Epigenetic regulation of cell fate during early mammalian development

Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Single cell RNA-sequencing has identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice is poorly understood. We are systematically charting this important developmental progression by single cell multi-omics, tracking simultaneously the transcriptome, DNA methylome and chromatin accessibility. We find that promoters or enhancers of lineage specific genes are epigenetically primed at early developmental stages to safeguard their future transcriptional activation. We have identified DNA binding proteins needed for multi-lineage priming of regulatory elements prior to gastrulation. Here, we will determine the molecular mechanisms of epigenetic priming, and the functional consequences of faulty priming in lineage and organ development. The first objective addresses how the DNA binding proteins DPPA2,4 target chromatin bivalency (H3K4me3 and H3K27me3) to developmental gene promoters, and the consequences of bivalency loss in vivo. The second objective characterises neuroectoderm enhancer priming which occurs already in the early epiblast, and identifies DNA binding proteins and chromatin complexes which prime these enhancers, preparing them for future gene activation. The third objective uses large-scale combinatorial epigenetic editing of promoters and enhancers in vitro and in vivo to determine their impact on cell fate decisions in gastrulation and early organogenesis. This ambitious programme of work will provide fundamental insights into how the epigenetic landscape in early development impacts cell differentiation. Our discoveries will inform strategies for ES or iPS cell based regenerative medicine, and improve our understanding of how developmental disorders arise in humans.