In striking contrast, macrophage-specific and B cell-specific PU.1-bound regions were significantly co-enriched for motifs for macrophage- and B cell-restricted, lineage-determining transcription factors, respectively (Figure 2A and 2B). This was evident to a similar degree in both promoter-proximal and promoter-distal regions (Table S2). Analysis of the spatial relationships between these co-enriched motifs and the PU.1 motif in each peak revealed that C/EBP and AP-1 motifs were highly enriched within 100 bp of macrophagerestricted distal PU.1 sites, while E2A, EBF, Oct and NF-κB motifs were correspondingly highly enriched near B cell-specific distal PU.1 sites (Figure 2B and 2C, Figure S2B). Conversely, the B cell-specific motifs were depleted in the vicinity of macrophage-specific PU.1 sites, while the regions around B cell-restricted PU.1 sites were depleted of macrophage-specific motifs (Figure 2C and Figure S2B). Secondary PU.1 motifs were also enriched within 100 bp of the central PU.1 motif, particularly at macrophage-specific and commonly bound sites (Figure S2B).
