Epigenetic regulation in extraembryonic lineage formation

DNA methylation is a crucial component of genome regulation and, together with other parts of the epigenome such as post-translational modifications of histones, essential for cell identity and viability. In virtually all somatic mammalian cells, DNA methylation at CpGs is distributed in a bimodal pattern where high genome-wide methylation is only interrupted by low levels at CpG islands (CGIs). This canonical methylation landscape is established by DNA methyltransferases (DNMTs) and propagated during cell division, ensuring its stability over the lifespan of the organism. In stark contrast, cells of the extraembryonic lineages deviate from this consensus by exhibiting globally reduced levels accompanied by elevated methylation over hundreds of CGIs at developmental gene promoters. These two methylomes are formed during early development and afterwards clearly separate embryonic from extraembryonic cell types. However, in contrast to the somatic landscape, it is largely unclear how the extraembryonic non-canonical methylome is established. We used inducible in vitro model systems that differentiate mouse embryonic stem cells into cell types representing the placental and extraembryonic endoderm lineages to follow the conversion between these two methylomes. This allowed us to directly and quantitatively compare the epigenetic regulatory principles that enforce the two methylation landscapes. We find that the methylation transition occurs concomitantly with cellular differentiation and is underpinned by drastic changes in the abundance of epigenetic modifiers. Results from functional assays demonstrate that global hypomethylation is not the result of slow deterioration over time but is instead rapidly established through a downregulation of key enzymes involved in methylation maintenance. We further mechanistically dissect the isoform-specific contributions of DNMTs and find evidence for a critical importance of their interaction with methylation at lysine 36 of histone 3. Together, our data delineate crucial roles of epigenetic regulators during the methylome conversion and suggest that methylation dynamics are part of a wider epigenetic rearrangement that accompanies extraembryonic cell type formation, providing a basis for comprehensive investigations into the principles of epigenetic regulation in distinct developmental lineages.