GSE203226
Mechanisms and function of de novo DNA methylation in placental development [snRNA-seq]
DNA methylation is a repressive epigenetic modification that is essential for development, exemplified by the embryonic and perinatal lethality observed in mice lacking de novo DNA methyltransferases (DNMTs). Here we characterise the role for DNMT3A, 3B and 3L in gene regulation and development of the mouse placenta. We demonstrate that each of the DNMTs is required to establish the placental methylome and is distinctly targeted to genome based on underlying chromatin features. Loss of Dnmt3b results in de-repression of germline genes in trophoblast lineages and impaired development of the placental maternal-foetal interface. Critically, loss of DNA methylation in the placenta did not lead to abnormalities in lineage specification or cell identity, but to defective formation and vascularisation of the placental labyrinth. Using Sox2-Cre to delete Dnmt3b in the embryo, leaving expression intact in placental trophoblast cells, we were able to rescue the placental phenotype and, consequently, the embryonic lethality, as Dnmt3b null embryos could now survive to birth. We conclude that the principal function of DNA methylation during embryogenesis is to regulate placental function, which in turn is critical for embryo survival. Overall design: Using low-input RNA-seq and post bisulphite adaptor tagging (PBAT), we then assayed gene expression and genome-wide DNA methylation in E7.5 ExE and epiblast from Dnmt3a KO, Dnmt3b KO, Dnmt3a/b double KO (DKO), Dnmt3l KO and wildtype (WT) controls.  The de novo DNMT enzymes have been shown to interact with modified histone tails, which modulates their catalytic activity and genome localisation in vitro. Thus, we generated ultra-low input ChIP-seq data for H3K4me1 and H3K27ac to combine with published datasets for H3K4me3, H3K27me3 and H3K36me3 in E6.5 ExE, immediately preceding the completion of de novo DNA methylation.  To investigate the placental phenotype of Dnmt3b KO at the molecular level, we generated single nuclei RNA sequencing data from E12.5 placentas from a Dnmt3b KO and WT control.