Site-specific DNA demethylation during spermatogenesis precedes nucleosome retention in mouse sperm

DNA methylation patterns are inherited from the parental germline to the embryo. In mature sperm, the sites of unmethylated DNA are tightly coupled to sites of histone retention at gene regulatory elements that are implicated in paternal epigenetic inheritance. The timing and mechanism of site-specific DNA demethylation in the male germline remains unknown. Here, we perform genome-wide profiling of DNA methylation during spermatogenesis by capturing methylated DNA through interaction with a methyl-DNA binding protein domain (MBD). Our data demonstrate a site-specific change in DNA methylation during the mitosis-to-meiosis transition. Importantly, demethylation at these genomic sites during this transition precedes nucleosome retention in spermatozoa. These results suggest that site-specific DNA demethylation during the mitosis-to-meiosis transition of spermatogenesis contributes to the establishment of sperm epigenetic states associated with embryonic gene expression. We therefore propose DNA demethylation during spermatogenesis as a novel phase of epigenetic reprogramming that contributes to embryonic gene regulation.