CBP Occupancy in Drosophila Embryos Figure 3. CBP peaks can be classified based on their change in gd7 embryos. CBP peak values in gd7 embryos were calculated within each CBP bound region from wild-type embryos. Up and down represent regions where CBP occupancy is altered more than 2-fold, unchanged are regions with less than a 2-fold change. In regions for which the gd7 peak values were below 0.5 fold enrichment in log2 scale, CBP was considered lost. A) Number of peaks for each category, their overlap with High Occupancy Target (HOT) regions, mean HOTness, and mean fold enrichment over input of wild-type CBP peaks in log2 scale. B) Fold-change (log2) in CBP occupancy between gd7 and wild-type plotted versus HOTness. Squares indicate mean HOTness and whiskers correspond to 95% confidence intervals. The less CBP occupancy in gd7 compared to wild-type, the lower the HOTness of the region. C–E) gd7 Up is shown in blue, Unchanged in red, Down in green, and Lost in purple. C) Percent overlap of the four categories of CBP peaks with the 300 strongest binding regions for each transcription factor in wild-type embryos. The three cut-offs for the CBP peaks are; 1) no cut-off (all regions included), 2) an average of cut-offs 1 and 3, 3) the highest cut-off corresponding to the ,5% most enriched peaks in wild-type embryos for each category. D) Percent overlap of the four categories of CBP peaks with histone modifications in 0–4 hour embryos (H3K18ac in 2– 4 hour embryos). Cut-offs as in C). E) Percent overlap of the four categories of CBP peaks with gene features. Promoters (+/2500 bp of transcription start site, TSS), introns, and intergenic regions are shown. Less than 3% of the peaks overlap coding regions and 39UTRs and are therefore not shown. Overlap with 59UTRs may result from CBP binding close to the TSS in promoters and is not included. The genome coverage illustrates how common each gene feature is in the genome and is shown in light blue. F) Mean expression of genes associated with the four categories of CBP peaks at different stages of embryo development. Each peak was associated with the closest TSS, and expression of the corresponding gene included in the analysis [46]. Log2 transformed expression values are plotted against developmental time point (0–2 hour embryos (E00-02), etc). Whiskers correspond to 95% confidence intervals. Arrows point to expression in 2–4 hour old embryos. doi:10.1371/journal.pgen.1002769.g003 PLoS Genetics | www.plosgenetics.org 6 June 2012 | Volume 8 | Issue 6 | e1002769