Figure 5.

Statistical PIC binding preferences to both TFIID-dominated and SAGA-dominated genes negatively correlate with the nonconsensus free-energy landscape, yet these two groups of genes are distinguishable based on the average free-energy profiles. (A) Correlation between the minimal value of the free energy of nonconsensus TF-DNA binding, $f_{\text{min}}=\text{min}\left(f\right)$, and the average GTF occupancy of 3068 TAF1-enriched genes. The correlation is computed for individual genes in nonoverlapping windows of 80 bp within the entire interval $(-990,990)$ around the TSS. The data are then sorted into 50 bins. (B) Similar to A, but with $f_{\text{min}}$ correlated with the nucleosome occupancy of these TAF1-enriched genes. (C) Correlation between $f_{\text{min}}$ and the average GTF occupancy of 877 TAF1-depleted genes. The correlation is computed for individual genes in nonoverlapping windows of 80 bp within the entire interval $(-990,990)$ around the TSS. The data are sorted into 50 bins. (D) Similar to C, but now $f_{\text{min}}$ is correlated with the nucleosome occupancy of these TAF1-depleted genes. (E) The average free energy of nonconsensus TF-DNA binding per bp, $\langle f\rangle$, for a larger set of 4755 TAF1-enriched genes, and 1135 TAF1-depleted genes, around the TSSs.