Selective RNA sequestration in P-bodies regulates cell identity

Post-transcriptional regulation is pivotal in guiding the gene expression programs that instruct cell fate decisions. Recent studies emphasize the significance of biomolecular condensates in modulating gene expression through RNA processing and translational control. However, the functional roles of RNA condensates in the context of cell fate specification are unknown. In this study, we profiled the coding and non-coding transcriptome within intact biomolecular condensates known as P-bodies in diverse developmental contexts and vertebrate species. Our analyses revealed the conserved, cell type-specific sequestration of RNAs encoding key cell fate specifiers. Notably, P-body contents did not directly reflect gene expression profiles for a given cell type, but rather were enriched for transcripts characteristic of the preceding developmental stage, which are translationally suppressed and stored within P-bodies. We demonstrate that the forced degradation of P-bodies stimulates the translation of transcripts encoding fate-instructive factors, ultimately re-activating a totipotency transcriptional program in human and mouse pluripotent cells. Mechanistically, microRNAs (miRNAs) facilitate the sequestration of specific RNAs into P-bodies in a context-dependent manner. Accordingly, perturbing AGO2, alternative polyadenylation, and miRNA function profoundly reshapes the RNA content of P-bodies and alters cell fate. Furthermore, we show that adding a miRNA target sequence is sufficient to redirect transcripts to P-bodies and influence stem cell self-renewal. Collectively, our findings establish a direct link between biomolecular condensates and cell fate decisions across vertebrate species.