Journal Article

Exploring the regulatory mechanisms of differentially expressed circRNAs during bovine intramuscular adipogenic differentiation

Abebe, Belete Kuraz, Wang, Jianfang, Cheng, Gong, Guo, Juntao, Li, Anning, Yu, Shencheng, Jilo, Diba Dedacha, Zan, Linsen

2025

Overview

Background Intramuscular fat (IMF) accumulation plays a crucial role in determining beef quality. However, the molecular mechanisms regulating adipogenesis within bovine tissue remain unclear. Results This study conducted a comprehensive reanalysis of circular RNAs (circRNAs) transcriptomes using Temporal Clustering Analysis (TCA) to characterize their dynamic expression during the differentiation of bovine intramuscular preadipocytes across four time points. TCA revealed eight distinct clusters. Clusters 2 and 6 were selected due to exhibiting inverse expression trajectories that suggest stage-specific regulatory functions during early differentiation and late adipocyte maturation, respectively. Differential expression analysis identified 40 circRNAs which were dynamically modulated during the early stages of differentiation, including 19 core circRNAs shared among clusters, which may play essential roles in adipogenic development. Functional enrichment analysis of the host genes associated with these circRNAs indicated pathways related to extracellular matrix remodeling, focal adhesion, glycosylation, and DNA repair. This highlights the complex regulatory landscape mediated by circRNAs in adipogenesis. Regulatory network analysis of miRNA–mRNA interactions has identified a competing endogenous RNA (ceRNA) network consisting of 19 circRNAs, 54 miRNAs, and 209 mRNAs. This network exhibits significant enrichment in the PI3K-Akt signaling pathway and includes key adipogenic regulators such as PPARGC1A , AKT2 , and STK11 . Notably, the circLMO7 –bta-miR-2442– STK11 axis has been identified as a critical regulatory module. Experimental validation confirmed the circular conformation, temporal expression dynamics, and tissue-specific enrichment of circLMO7 , particularly within intramuscular fat. Functional knockdown of circLMO7 in bovine preadipocytes resulted in the significant downregulation of adipogenic markers such as FABP4 , SREBP1 , C/EBPβ ), indicating that circLMO7 acts as a positive regulator of adipogenesis. Conclusions This study identified a novel circLMO7 regulatory mechanism underlying the development of intramuscular fat in bovines and suggests promising molecular targets for genetic strategies aimed at enhancing meat quality. This study may serve as a foundation for studying the differential regulatory roles of ncRNAs in the development and function of adipose tissue.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: 1-Phosphatidylinositol 3-kinase / Adipocytes / Adipocytes - cytology / Adipocytes - metabolism / Adipogenesis / Adipogenesis - genetics / Adipose tissue / Adipose tissues / AKT protein / AKT2 protein / Animal genetics / Animal Genetics and Genomics / Animals / Biomedical and Life Sciences / Biotechnology / Cattle / Cell culture / Cell Differentiation - genetics / Cell growth / CeRNA network / Circular RNA / Cluster analysis / Clustering / Conformation / Differentiation / DNA repair / Enrichment / Extracellular matrix / Gene Expression Profiling / Gene Regulatory Networks / Gene set enrichment analysis / Genes / Genetic aspects / Genetic research / Glycosylation / Insulin / Intramuscular adipogenic differentiation / Life Sciences / Metabolism / Microarrays / Microbial Genetics and Genomics / MicroRNA / MicroRNAs / MicroRNAs - genetics / miRNA / Molecular modelling / Network analysis / Physiological aspects / Plant Genetics and Genomics / Preadipocytes / Proteomics / Regulatory mechanism / RNA / RNA, Circular - genetics / RNA, Circular - metabolism / Signal transduction / Transcriptomes