To confirm that the PU.1-co-enriched motifs were occupied by the associated cell type-restricted transcription factors, we carried out ChIP-Seq for C/EBPα and C/EBPβ in peritoneal macrophages and for Oct-2 in splenic B cells. For C/EBPα and C/EBPβ, which displayed an almost identical genomic binding pattern, we identified approximately 40000 binding sites (Table S1 and Figure S2C). Of these sites, 13840 (34.6%) were located within 100 bp of a PU.1-bound site, 60% of which were specific to macrophages, while only 1% were localized to B cell-specific PU.1 peaks (4× PU.1 tag difference) (Figure 2D). For Oct-2, the number of identified sites (1191) was smaller than for the C/EBPs, however the results complemented the above findings in that 596 (50%) of all Oct-2 sites were located within 100 bp of a PU.1 peak, of which 43% were B cell-specific and less than 1% macrophage-specific (4× PU.1 tag difference) (Figure S2D). C/EBP and Oct-2 binding sites exhibited similar relationships with gene expression as observed for PU.1 (Figure S2E). C/EBP- and Oct-2-bound regions were highly enriched for C/EBP and octamer motifs, respectively (Figure 2E).
