Preventing CpG hypermethylation in oocytes safeguards mouse development [WGBS 4-cell]

Except for regulatory CpG-island sequences, genomes of most mammalian cells are widely DNA-methylated. In oocytes though, DNAme is largely confined to transcribed regions. The mechanisms restricting de novo DNAme in oocytes and the relevance thereof for zygotic genome activation and embryonic development are largely unknown. Here we show that KDM2A and KDM2B, two histone demethylases, prevent genome-wide accumulation of histone H3 lysine 36 di-methylation, thereby impeding DNMT3A-catalyzed DNAme. We demonstrate that aberrant DNAme at CpG-islands inherited from Kdm2a/Kdm2b double mutant oocytes represses gene transcription in two-cell embryos. Aberrant maternal DNAme impairs pre-implantation embryonic development which is suppressed by Dnmt3a deficiency during oogenesis. Hence, KDM2A/KDM2B are essential for confining the oocyte methylome, thereby conferring competence for early embryonic development. Our research implies that the reprogramming capacity eminent to early embryos is insufficient for erasing aberrant DNAme from maternal chromatin, and that early development is vulnerable to gene dosage haplo-insufficiency effects. To study the function of KDM2A and KDM2B in regulating genome-wide DNA methylation in oocytes, we conditionally altered their expression in growing oocytes in several ways. First, by using Zp3-driven CRE recombinase-mediated excision, we removed exons encoding the histone demethylase JmjC domains of Kdm2a or Kdm2b, which fully abrogated expression of either protein. We also generated mice expressing a KDM2B protein lacking its CxxC domain, unable to be recruited to CpG island regions of the mouse genome. To address possible combinatorial roles of both proteins, we generated oocytes conditionally deficient for Kdm2a in combination with either Kdm2b mutation. We profiled genome-wide mCpG methylation in fully grown germinal vesicle oocytes of following genotypes: (1) Kdm2b-deltaCxxC, (2) Kdm2a-KO; Kdm2b-deltaCxxC, (3) Kdm2a-KO; Kdm2b-KO and (4) controls. To study the impact of Kdm2a-KO and Kdm2b-KO double mutations introduced in oocytes on preimplantation embryo development, we profiled genome-wide CpG methylation in genetically hybrid, morphologically normal four-cell embryos generated by in vitro fertilization using spermatozoa from JF1 strain male mice.