Germline epigenome editing identifies H3K9me3 as a mediator of intergenerational DNA methylation recovery

Inter/transgenerational epigenetic inheritance is a crucial and controversial theory that could reshape the concept of genetics. To validate this theory directly, we invent a system for targeted reprogramming of epigenetic memory in sperm. Using this system, we erased DNA methylation at the differentially methylated region of H19 gene (H19-DMR) in sperm, which causes Silver-Russell syndrome-like phenotypes in the F1 offspring. Surprisingly, although DNA methylation is fully lost in the sperm, it is partially restored during early F1 embryogenesis, suggesting the existence of epigenetic memory other than DNA methylation. Importantly, targeted removal of histone modifications reveals that de novo deposition of tri-methylation at lysine 9 of histone H3 (H3K9me3) is required for the DNA methylation recovery. Thus, our study provides a robust tool of germline epigenome editing and identifies H3K9me3 as a mediator of intergenerational DNA methylation recovery.