Untangling early embryo development using single cell genomics

The zygote undergoes five cell divisions prior to the first signs of lineage segregation. Blastocyst formation requires segregation of the trophectoderm, needed for implantation, and the inner cell mass, which differentiate towards the major lineages of the fetus. This process is broadly conserved in mammals, however, in recent years investigations using high throughput single cell transcriptomics have provided new insights on the gene regulatory networks and epigenetic mechanisms controlling these processes in different species, highlighting novel unique evolutionary adaptations. Although analysis of single cell datasets is inherently challenging due to stochastic gene expression in single cells, continuous development of novel computational tools have contributed to improving the quality of these datasets. Single cell -omics provides detailed information on discrete cellular states, and when combined with spatial transcriptomics it can inform on the relationship between cellular compartments and fate determination. This technology has recently been used to shed new light into the progression of lineage segregation, establishment of pluripotency, epigenetic regulation and signalling pathways participating in mammalian pre-gastrulation development. The adoption of these new technologies for generating high-resolution maps of embryogenesis will readily translate into biotechnological applications that will have significant impact in livestock production.