Chromatin Binding Regulates Phase Behavior and Morphology of Condensates Formed by Prion-Like Domains

Abstract

Many transcription factors (TFs) contain intrinsically disordered regions (IDRs) and are thought to form biomolecular condensates in the nucleus. These proteins can be conceptualized as di-block polymers, with the IDR driving homotypic protein-protein interactions and the DNA-binding domain (DBD) mediating heterotypic interactions with chromatin. While in vitro studies have predominantly reported micron-scale, spherical condensates in the absence of chromatin, TF condensates in live cells exhibit strikingly different behavior—adopting diverse, nanoscale, often aspherical morphologies and displaying sub-diffusive dynamics. Here, we show that this distinct phase behavior can arise from TF-chromatin interactions, using engineered fusion proteins with tunable IDR-DBD architectures. Specifically, we fused the prion-like domain (PLD) of the SS18 subunit from the mammalian SWI/SNF complex—a domain known to drive homotypic phase separation—to the DBD of the pioneer factor FOXA1. While SS18PLD alone forms large, spherical condensates in cells, its fusion with FOXA1DBD leads to condensates that re-localize to chromatin, adopt aspherical morphologies, and exhibit chromatin-wetting behavior. Disruption of DBD-chromatin binding shifts condensate morphology toward a mixed or spherical state, implicating chromatin affinity as a key regulator of condensate coarsening and spatial organization. Coarse-grained simulations recapitulate these observations, revealing a finely balanced interplay between PLD-PLD and DBD-DNA interactions that collectively determine condensate dynamics and structure. Together, our findings demonstrate that chromatin binding is a critical modulator of transcriptional condensate behavior in vivo.

Keywords: Phase separation, Transcription factor, DNA-binding proteins, Intrinsically disordered proteins, viscoelastic condensates