Spatiotemporal dissection of cell-fate decisions during gastrulation, at single cell resolution

In mammals, implantation marks the initiation of cellular differentiation and robust acquisition of specialized cellular properties by individual cells, that specify the basic embryonic lineages. Cell specification is shaped by complex layers of epigenetic modifications that specify, memorize and modulate functional embryonic programs. New technologies now offer unprecedented view into cell specification at the molecular level. One aspect of these technologies involves transcriptional analysis at single cell resolution, which has recently enabled charting the mouse post-implantation development at unparalleled resolution. Yet, it remains a challenge to dissect the relative roles of intrinsic cellular processes from extrinsic effects of the localized environment upon cell-fate choices. In additions, disentangling the Gordian knot of epigenetic cause and effect still remains a formidable task.

To address these challenges, we developed a novel method that uses fluorescent dyes to index spatial information in the early embryo. Analyzing multiple individual embryos at different time points, established first precise spatiotemporal characterization of post-implantation development. To study how epigenetics may be involved in regulating cell-fate and function, we established isogenic pairs of mouse embryonic stem cell, harboring knockouts of key factors involved in writing, maintaining and erasing of DNA methylation. Analyzing chimeric embryos derived from isogenic clones, enabled us to critically evaluate and substantiate casual relationships between DNA methylation changes and gene-expression. Taken together, synthesizing ideas from developmental biology, epigenetics, computational biology, microscopy and single cell genomics, enabled separating extrinsic signaling from intrinsic cellular commitment around some of the most fundamental lineage decision choices in mammals.