Fig. 4

Effects of linker histones on nucleosome repositioning in breast cancer. A Correlation of GC content and H1 occupancy in 10-kb regions genome-wide. H1 variants H1.0, H1.2 and H1.5 preferentially bind AT-rich regions, while H1.4 and H1X have a higher affinity for GC-rich regions. B–D Averaged aggregate profiles of H1 occupancy around different types of DNA fragments protected from MNase digestion. These profiles were first calculated individually for each MNase-seq tumour tissue sample reported in this study, and then averaged across all patients. B Occupancy of H1 variants around nucleosome dyads calculated for different DNA fragment sizes. C H1 occupancy in the region [-50, 50] bp around nucleosome dyad calculated for different H1 variants as a function of DNA fragment size. D Average H1X occupancy in T47D breast cancer cell line calculated around DNA fragments of 160–180 bp in normal (black lines) and tumour breast tissues (red). E Average H1X occupancy profiles around the consensus set defined based on all tissue samples from this study, of common nucleosomes (black), and nucleosomes which are gained (blue) and lost in cancer (orange)