Transgenerational Sperm DMRs and Low CpG Density Sites Escape Methylation Erasure in Embryonic Epigenetic Inheritance

Previous studies have suggested an erasure of DNA methylation is required to develop the stem cells in the morula embryo. An exception involves imprinted genes that escape this DNA methylation erasure. Transgenerational differential DNA methylation regions (DMRs) have been speculated to also escape this erasure. The current study was designed to assess if morula embryos escape erasure of DDT (dichloro-diphenyl-trichloroethane)-induced transgenerational sperm DMRs. Observations demonstrate that the transgenerational sperm DMR sites are not erased, so are imprinted-like DMR sites. Interestingly, we also found that the majority of low-density CpG genomic sites had a significant increase in DNA methylation in the morula embryo compared to sperm. The general erasure of DNA methylation during embryogenesis appears applicable for high-density CpG islands, but not low-density CpG deserts. The current study used intracytoplasmic sperm injection (ICSI) of control and DDT transgenerational (F3 generation) sperm to generate morula stage embryos for analysis of DNA methylation status of the DMRs. Sperm and morula samples were collected from both control and DDT exposure lineage rats. The DNA was extracted from the sperm and morula embryo pools. A methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) was performed on each of the control and DDT sperm and ICSI morula embryo pools.