Size Control of hnRNPK-based Nucleolar Condensates by RNA-Regulated Fusion Dynamics

Abstract

Nucleoli are liquid-like condensates whose size is actively conserved--they remain small, numerous, and resistant to coalescence--yet the molecular mechanisms that constrain their fusion remain poorly understood. Heterogeneous nuclear ribonucleoprotein K (hnRNPK), an RNA-binding protein implicated in nucleolar organization and cancer, interacts directly with the scaffold protein Nucleolin. Combining residue-resolution coarse-grained simulations with biochemical experiments, we find that hnRNPK and Nucleolin condense through distinct interaction networks--a localized cation-{pi}/electrostatic hotspot in hnRNPK versus broadly distributed electrostatic contacts in Nucleolin, reorganized upon co-assembly. To probe how RNAs reshape these condensates, we develop and validate, against re-entrant phase-separation experiments and AlphaLISA binding data, a nucleotide-resolution coarse-grained model for single-stranded RNA. Using this framework, we show that RNA is asymmetrically and preferentially recruited by hnRNPK over Nucleolin, an asymmetry that grows stronger when the two proteins compete for the same RNAs. This selective recruitment sustains a dynamic fission-fusion equilibrium: hnRNPK-containing condensates repeatedly fuse and split rather than coalescing into a single condensate, whereas Nucleolin-containing and ternary condensates fuse into one dominant cluster. These results reveal a molecular mechanism, grounded in sequence-encoded, RNA-controlled fusion dynamics, by which nucleolar condensates conserve a controlled, non-coalescing size despite their liquid-like character.