David Taborsky, Fabiola Valdivia-Francia, Pablo Serrano, Sukalp Muzumdar, Neguin Ranjbar, Laura Llop-Grau, Guillermo Tellez, Pjeter Gjonlleshaj, Clara Duré, Peter F. Renz, Ramona Weber, Merve Yiğit, Umesh Ghoshdastider, Aleksei Mironov, Katie Hyams, Stefano Vianello, Mihaela Zavolan, Ori Bar‐Nur, Matthias P. Lütolf, Ataman Sendoel
Abstract The establishment of the body plan during gastrulation represents a hallmark of animal life. It emerges from the interplay of gene-regulatory programs and positional cues, yet how these signals are integrated post-transcriptionally remains largely unexplored. Here, we combine the scalability of mouse gastruloids with a single-cell CRISPR screening platform to functionally dissect germ layer specification at single-cell transcriptomic resolution. Focusing on post-transcriptional regulation, we systematically map drivers of mesodermal and endodermal fate and identify the deadenylase Cnot8 . Loss of Cnot8 leads to widespread poly(A) tail elongation and transcript stabilization, shifting mesoderm differentiation toward ectopic notochord fate, thereby profoundly impacting axial patterning. Collectively, our findings identify mRNA deadenylation as a fundamental mechanism linking cellular identity with morphogenetic signaling during mammalian body plan formation.