DNA bendability regulates transcription factor binding to nucleosomes

Cell fates are controlled by ‘pioneers’, sequence-specific transcription factors (TFs) that bind recognition motifs on nucleosomes (‘pioneer binding’). Pioneers occupy a minority of their recognition sequences in the genome, suggesting that the sequence context regulates their binding. Here we developed PIONEAR–seq, a high-throughput biochemical assay to characterize pioneer binding. We used PIONEAR–seq to assay 11 human TFs for binding to nucleosomes based on Widom 601 versus genomic sequences. We found that pioneer binding, while mediated primarily by the recognition motifs of TFs, is regulated by the broader nucleosome sequence context. Certain TFs, found to be dyad or periodic binders on nucleosomes assembled on synthetic sequences, exhibited end binding to nucleosomes based on genomic sequences. We propose a model where the local bendability of the DNA sequence in nucleosomes is involved in positioning pioneer binding, and thus represents another cis-regulatory layer in eukaryotic genomes.