To investigate whether the remodelling of H3K4me1-marked nucleosomes in the Group II peaks were consistent with changes in nucleosomal occupancy, we mapped nucleosome positions using MNase-Seq (Schones et al., 2008) in PUER cells at 0 h and 1 h after treatment with tamoxifen. Analysis of the nucleosome pattern before tamoxifen treatment at the 7428 regions where PU.1 is maximally gained at 1 h revealed a semi-regular pattern exposing the prospective PU.1 binding site on an expanded linker region between adjacent nucleosomes (Figure 4D). This pre-existing pattern is possibly due to low levels of PU.1 binding that are below detection by ChIP-Seq at the current sequencing depth, as it is possible to detect PU.1 at many of these sites in untreated PUER cells using qPCR-based ChIP assays (data not shown). Induction of PU.1 binding led to nucleosome remodelling across the entire set of induced sites, analogous to that suggested by the Group II H3K4me1-marked nucleosomes, resulting in further expansion of the linker region centered on the PU.1 binding site and compression of nucleosomes in either direction along the DNA for approximately
