Promoters bound by both SUZ12 and OCT4 in Ntera2 cells. DAVID analysis of the set of (A) OCT4+ RNAPII+ and (B) OCT4+ RNAPII− promoters in Ntera2 cells. Shown in parentheses are the P-values, which indicate the probability that the category has been identified by random chance. The entire list of OCT4 targets (having known function) can be found as Supplemental Table S8. (C) PCR analysis of amplicons prepared from Ntera2 ChIP samples obtained using antibodies to the indicated proteins. The NANOG promoter was used for a known OCT4 target gene; NANOG was not expected to be bound by SUZ12 because it is expressed at high levels in Ntera2 cells (i.e., it is an OCT4+ RNAPII+ promoter target). (D) PCR analysis of amplicons prepared from SUZ12 ChIP samples after siRNA-mediated knockdown of OCT4 (hatched bars) or introduction of a control siRNA (black bars) in Ntera2 cells. The horizontal black bar indicates the SUZ12/Total ratio that is expected for nontarget promoters such as NANOG (nontarget genes should show a ratio of ∼1 when equivalent amounts of amplicons prepared from ChIP and total samples are analyzed).
