Elite bull semen is widely used in cattle artificial insemination and reproductive technologies. Beyond genetic variation, sperm epigenetic changes can be transmitted to embryos, potentially affecting embryo methylome, tran-scriptome, development, and calf phenotypic performance. This study evaluated the impact of sperm DNA methyl-ation on in vitro produced (IVP) embryo methylome and transcriptome using a paired experimental design. Ten replicates used oocyte pools from five cows fertilized with sperm from two bulls with extreme CpG methylation differences across ~115,000 sites, generating a total of 20 pools of Day-7 expanded blastocysts (10 pools per bull) for RRBS and RNA-seq analysis (ARS-UCD2.0).
RRBS identified 5,077 hypermethylated and 4,929 hypomethylated DMCs, predominantly in intronic regions, followed by exonic, intergenic, and promoter regions. GO enrichment revealed hypermethylated DMCs enriched for tissue development, neurogenesis, and DNA-binding transcription factors, while hypomethylated DMCs were associated with transcription regulation and RNA biosynthesis. RNA-seq detected 38,001 genes, yielding 44 dif-ferentially expressed genes (FDR<0.05). Weighted Gene Co-expression Networks (WGCNA) with top 25% varia-ble genes and power=18, R²≥0.70, identified 29 modules, three of which were significantly correlated with bull origin (|r|≥0.60, adj.P≤0.05).
These findings suggest that contrasting sperm methylomes are associated with broad embryo epigenetic repro-gramming, affecting both individual gene expression and co-expression networks, establishing a framework for studying paternal epigenetic transmission in cattle IVP embryos.

Co-authors: Aurélie Bonnet, Aurélie Chaulot Talmon, Valentin Costes, Marie-Christine Deloche, Anne Frambourg, Udayaraja Gk, Laurent Schibler, Hélène Kiefer, Véronique Duranthon, Haja N. Kadarmideen