The intrinsic and extrinsic effects of Tet proteins during gastrulation

To isolate cell-autonomous effects of TET loss during gastrulation, we utilized a chimeric embryo platform in which fluorescently tagged Tet-deficient and control mouse embryonic stem cells (mESCs) were either injected into tetraploid (4N) or diploid (2N) blastocysts, and allowed to develop in utero. In 4N complemented embryos, the resulting embryonic compartment is solely comprised of the injected mESCs derivatives (hereinafter denoted as whole-embryo chimera), whereas in chimeras obtained using 2N host blastocysts, the embryonic compartment contains both wild-type (WT) and injected cell derivatives (hereinafter denoted as mixed chimera). We performed single-cell RNA-seq for each whole-embryo and mixed chimera embryo, and compared the transcriptomes to a defined single-cell/single-embryo atlas. We further performed methylation analysis using post-bisulfite adaptor tagging (PBAT) for sorted Tet-TKO mutant and control from E8.5 mixed chimeras. Our work demonstrates an unbiased approach for defining intrinsic and extrinsic embryonic gene function based on temporal differentiation atlases, and disentangles the intracellular effects of the demethylation machinery from its broader tissue-level ramifications. Overall design: We individually imaged each chimeric embryo and performed index-sorting for them. To map the developmental potential for Tet-TKO cells in the whole-embryo chimera context, embryos were sampled at E7.5-8.5. Mixed chimera embryos were collected at E7.5. We then perform combined analysis of timed chimeric embryos in the context of a precise single embryo/single-cell temporal gastrulation atlas. To map the impact of Tet deficiency on embryonic DNA methylation while focusing on intrinsic effects, we injected a mixture of TKO and control cells to 2N blastocysts, generating chimeric embryos that were harvested at E8.5 when substantial differentiation is already established. We then sorted apart Tet-TKO mutant and control cells for analysis using PBAT protocol.