Figure 4

PU.1 binding sites with short motif selectively targeted by other factors including PML/RARα. (A) Venn diagram displaying the overlap of PU.1 binding regions and PML/RARα binding regions in NB4 cells. (B) Schematic illustration of the PU.1 motif comparison between PU.1 binding regions and PML/RARα binding regions. PU.1-specific is the subpopulation of PU.1 binding regions that do not overlap with PML/RARα binding regions. PU.1&PR is the subpopulation of PU.1 binding regions that overlap with PML/RARα binding regions. The color bars indicate the percentages of the regions with the long, only short PU.1 motif and neither, with green, orange and gray, respectively. (C) Bar plot of Motif RARE half (RAREh) enrichment in three subpopulations. PU.1-specific and PU.1&PR mean the same as above. PR-specific is the subpopulation of PML/RARα binding regions that do not overlap with PU.1 binding regions. (D) Scatter plot showing the covered percentages of PU.1-specific binding sites with the long motif versus that with the short motif by ENCODE ChIP-seq data sets of transcription factors except PU.1. (E and F) Box plot of the covered percentages in three PU.1 binding sets, including PU.1&PR, Long and Short, by ENCODE ChIP-seq data sets of PU.1 and other factors, respectively. The “Long” represents the PU.1-specific binding set with the long motif, while the “Short” represents those only with the short motif. The differences between the two binding sets were assessed using the paired t-test. The p-values are shown in the panels. (G and H) Heat map of functional enrichment with the items of PANTHER gene ontology in biological process and KEGG pathways. The enrichment level (-10*log10 (p-value)) was indicated with red color. The “PU.1&PR”, “Long” and “Short” represent the corresponding gene sets to the sets of binding sites defined above.