Integrated MeRIP-seq and RNA-seq analyses identify candidate m6A-associated genes during developmental coat color transition in Junken meat sheep

Junken meat sheep undergo a developmental coat color transition from black fleece at birth to white body fleece by approximately 179 days of age, but the associated epitranscriptomic features remain unclear. Here, integrated MeRIP-seq and RNA-seq analyses were performed using skin samples from three newborn black-fleeced lambs and three 179-day-old white-fleeced lambs. m6A peaks were mainly enriched in CDS regions and near stop codons, with the canonical GGACU motif detected in both groups. Across three paired comparisons, 1,273–1,716 differential m6A peaks and 400–1,657 differentially expressed genes were identified. Functional enrichment analysis highlighted processes related to hair follicle development, epidermal morphogenesis, extracellular matrix remodeling, focal adhesion, and Wnt, TGF-β, PI3K-Akt, Notch, and melanogenesis-related pathways. Integrative analysis revealed comparison-dependent m6A–expression coupling patterns, including hyper-down in C11 vs. C1 and predominant hypo-up patterns in C22 vs. C2 and C33 vs. C3. Candidate m6A-associated genes, including FZD7 , GAS1 , COL4A1 , PXDN , LAMC3 , ARID1A , FA2H and RAPGEFL1 , were prioritized, and qRT-PCR supported the RNA-seq expression trends of selected genes. Given the confounding between age and coat-color stage, these findings represent candidate molecular features associated with developmental coat color transition and provide a basis for future m6A-site validation and functional studies.