DNA demethylation in spermatogenesis presets the sites of nucleosome retention in mouse sperm

DNA methylation is a heritable epigenetic mark from the parental germline to the embryo. In the male germline, it remains unknown how the site-specificity of DNA methylation conversely defines the sites of unmethylated DNA in mature sperm, which are tightly coupled to histone retention sites at gene regulatory elements implicated in paternal epigenetic inheritance. Here, we perform genome-wide profiling of DNA methylation during spermatogenesis based on the capture of methylated DNA by the methyl-DNA binding protein domain (MBD) and demonstrate that there is a site-specific change in DNA methylation during the mitosis-to-meiosis transition in spermatogenesis. Importantly, DNA demethylation sites during the mitosis-to-meiosis transition predetermine nucleosome retention sites in spermatozoa. These results suggest that site-specific DNA demethylation during the mitosis-to-meiosis transition of spermatogenesis prepares embryonic gene expression after fertilization. We propose that DNA demethylation in spermatogenesis is a novel phase of epigenetic reprogramming that contributes to embryonic gene regulation. Overall design: MethylCap-seq for capturing MBD-bound DNA methylated regions in mouse male germ cells