Fig. 5

NRL shortening as a novel breast cancer marker. A–E NRL values calculated for each individual sample from this study inside different types of genomic regions. A Transcriptionally active A-compartments of chromatin annotated in breast cancer MCF-7 cells; B Regions surrounding gene promoters. C Genomic regions around Alu repeats; D Regions enriched with H1X linker histones in breast cancer T47D cells; E Differentially methylated DNA regions annotated based on cell lines MCF-10A, MCF-7 and MDA-MB-231. Open squares—average NRL values for a given condition; horizontal lines—median values. The colours of the points are assigned per sample as in Fig. 3A. F A scheme of the global change of nucleosome compaction in breast cancer tissues. DNA (black) is wrapped around histone octamers (grey) in contact with linker histones (blue). MNase used in this study or apoptotic nucleases present in situ (orange) cut DNA not protected by nucleosomes and linker histones. Cancer cells have shorter NRL and contain more nucleosomes which are less protected from MNase digestion due to redistribution of linker histone variant H1X, changes in DNA methylation and other factors