Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during early mammalian organogenesis [scNMT BS-seq]

Perturbation of DNA methyltransferases and of the active demethylation pathway via TET enzymes results in severe developmental defects and embryonic lethality. Dynamic control of DNA methylation is therefore vital for embryogenesis, yet the underlying mechanisms remain poorly understood. Here we report a single-cell transcriptomic atlas from a variety of DNA methylation mutant mouse embryos during mouse early organogenesis. We show that both the maintenance and de novo methyltransferase enzymes are dispensable for the formation of all major cell types at E8.5. However, DNA methyltransferases are required for silencing of prior or alternative cell fates such as pluripotency and extraembryonic programmes. Deletion of all three TET enzymes produces substantial lineage biases, in particular, a failure to generate primitive erythrocytes. Single-cell multi-omics profiling moreover reveals that this is linked to a failure to demethylate distal regulatory elements in Tet triple-knockout embryos. This study therefore provides a detailed analysis of the effects of perturbing DNA methylation on mouse organogenesis at whole organism scale, and affords new insights into the regulatory mechanisms of cell fate decisions. 768 single cells isolated from TET triple knockout chimeric mouse embryos at E8.5 and processed using either scNMT-seq (640 cells, Clark et al 2018) or scM&T-seq (128 cells, Angermueller et al 2016)