Comparative analysis of sperm DNA methylation supports evolutionary acquired epigenetic plasticity controlling organ speciation

Gametic DNA methylation is essential to the viability of the embryo and participates in developmental programming. Here, we performed a comparative epigenomic analysis of DNA methylation in spermatozoa from humans, mice, rats and mini-pigs to get insight into species specificity of the gametic epigenetic blueprint. Using data from whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS), we compared the methylation profiles of orthologous single-CpG sites. Transcription profiles of early embryo development were analyzed to provide insight into the association between sperm methylation and gene expression programming. We identified DNA methylation variation near genes related to the central nervous system and signal transduction. Gene expression dynamics at different time-points of preimplantation stages were modestly associated with spermatozoal DNA methylation at nearest promoters. Our analysis revealed that conserved genomic regions subject to epigenetic variation across different species were associated with specific organ functions, suggesting their potential contribution to organ speciation and long-term adaptation to the environment We performed our analyses on a panel of publically available datasets, generated for different studies. In addition, we performed RRBS on mini-pigs sperm. Sperm samples were collected from four adult mini-pigs.