Transcription factor interactions promote binding to non-cognate DNA sites

Recruitment of transcription factors (TFs) to non-cognate DNA sequences is widely observed, but the underlying mechanisms remain poorly understood. Here, we show that, within the nucleosome, Sox2 can bind an Oct4 motif, interact with the Oct4 POU-specific domain, and displace the Oct4 homeodomain. We also observe Sox2 binding at multiple near-canonical and non-canonical DNA sites, with these interactions promoted by a second Sox2 molecule or by nearby nucleosome-bound Oct4. The TF-TF interactions can bridge across DNA gyres, bringing together binding sites that are distant in linear DNA but spatially proximal on the nucleosome. We further find that Sox2 can engage across nucleosomal DNA gyres through loop regions and/or intrinsically disordered segments, providing an additional mode of chromatin binding. Together, our structural and biochemical data reveal how TF-TF interactions change DNA recognition on the nucleosome, enabling binding to non-cognate sequences and expanding the repertoire of pioneer factor interactions on chromatin.