Integrated analysis of differential m6A methylation and transcriptome profiles in ovaries of young and aged Qira black sheep

Ovarian aging leads to follicular atresia and a decline in both the quantity and quality of oocytes, yet its molecular regulatory mechanisms remain incompletely understood. N6-methyladenosine (m6A), one of the most prevalent RNA modifications in mammals, is thought to play a key role in ovarian function and aging. In this study, ovarian tissues from 1–2-year-old and 5–6-year-old Qira black sheep were collected, and an m6A methylation transcriptomic atlas was constructed based on MeRIP-seq and RNA-seq. A total of 660 differential methylation peaks (DMPs) and 2,018 differentially expressed genes (DEGs) were identified between the two groups, most of which were enriched in pathways associated with ovarian development, cellular senescence, and immune responses. GO and KEGG enrichment analyses showed that DMPs were significantly enriched in the positive regulation of the BMP signaling pathway, in utero embryonic development, and VEGF and Wnt signaling pathways. DEGs were mainly enriched in processes related to cellular senescence, NF-κB/MAPK signaling pathways, RNA binding, and transcriptional regulation. Integrated analysis revealed 109 overlapping differential genes between DMPs and DEGs, several of which (such as CEBPB, COL6A3, and PLCG1) were associated with aging, inflammatory responses, and the maintenance of ovarian function. This study provides the first m6A methylation transcriptomic profile of the ovaries of Qira black sheep and offers new insights into the regulatory mechanisms of m6A in ovarian aging.