The unique interactions with nucleosome and hexasome of pioneer transcription factor RFX5

Among the Regulatory Factor X (RFX) transcription factor family, RFX5 is the only reported member capable of binding to the nucleosome and inducing nucleosome remodeling n vivo. Dysfunctions in RFX5 have been implicated in various diseases. Here, we present the cryo-EM structure of the RFX5-nucleosome complex, revealing that RFX5 binds to the nucleosome at the superhelical location (SHL) +2. By forming extensive interactions with both histones and the nucleosomal DNA, RFX5 locally distorts DNA and detaches DNA termini, which could potentially increase DNA accessibility and transcription in vivo. Interestingly, our cryo-EM analysis of the RFX5-nucleosome dataset revealed the presence of a RFX5-hexasome complex, whereas no hexasome was observed in the free nucleosome dataset, suggesting that RFX5 may induce the formation of the hexasome. Notably, compared to the RFX5-nucleosome structure, the RFX5-hexasome structure lacks the proximal histones H2A and H2B, resulting in longer nucleosome DNA detaching from the histones. Overall, our findings provide insights into the mechanisms by which RFX5 binds to and remodels nucleosomes.