A single embryo, single cell time-resolved model for mouse gastrulation

Mouse embryonic development is a canonical model system for studying mammalian cell fate acquisition. Recently, single-cell atlases comprehensively charted embryonic transcriptional landscapes, yet inference of the coordinated dynamics of cells over such atlases remains challenging. Here we introduce a temporal model for mouse gastrulation, consisting of data from 153 individually sampled embryos spanning 36 hours of molecular diversification. Using new algorithms and precise timing we infer differentiation flows and lineage specification dynamics over the embryonic transcriptional manifold. Rapid transcriptional bifurcations characterize the commitment of early specialized node and blood cells. However, for most lineages, we observe combinatorial multi-furcation dynamics rather than hierarchical transcriptional transitions. In the mesoderm, dozens of transcription factors combinatorially regulate multi-furcations, as we exemplify using time-matched chimeric embryos of Foxc1/Foxc2 mutants. Our study rejects the notion of differentiation being governed by a series of binary choices, providing an alternative quantitative model for cell fate acquisition. Overall design: Single cells from 153 WT mouse embryos (E6.5 - E8.25) were sequenced using MARS-seq2.0 which allowed to record each single cell's embryo identity during FACS cell-sorting. Using chimera and tetraploid complementation assays we analyzed the role of Foxc1 and Foxc2 during mesoderm specification. For both assays, we injected Foxc1/2 DKO and control cells into the blastocyst and performed scRNA-seq at ca. E7.5. Fluorescence intensity and embryo identity of each single cell from chimera and tetraploid embryos was recorded during FACS index-sorting.