Meiotic prophase I (MPI) is a unique phase of the cell cycle, specific to germ cells and defining of sexual reproduction. MPI is a period of extensive and specialized homologous chromosome interactions and genetic exchange. Proper progression of MPI requires elaborate epigenetic control, deficiencies in which often lead to infertility. Changes in DNA methylation during MPI can endanger genome integrity by activating transposable elements (TEs) that when mobilized induce DNA breaks and mutations. Therefore, MPI was thought to be under strict surveillance by DNA methylation, whose levels were assumed to be high and stable throughout MPI. Interestingly, expression of LINE retrotransposons, specifically LINE-1 (L1)-encoded protein ORF1p has been observed in MPI germ cells of wild-type male mice. Since tight epigenetic regulation is associated with transposon silencing, we hypothesized that L1 expression in MPI may indicate relaxation of epigenetic silencing in meiotic germ cells. Thus, we investigated the dynamics of CpG DNA methylation during MPI. We enriched and isolated individual MPI stages by Fluorescence Activated Cell Sorting (FACS) and profiled individual MPI germ cells using whole-genome bisulfite sequencing, and RNA-sequencing. Using this approach we uncovered transient and stage-specific changes in DNA methylation dynamics. In contrast to the prevailing view, we show that male germ cells undergo genome-wide transient relaxation of DNA methylation (TRDM) during early MPI. Specifically, we find that a transition from pre-meiotic spermatogonia to meiotic onset in preleptotene spermatocytes is accompanied by genome-wide hypomethylation. Gradual, but uneven remethylation of the genome creates hypomethylated domains throughout meiotic prophase, with pre-meiotic levels of DNA methylation achieved only by late MPI. Our data are most consistent with a DNA replication- coupled mechanism of DNA demethylation in pre-meiotic S-phase. Intriguingly, a TRDM- independent set of hypomethylated domains emerges in mid to late MPI and is enriched in transcriptionally upregulated spermatogenic genes. Using Mael -/- mice defective in piRNA pathway, we show that early MPI offers an opportunity for TE expression and reactivation. We
demonstrate that if germ cells enter MPI with insufficient levels of DNA methylation at L1 elements, then during TRDM, meiotic onset can be hijacked to reactivate potentially active L1s. Cumulatively, we demonstrate that early MPI is epigenetically relaxed, exhibits dynamic DNA methylation pattern in MPI and that transient genome-wide DNA hypomethylation at meiotic onset might have implications in gamete quality control
