The intrinsic and extrinsic effects of TET proteins during gastrulation

• Published in: Cell Vol. 185; no. 17; pp. 3169 - 3185.e20
• Main Authors: Cheng, Saifeng, Mittnenzweig, Markus, Mayshar, Yoav, Lifshitz, Aviezer, Dunjić, Marko, Rais, Yoach, Ben-Yair, Raz, Gehrs, Stephanie, Chomsky, Elad, Mukamel, Zohar, Rubinstein, Hernan, Schlereth, Katharina, Reines, Netta, Orenbuch, Ayelet-Hashahar, Tanay, Amos, Stelzer, Yonatan
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 18.08.2022; Cell Press
• Subjects: cell fate decisions; developmental biology; DNA demethylation; epigenetics; genome editing; mouse gastrulation; single-cell genomics; stem cells; stem cells; genome editing; developmental biology; mouse gastrulation; single-cell genomics; DNA demethylation; cell fate decisions; epigenetics
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2022.06.049

Mice deficient for all ten-eleven translocation (TET) genes exhibit early gastrulation lethality. However, separating cause and effect in such embryonic failure is challenging. To isolate cell-autonomous effects of TET loss, we used temporal single-cell atlases from embryos with partial or complete mutant contributions. Strikingly, when developing within a wild-type embryo, Tet-mutant cells retain near-complete differentiation potential, whereas embryos solely comprising mutant cells are defective in epiblast to ectoderm transition with degenerated mesoderm potential. We map de-repressions of early epiblast factors (e.g., Dppa4 and Gdf3) and failure to activate multiple signaling from nascent mesoderm (Lefty, FGF, and Notch) as likely cell-intrinsic drivers of TET loss phenotypes. We further suggest loss of enhancer demethylation as the underlying mechanism. Collectively, 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. [Display omitted] •Chimeras with full or partial Tet deficiency are mapped over the course of gastrulation•Tet-TKO cells disrupt signaling, leading to skewed whole-embryo mutant gastrulation•Tet-TKO cells retain near-complete differentiation potential in a chimera context•Loss of TET leads to pervasive hypermethylation and mildly perturbed gene expression Single-embryo, single-cell temporal models of embryos lacking Tet contribution, either partially or fully, clarify the cell-intrinsic effects of the TET machinery from its subsequent tissue-level ramifications. TET-mediated demethylation alters gene expression in a lineage- and time-specific fashion, but such alterations can be overcome in the presence of inter-cellular signals from neighboring cells.