Selective RNA sequestration in biomolecular condensates directs cell fate transitions

Pessina, P.; Nevo, M.; Shi, J.; Kodali, S.; Casas, E.; Cui, Y.; Richards, A. L.; Park, E. J.; Chen, X.; Levin-Ferreyra, F.; Stevenson, E.; Krogan, N. J.; Swaney, D. L.; Ying, Q.; Chen, Q.; Brumbaugh, J.; Di Stefano, B.

doi:10.1101/2025.05.08.652299

bioRxiv · 10.1101/2025.05.08.652299

Selective RNA sequestration in biomolecular condensates directs cell fate transitions

Pessina, P.·Nevo, M.·Shi, J.·Kodali, S.·Casas, E.·Cui, Y.·Richards, A. L.·Park, E. J.·Chen, X.·Levin-Ferreyra, F.·Stevenson, E.·Krogan, N. J.·Swaney, D. L.·Ying, Q.·Chen, Q.·Brumbaugh, J.·Di Stefano, B.

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Abstract

Recent studies have emphasized the significance of biomolecular condensates in modulating gene expression through RNA processing and translational control. However, the functional roles of RNA condensates in cell fate specification remains poorly understood. Here, we profiled the coding and non-coding transcriptome within intact biomolecular condensates, specifically P-bodies, in diverse developmental contexts, spanning multiple vertebrate species. Our analyses revealed the conserved, cell type-specific sequestration of untranslated RNAs encoding key cell fate regulators. Notably, P-body contents did not directly reflect active gene expression profiles for a given cell type, but rather were enriched for translationally repressed transcripts characteristic of the preceding developmental stage. Mechanistically, microRNAs (miRNAs) direct the selective sequestration of RNAs into P-bodies in a context-dependent manner, and perturbing AGO2 or alternative polyadenylation profoundly reshapes P-body RNA content. Building on these mechanistic insights, we demonstrate that modulating P-body assembly or miRNA activity dramatically enhances both activation of a totipotency transcriptional program in naive pluripotent stem cells as well as the programming of primed human embryonic cells towards the germ cell lineage. Collectively, our findings establish a direct link between biomolecular condensates and cell fate decisions across vertebrate species and provide a novel framework for harnessing condensate biology to expand clinically relevant cell populations.

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Pessina, P., Nevo, M., Shi, J., Kodali, S., Casas, E., Cui, Y., Richards, A. L., Park, E. J., Chen, X., Levin-Ferreyra, F., Stevenson, E., Krogan, N. J., Swaney, D. L., Ying, Q., Chen, Q., Brumbaugh, J., Di Stefano, B.. 2025-05-10. Selective RNA sequestration in biomolecular condensates directs cell fate transitions. https://doi.org/10.1101/2025.05.08.652299

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