Fig. 6

ΔNp63 binds to nucleosome edges. a A 217-bp dsDNA library was designed containing p63BS in various nucleosomal positions. A 20-bp-long p63BS (intermediate and high affinity) was placed at different positions 0, 5, 41, 46, 66, 71, and 81 bp away from the dyad. The superhelix location (SHL) is designated for each nucleosome sequence. Within the nucleosome, three different positions (dyad, intermediate, and edge) were chosen with increasing distance to nucleosome dyad. b Nucleosomes containing 16 different sequences were bound to increasing amounts of ΔNp63 and separated by native PAGE. Lanes contain the following: 1–0.25 pmol nucleosomes, 2–5 contain 0.25 pmol of nucleosomes with 18, 36, 71, 142, or 286 nM of ΔNp63 (0.125, 0.25, 0.5, 1, or 2 pmol). Nucleosome and the supershift (Ss) bands are indicated. c, d Relative shift for each nucleosome is determined by counting the frequency of each sequence within the nucleosome band and comparing it to non-specific binding to the 601 sequence. This value is then normalized to the input ratios of nucleosomes. The alternative control sequence 601-modified (601 M) is plotted. Results for each experimental replication are plotted in c, d