Comprehensive epigenetic analysis on 5-methylcytosine modification of circRNAs in the mouse cerebral ischemia model

A growing body of research suggests that circular RNAs (circRNAs) and 5-methylcytosine (m 5 C) play crucial roles in the onset and progression of stroke. This includes their potential regulation of neuronal damage and repair under cerebral ischemic conditions. However, the specific features of m 5 C modification in circRNAs associated with stroke remain unclear. In this study, we established a mouse model of cerebral ischemia (MCAO) and utilized methylated RNA immunoprecipitation sequencing (MeRIP-Seq) to identify m 5 C peaks. In comparison to the control group, MCAO exhibited significant changes in 1982 m5C peaks, with 1096 peaks upregulated and 886 peaks downregulated. Differentially expressed genes in m5C were identified to have significant involvement in the MAPK signaling pathway, GABAergic synapse, and foxO signaling pathway. Additionally, through integrated analysis of MeRIP-Seq and RNA-Seq data, we identified 24 circRNAs that underwent significant changes in both methylation and expression. This suggests a potential association between stroke and circRNA m 5 C modification, providing insights into the prognosis of stroke patients and the identification of novel intervention targets. • This study presents the first comprehensive profile of m5C modification in circRNAs during ischemic stroke. • Integrated MeRIP-seq and RNA-seq analysis reveals 1982 differentially m5C-methylated circRNA peaks.24 circRNAs show concurrent changes in both m5C methylation and expression levels after MCAO.m5C-modified circRNAs are enriched in MAPK, FoxO, and GABAergic synapse pathways. • The findings suggest m5C in circRNAs as a potential novel epigenetic mechanism in stroke pathology.