Blurring of High-Resolution Data Shows that the Effect of Intrinsic Nucleosome Occupancy on Transcription Factor Binding is Mostly Regional, Not Local
Figure 3
Some of the nucleosome position information correlated with transcription factor binding is intrinsic to genomic sequence.
(A) ROC AUC values quantifying the predictive value of low nucleosome occupancy based on chromatin in vivo (x-axis) or chromatin reconstituted in vitro from genomic DNA and histones (y-axis). The in vivo data are as shown in Figure 1; values based on the in vitro reconstituted chromatin were calculated in the same manner. The positions of four TFs that are used in panel B are indicated by colored circles. The solid line is the best linear fit through the data (R = 0.90), excluding outliers Abf1 and Reb1 (gray circles). That Abf1 and Reb1 are truly outliers was established by assessing the deviation from a fit to all the data: these two TFs deviate from that line by a distance that exceeds the average distance by more than 2.5 standard deviations. The dashed line, y = x, corresponds to the expected fit if in vitro and in vivo nucleosome data were entirely equivalent. (B) Correlation between the ChIP enrichment value at perfect consensus binding sites and tag counts from nuclease-protected mono-nucleosome-sized DNA obtained from in vivo chromatin (left panels) or in vitro reconstituted chromatin (right panels). The best linear fits between log(ChIP-qPCR enrichment value) and tag count are shown.