Yeast Pioneering Transcription Factors Rely On Slowed Dissociation Kinetics To Efficiently Target Nucleosomal Sites

Nucleosomes are key regulators of transcription factor (TF) occupancy by restricting binding and accelerating dissociation rates, while pioneer transcription factors (PF) somehow circumvent nucleosome regulation. Here, we investigate the essential S. cerevisiae TF Reb1, which binds nucleosome entry-exit sites with high occupancy. We show that Reb1 binds its site within nucleosomes, trapping a partially unwrapped state without histone eviction. Reb1 binds nucleosomes and DNA with the same affinity, while surprisingly the binding and dissociation kinetics are 50-fold slower at nucleosome sites relative to DNA. We then found similar results for a separate S. cerevisiae TF, Cbf1. From these results, we propose that Reb1 and Cbf1 are pioneer factors that target sites within nucleosome entry-exit regions by decreasing their dissociation rates to compensate for reduced nucleosome binding. This allows these PFs to induce nucleosome unwrapping and reside at nucleosome entry-exit sites for minutes to facilitate the recruitment of transcription coactivators.