Hierarchical Nuclear Architecture in Pre-mRNA Splicing: From IDRs to Speckles and Meshworks

The spatial organization of the eukaryotic nucleus plays a pivotal role in regulating pre-mRNA splicing; however, the underlying principles governing this organization remain incompletely understood. Recent advances in imaging and sequencing technologies have revealed that splicing regulation is orchestrated across multiple hierarchical levels, from nanoscale protein–RNA interactions to large-scale nuclear architecture. Intrinsically disordered regions (IDRs) in RNA-binding proteins (RBPs) mediate multivalent interactions that drive liquid–liquid phase separation, leading to the formation of dynamic biomolecular condensates, such as nuclear speckles, paraspeckles, and nuclear stress bodies (nSBs). These structures act as functional hubs that modulate RNA processing efficiency and respond to cellular stress. In addition, emerging evidence highlights nucleus-wide RBP meshworks that spatially organize co-transcriptional splicing through dynamic RNA-dependent interactions. The interplay between these condensates and meshworks forms a spatially organized network that fine-tunes the efficiency and fidelity of pre-mRNA splicing. Collectively, this review presents a unified model in which phase separation and higher-order nuclear architecture coordinately regulate transcriptomic output in space and time.