Figure 4. Evidence for competition between Rap1 and nucleosomes.

(a) Colorimetric representation of in vivo nucleosome occupancy centered on Rap1 binding motifs. Loci ordered by Rap1 residence time (top) or Rap1 occupancy (bottom). The total number of Rap1 targets in each group is shown in parentheses. To the right are plots of the average nucleosome occupancy for each group centered on the Rap1 motif. Targets with multiple Rap1 motifs are represented by one randomly chosen motif. (b) Same as (a) for in vitro nucleosome occupancy. (c) Histone H3 turnover vs. Rap1 residence for ribosomal protein genes (red) and other targets (blue). (d) The number of Rap1-nucleosome interactions²² detected within each Rap1 target peak boundary on a log₁₀ scale. (e) Relative change in nucleosome occupancy following Rap1 depletion²³ centered on Rap1 motifs grouped residence. A value of zero represents no relative change in nucleosome occupancy. (f) in vitro Rap1 affinity for its cognate target as measured by Protein Binding Microarray (PBM)²⁴ compared to Rap1 residence. Colors represent histone H4 occupancy z-scores (> −1.5 purple (high),< −1.5 green (low)¹⁷. (g) Top position weight matrix motifs discovered for Rap1 targets grouped by residence. The number of targets for each group is in parentheses. (h) All motifs from the top position weight matrix for each residence group are colored by their A/T (purple) or G/C (green) content at each motif base position. (i) Percentage of A/T content for the entire motif (blue), AA/AT/TA/TT at the 12^th and 13^th motif position (green), TT at the 12^th and 13^th position (purple) and GG/GC/CG/CC at the 12^th and 13^th position (red) for Rap1 targets grouped by residence and telomeric regions.