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

Nucleoli are small, numerous, and resistant to coalescence. They remain small and actively conserved. The size regulation of nucleoli is a subject of ongoing research. Heterogeneous nuclear ribonucleoprotein K (hnRNPK) is an RNA-binding protein that plays a role in nucleolar organization and cancer. hnRNPK interacts with Nucleolin, another protein.

Coarse-grained simulations and biochemical experiments were used to study the interaction networks between hnRNPK and Nucleolin. These interactions lead to condensation of nucleoli through distinct mechanisms - a localized cation-{pi}/electrostatic hotspot in hnRNPK and broadly distributed electrostatic contacts in Nucleolin, which are reorganized upon co-assembly.

A nucleotide-resolution coarse-grained model for single-stranded RNA was developed and validated to understand how RNAs reshape these condensates. The model revealed that RNA is asymmetrically and preferentially recruited by hnRNPK over Nucleolin. This asymmetry strengthens when the two proteins compete for the same RNAs.

This selective recruitment results in a dynamic fission-fusion equilibrium. Condensates containing hnRNPK repeatedly fuse and split rather than coalescing into a single condensate. In contrast, condensates containing Nucleolin and ternary condensates fuse into one dominant cluster. These findings unveil a molecular mechanism based on RNA-encoded sequence dynamics, which maintains nucleolar condensates at a controlled, non-coalescing size.