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

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.