Nucleosome repositioning in breast cancer.

Liquid biopsies based on cell-free DNA (cfDNA) extracted from body fluids are becoming increasingly popular in the clinic. cfDNA can be released into the blood during apoptosis, necrosis and active secretion by healthy and malignant cells. These cfDNA fragments are not random, they mostly come from nucleosome-protected DNA, because when the genomic DNA is being shredded into pieces these pieces follow the chromatin organization in the cells of origin when they were still alive. Here I analysed high-resolution nucleosome maps in paired tumour and normal tissues and compared these with the corresponding cfDNA from the same breast cancer patients. To evaluate DNA fragmentation patterns, the MNase-seq, MNase-assisted histone H3 ChIP-seq and cfDNA sample reads were classified into fractions with different fragment sizes. I identified an effect of cancer specific shortening of DNA fragments protected from MNase digestion. This cancer-specific cfDNA shortening can be explained by a higher fraction of partially unwrapped/less stable nucleosomes that are more susceptible to digestion. I explored the specific roles of the linker histone variants, nucleotide content, DNA methylation and different DNA sequence repeats in nucleosome repositioning of breast cancer patients. These results suggest that the redistribution of linker histone variants H1.4 and H1X may have particularly pronounced effect on the nucleosome reorganisation in breast cancer patients. These findings highlight the possible explanation for the cancer specific shortening of cfDNA fragments and provide theoretical foundations for cfDNA based diagnostics.