Single-cell multiomics sequencing during mouse embryogenesis

Abstract Single-cell sequencing technologies are transforming our understanding of the gene expression dynamics of devel-opmental biology, yet the role of the epigenome is less well understood. We recently developed a technique, named scNMT-seq for profiling DNA methylation, chromatin accessibility and gene expression from the same single-cells. Applying this method to cells collected from early mouse embryos we discovered an asymmetry in the for-mation of the three primary germ layers with the mesendoderm epigenome arising upon differentiation but the ecto-derm profile being pre-specified in the early epiblast. Using genetic perturbations we next revealed a role of active TET-dependent demethylation in the enhancer landscape of early organogenesis which is necessary for the for-mation of the primitive blood lineage. Finally we developed a computational tool to predict transcription factor bind-ing events and infer gene regulatory networks. We show that these can be used to generate in silico predictions of the effect of transcription factor perturbations which we validate experimentally by showing that Brachyury is essen-tial for the differentiation of neuromesodermal progenitors to somitic mesoderm by priming cis-regulatory elements. In conclusion, single-cell multi-omics are powerful technologies for investigating the role of the epigenome in cell fate decision making.