Comparison of histone modification profiles in mES, neuronal progenitor and mouse embryonic fibroblast cells. The repeat types were clustered based on their enrichment profiles across four different histone marks in three cells, so that the order of repeat types is the same for each histone methylation mark shown. Green bars mark major clusters of enrichment, with numbers corresponding to mES clusters from Figure 3a. The orange bar marks a set of repeats, composed predominantly of LTRs, that acquires H3K27me3 in NP cells. See Figure S7 in Additional file 1 for a complete plot.