Comparison of epigenetic differences in genomes of cloned cattle from different donor cell sources

Despite its potential, somatic cell nuclear transfer (SCNT) remains limited by low efficiency and frequent developmental abnormalities, with donor cell selection being a key contributing factor. To address this, we investigated epigenetic differences in cloned cattle derived from fetal fibroblasts (FFBs) versus fetal oviduct epithelial cells (FOVs). Using multi-omics profiling-including Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq), RNA sequencing (RNA-seq), and 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) analysis-we systematically compared the two groups. Notably, clones derived from FOVs (FOV group) exhibited enhanced chromatin accessibility and more active gene expression patterns relative to FFB-derived clones (FFB group). Integrative omics analysis identified differential genomic regions associated with cell differentiation, embryonic development, and epigenetic regulation, along with putative transcription factor binding motifs. Intriguingly, while original FFB and FOV cells showed comparable 5mC levels, FOV-derived clones displayed significantly reduced 5mC post-SCNT, suggesting distinct epigenetic reprogramming dynamics. Furthermore, surviving FFB clones exhibited elevated 5hmC (>4 ‰), whereas deceased clones had markedly lower levels (<2 ‰). Together, these findings elucidate donor cell-dependent molecular mechanisms in SCNT, offering novel perspectives and valuable clues for subsequent research.