Homotypic RNA clustering accompanies a liquid-to-solid transition inside the core of multi-component biomolecular condensates.

RNA-driven condensation plays a central role in organizing and regulating ribonucleoprotein granules within cells. Disruptions to this process-such as the aberrant aggregation of repeat-expanded RNA-are associated with numerous neurological disorders. Here we study the role of biomolecular condensates in irreversible RNA aggregation. We find that physiologically relevant and disease-associated repeat RNAs spontaneously undergo an age-dependent percolation transition inside multi-component condensates to form nanoscale clusters. Homotypic RNA clusters drive the emergence of multi-phasic condensate structures, with an RNA-rich solid core surrounded by an RNA-depleted fluid shell. The timescale of RNA clustering is determined by sequence, secondary structure and repeat length. Importantly, G3BP1, the core scaffold of stress granules, introduces heterotypic buffering to homotypic RNA-RNA interactions and prevents RNA clustering in an ATP-independent manner. Our work suggests that biomolecular condensates can act as sites for RNA aggregation and highlights the chaperone-like function of RNA-binding proteins against aberrant RNA phase transitions.