One of the mostremarkable processes in biology is the development of a single fertilized egginto a complete multi-cellular embryo within a short time period of rapidgrowth and cellular diversification. Yet, how variation is achieved while basicunits (cells) in this system comprise identical genetic information, representsa deep and fundamental open question in biology. Single-celltechnologies are transforming our ability to elucidate embryonic cellspecification. We recently generated a time-resolved transcriptional model ofmouse gastrulation based on single-cell data from over 150 individually isolatedand processed embryos. Since each embryo independently progresses at its ownpace, toward ultimate convergence at a common outcome, individual cells makingup each embryo could be placed on a bona fide time continuum. This facilitateda unified flow model that considers continuous, parallel, and convergeddifferentiation towards multiple lineages. Based on the detailed temporalmodel, we devised a robust experimental framework for interpreting embryonicphenotypes resulting from genetic or epigenetic alterations. In this manner, weutilize individual mouse chimera embryos to systematically dissect thecell-intrinsic effects of Tet-mediated DNA demethylation on embryonic cellspecification. We demonstrate that interpretation of Tet function is dependenton separating temporal, lineage, and cell-autonomous/inter-cellular effects.Knocking out the three Tet genes (Tet-TKO) in the entire embryo gives rise tomajor gastrulation defects. But when Tet-TKO cells are allowed to develop in aWT niche, they retain differentiation capacity to nearly all embryonic lineages.This leads to a revised conceptual framework supporting the notion thatTet-mediated demethylation is dispensable towards most differentiationprograms, but rater involves fine-tuning of gene expression pervasivelythroughout the genome. Our work demonstrates an unbiased approach for definingintrinsic and extrinsic embryonic gene function based on temporaldifferentiation atlases, and disentangles the intracellular effects of thedemethylation machinery from its broader tissue-level ramifications.
Host: Sagi Levy
