Characterization of the promoters that contain E2F consensus motifs but are not bound by E2F1 in MCF7 cells. The set of 1566 consensus E2F1 motifs that were unoccupied by E2F1 in MCF7 cells was compared with the top 2000 targets identified in ChIP-chip assays for E2F4, E2F6, H3me3K7, H3me3K9, and 5-meC (Xu et al. 2007; Komashko et al. 2008). The percentage of promoters in the “unoccupied E2F motif” set that was bound by E2F4 or E2F6, which was found in silenced chromatin (but not bound by E2F4 or E2F6), or was in silenced chromatin and bound by E2F4 or E2F6 is shown. The number of the 1566 promoters bound by the various combinations of silencing marks and E2Fs are shown in Supplemental Table S4. For comparison, the overlap between the silencing marks and a set of 1566 randomly chosen promoters is shown in Supplemental Figure S1.
