Blurring of High-Resolution Data Shows that the Effect of Intrinsic Nucleosome Occupancy on Transcription Factor Binding is Mostly Regional, Not Local
Figure 2
Crosslinking of chromatin preferentially protects sites that are otherwise nuclease sensitive and correlated with transcription factor binding.
(A) (top): Tag counts of uncrosslinked chromatin (orange) and crosslinked chromatin (gray) in the region of bound Abf1 sites. Tag counts have been symmetrized around the Abf1 site. Tag counts for the crosslinked sample were normalized to the uncrosslinked sample between 100–600bp from the Abf1 site to highlight the concordance in the phased nucleosome locations and occupancies. (bottom): Tag count difference map (green) in the vicinity of bound Abf1 sites showing excess tags in crosslinked chromatin vs. uncrosslinked. (B) Predictive value of nuclease-resistant tag counts for binding of 41 TFs. ROC AUC values on the y-axis were calculated based on the difference map (excess tag counts found in the crosslinked sample compared to the uncrosslinked). ROC AUC values on the x-axis were calculated as in Figure 1. The dashed line is for y = x. Binding of most TFs is predicted by the difference map well as well as, or even better than, by the under-representation of tags in the normal chromatin preparation.