Fig. 7.

Comparative topology of H3K9me3, a global marker for transcriptionally repressed (hetero)chromatin and H3K4me3 in relation to chromatin density maps. a 3D-SIM light optical mid-sections from whole 3D acquisitions of nuclei and representative inset magnifications delineating DAPI stained DNA (gray), immuno-stained H3K4me3 (green) and H3K9me3 (red). H3K4me3 marks decondensed chromatin sites and lines compacted CDCs (compare Fig. 5). H3K9me3 marks highly compacted chromatin clusters but is also seen at decondensed sites (arrows). Scale bars 2 µm; insets 0.5 µm. b Graphs highlighted with yellow background relative signal distribution of H3K4me3 (green) and H3K9me3 (red) within respective DAPI defined DNA intensity classes. p < 0.001 for DAPI vs. H3K4me3 and H3K4me3 vs. H3K9me3. Graphs highlighted with light-blue background quantified levels of relative enrichment (positive values) or depletion (negative values) of H3K4me3 (green) and H3K9me3 (red) signals relative to DAPI signals reveal a relative depletion of H3K9me3 signals in classes 1 and 2 in undifferentiated cells (progenitors and precursors) and a relative enrichment of H3K9me3 signals in classes 6 and 7 in monocytes. In both cases the signals are distributed similar to the DAPI intensity classified distributions for the remaining classes. n Number of analyzed nuclei; error bars standard deviation