Blurring of High-Resolution Data Shows that the Effect of Intrinsic Nucleosome Occupancy on Transcription Factor Binding is Mostly Regional, Not Local
Figure 4
The effect of intrinsic sequence-dependent chromatin structure on TF binding is not dependent on exact nucleosome positioning.
(A) Windowing scheme to simulate lower resolution data. Nucleosome tag counts around genomic loci (TF binding sites or control loci) were averaged over windows of 15, 40, 75, 150, 300 and 600bp as indicated by the lines at the bottom of the panel. Average tag counts around Abf1-bound sites are shown as in Figure 1A, along with the locations of nucleosomes inferred from those data. (B) ROC AUC values for the prediction of Abf1 binding sites based on low nucleosome occupancy, averaged over the indicated window sizes. The difference in ROC AUC in going from high resolution data (15bp) to simulated low resolution data (600bp) is indicated by the arrow. This measure of the effect of data blurring was used in panels C and D. (C) Effect of averaging in vivo nucleosome data on the correlation between nucleosome occupancy and TF binding for 41 TFs. Coloring of the histogram bars is based on the standard deviation of the values for abs(Δ(ROC AUC)), as indicated in the legend. (D) Same as panel C except that data from in vitro reconstituted chromatin was used rather than in vivo chromatin.