Preliminary Study of Differential circRNA Expression and Investigation of circRNA–miRNA–mRNA Competitive Endogenous Network in Rumen Acidosis of Holstein Cattle

Rumen acidosis is a widespread digestive disorder in livestock, causing inflammation and lowering animal performance. Unraveling its molecular mechanisms is vital for improving cattle health and welfare. Circular RNAs (circRNAs) are noncoding RNAs functioning as miRNA or protein sponges. This study employed high-throughput RNA sequencing to identify differentially expressed (DE) circRNAs in subacute rumen acidosis (SARA) in Holstein cattle, revealing 65 DE-circRNAs. We constructed a competitive endogenous RNA (ceRNA) network comprising 57 circRNAs, 14 miRNAs, and 22 mRNAs. Key hub nodes included circRNAs (8:69996068-69996853, 16:2614111-2615445, 5:109525933-109531380, 20:63115665-63116774), miRNAs (bta-miR-146b, bta-miR-181a, bta-miR-223, bta-miR-130b), and mRNAs (SLC2A3, SOCS3, DLC1, ARRDC4). Examination of hub circRNA host genes identified 30 DE transcription factors (TFs). Functional and pathway enrichment analysis pinpointed inflammation and immune response pathways, such as NF-kappa B and TNF signaling. This pioneering study offers the first circRNA expression profile and ceRNA network in SARA cattle, indicating circRNAs' role in inflammation regulation, thus enhancing our understanding of SARA's systems biology and potential treatment strategies.