To examine the relationship of PU.1 binding sites and gene expression patterns, we performed transcriptome analysis of elicited macrophages and splenic B cells and correlated binding at each PU.1 site with the mRNA level of the closest gene. Out of 17004 genes analyzed, 58.0% and 54.9% were associated with at least one PU.1 peak in macrophages and B cells, respectively, with most of these genes exhibiting multiple peaks (Figure 1E). Genes associated with PU.1 binding were more likely to be expressed (Figure 1E) and the number of peaks per gene was positively associated with gene expression in both cell types (Figure 1F). Cell type-specific PU.1 binding was also correlated with cell type-specific gene expression (Figure 1G and Figure S1D). While this relationship was significant (Pearson correlation coefficient r2 = 0.30, p < 10−100), even cell type-specific genes often exhibited a mix of cell type-specific and commonly bound PU.1 peaks (e.g., Figure 1B, peak position (b)). The association between cell-specific PU.1 binding and cell-specific gene expression was strongest for peaks close to the TSS (Pearson correlation coefficient r2 = 0.45, p<10−100),
