YY1-concentration-dependent formation of mechanically distinct DNA condensates through different interaction mechanisms

Abstract

The transcription factor Yin Yang 1 (YY1) plays roles in chromatin organization, combining sequence-specific DNA recognition via zinc finger domains with multivalent interactions mediated by intrinsically disordered regions. While YY1 has been implicated in phase separation and enhancer-promoter communication, how its structured and intrinsically disordered regions cooperate to shape DNA-protein assemblies remains unclear. Here, we used single-molecule DNA curtain fluorescence imaging to dissect the molecular basis of YY1-DNA assembly. We found that YY1 induces higher-order assembly in a concentration-dependent manner. At moderately high concentrations, YY1 formed weakly-linked DNA condensates in which dynamic, liquid-like YY1 molecules are scaffolded by relatively immobile, solid-like DNA. At high concentrations, zinc finger-mediated bridging dominates, producing strongly-linked condensates. Distinct domain-deletion mutants selectively impaired either weakly-(soft) or strongly-linked (hard) DNA condensate formation, indicating that these architectures are generated by separate domain-dependent mechanisms. Our findings establish a domain-level framework for DNA condensate formation and highlight how transcription factors can integrate specific and non-specific DNA interactions to control the material state of chromatin and would influence genome regulation.