took precedence, followed by ECM-receptor interaction and endocytosis, while other involved pathways included mTOR and AMPK. Following the construction of competitive endogenous RNA (ceRNA) networks, the researchers identified four regulatory networks (circ0001122/miR-12043/ LIPG , circ0007367/miR-331-3p/ CIDEA and PML , and circ0018269/miR-11989/ RORC and HPX ), underscoring their pivotal roles in regulating milk lipid metabolism [ 31 ]. Similar outcomes were obtained through RNA-seq analysis of mammary epithelial cells (MECs) isolated from cows’ milk with varying milk fat percentages.…”

The emerging roles of circRNAs in traits associated with livestock breeding

“…The expression level of circMYBPC1 in the longissimus dorsi muscle is higher than that in other tissues, and it encourages the differentiation of bovine muscle cells (M. Chen, Wei, et al, 2021). The highest expression levels of circ‐0001122 and circ‐007367 are found in the bovine mammary gland, but they differ in other tissues (Feng, Cai, et al, 2022). The expression of circMARK3 in fat is higher than that of other tissues, and it aids in the differentiation of bovine adipocytes (Feng, Zhao, et al, 2022).…”