Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence

Understanding cellular coordination remains a challenge despite knowledge of individual pathways. The RNA exosome, targeting a wide range of RNA substrates, is often downregulated in cellular senescence. Utilizing an auxin-inducible system, we observed that RNA exosome depletion in embryonic stem cells significantly affects the transcriptome and proteome, causing pluripotency loss and pre-senescence onset. Mechanistically, exosome depletion triggers acute nuclear RNA aggregation, disrupting nuclear RNA-protein equilibrium. This disturbance limits nuclear protein availability and hinders polymerase initiation and engagement, reducing gene transcription. Concurrently, it promptly disrupts nucleolar transcription, ribosomal processes, and nuclear exporting, resulting in translational shutdown. Prolonged exosome depletion induces nuclear structural changes resembling senescent cells, including aberrant chromatin compaction, chromocenter disassembly, and intensified heterochromatic foci. These effects suggest that dynamic turnover of nuclear RNA orchestrates crosstalk between essential processes to optimize cellular function. Disruptions in nuclear RNA homeostasis result in systemic functional decline, altering the cell state and promoting senescence. To explore the systems-level function of RNA metabolism, we investigated the effects of depleting the RNA exosome over time in mouse embryonic stem cells using an auxin-inducible system. We established AID-FBEXOSC2 ESCs to deplete the essential exosome component, EXOSC2. Addition of the auxin analog indole-3-acetic acid (IAA) induced rapid degradation of EXOSC2 protein. To investigate the impact of EXOSC2 on nuclear functions, we performed profiling of RNA subcellular localization, nascent transcription, gene expression, epigenetic landscape and chromatin organization in AID-FBEXOSC2 ESCs treated with IAA for a period of 20 hours. All experiments were designed to reveal the differences between control and EXOSC2-depleted ESCs.