To conversely investigate whether PU.1 itself can also promote binding of one of its cistrome-associated factors, we assessed the genome-wide effects of inducing PU.1 activity on C/EBPβ binding in a PU.1-deficient (PU.1KO) myeloid progenitor cell line (Walsh et al., 2002). In the absence of PU.1, C/EBPβ exhibited a reduced overall binding pattern (22641 peaks), with loss of numerous binding sites associated with locations of PU.1 binding in primary macrophages, illustrated for the macrophage-specific CD14 gene (PU.1KO-Cebpb vs. Mac-Cebpb, Figure 3E). Motif analysis of the C/EBPβ-bound regions in PU.1−/− cells recovered C/EBP, C/EBP:AP-1, AP-1 and RUNX motifs, as well as a non-PU.1 Ets motif (AACAGGAAGT), but not the PU.1 binding motif found in primary macrophages (Figure S3G).
