Spatiotemporal dissection of cell specification processes during gastrulation and early organogenesis
Bioinformatics and Theoretical Biology
Final Report Abstract
This project aimed at reconstructing cellular differentiation trajectories from single-cell RNA- sequencing data and dissecting the effect of intracellular epigenetic changes and intercellular signals on cell fate decisions during early mammalian embryonic development. We developed a detailed temporal model of mouse gastrulation, analyzing data from 253 individually sampled embryos over 72 hours. This model revealed the dynamic transcriptional changes and differentiation flows within the developing embryo. Our findings showed that during gastrulation, early specialized cells, such as those in the node and blood, undergo rapid transcriptional bifurcations, while at the same time other lineages such as nascent mesoderm exhibit complex multi-furcation dynamics, regulated by numerous transcription factors acting in combination. Investigating the role of TET proteins during early development, we found that embryos deficient in these proteins fail during gastrulation by only generating cells of the endoderm and extra-embryonic mesoderm lineages. In contrast, when developing in a chimera setting within a wildtype host environment, Tet-mutant cells retain near-complete differentiation potential giving rise to almost all embryonic lineages. By comparing time-matched single-cell RNA-seq profiles of mutant and wild type cells, we identified early epiblast factors (e.g., Dppa4 and Gdf3) and a reduction in expression levels of multiple signaling factors in nascent mesoderm (Lefty2, FGF) as likely cell-intrinsic drivers of the TET loss phenotypes. On the DNA methylation level TET loss leads to pervasive hypermethylation of putative enhancer elements. Studying the role of BMP4 signaling in both embryonic and extraembryonic tissues, we found that early BMP4 signals from the extraembryonic ectoderm (ExE) are crucial for the proper differentiation of ectoplacental cone cells and the specification of trophoblast giant cells. In the embryo, BMP4 signaling regulates the bifurcation of endoderm and mesoderm and the development of primordial germ cells (PGCs). Our results emphasize the intertwined nature of embryonic and extraembryonic development and the importance of BMP4 signaling in coordinating these processes. In summary, this research enhanced quantitative modelling of the differentiation landscapes of early mammalian development, resulting time-resolved trajectory models that can be used to study quantitatively the effect of epigenetic regulators and intercellular signals during development.
Publications
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A single-embryo, single-cell time-resolved model for mouse gastrulation. Cell, 184(11), 2825-2842.e22.
Mittnenzweig, Markus; Mayshar, Yoav; Cheng, Saifeng; Ben-Yair, Raz; Hadas, Ron; Rais, Yoach; Chomsky, Elad; Reines, Netta; Uzonyi, Anna; Lumerman, Lior; Lifshitz, Aviezer; Mukamel, Zohar; Orenbuch, Ayelet-Hashahar; Tanay, Amos & Stelzer, Yonatan
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DNA methyltransferases 3A and 3B target specific sequences during mouse gastrulation. Nature Structural & Molecular Biology, 29(12), 1252-1265.
Mukamel, Zohar; Lifshitz, Aviezer; Mittnenzweig, Markus; Chomsky, Elad; Schwartzman, Omer; Ben-Kiki, Oren; Zerbib, Mirie & Tanay, Amos
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The intrinsic and extrinsic effects of TET proteins during gastrulation. Cell, 185(17), 3169-3185.e20.
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
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Time-aligned hourglass gastrulation models in rabbit and mouse. Cell, 186(12), 2610-2627.e18.
Mayshar, Yoav; Raz, Ofir; Cheng, Saifeng; Ben-Yair, Raz; Hadas, Ron; Reines, Netta; Mittnenzweig, Markus; Ben-Kiki, Oren; Lifshitz, Aviezer; Tanay, Amos & Stelzer, Yonatan
