Fig. 2

Nucleosome repeat length shortening in cancer. A Frequencies of distances between dyads of DNA fragments protected from MNase digestion in paired normal and tumour breast tissue samples from patient P2. B Genome-wide NRL values calculated for each sample reported in this study. The difference of NRLs between normal and tumour tissues is statistically significant (p = 0.014, paired sample t test). Open squares—average values across all samples in a given condition; horizontal lines—median values for a given condition. The colours of the points corresponding to NRL values in N/T tissues are assigned per patient and per experiment type as follows: MNase-seq: patient P1 (black), P2 (red), P3 (blue), P4 (green); MNase-assisted H3 ChIP-seq: patient P1 (violet), P3 (brown), P4 (cyan). Panels A and B use DNA fragments of sizes 120–180 bp. C NRL in normal (grey violins) and tumour (beige violins) breast tissue calculated inside genomic regions enriched with 160–180 bp DNA fragments (“long nuc”) and depleted of 160–180 bp fragments (“short nuc”). The colours of the points are assigned per patient and per experiment type in the same way as in B. Paired-sample t test p values are indicated on the figure. Open squares—average values across all samples in a given condition; horizontal lines—median values for a given condition. D NRL in normal and tumour breast tissue samples from patient P2 inside genes which are marked by nucleosome loss or gain at their promoters (black), compared with NRL calculated genome-wide in 10 kb regions with low-GC content (< 40%) (red) and high-GC content (> 40%) (blue). E NRL in normal (black) and tumour breast tissues from patient P2 from this study (red), calculated inside genes which are highly- or lowly expressed in a healthy state (circles) or breast cancer (squares). This analysis is based on 3,000 genes with largest and smallest RSEM values in normal/cancer cells reported by the TCGA Cancer Atlas. F NRL in MCF-7 and T47D breast cancer cells as well as human embryonic stem cells (hESC), compared with NRL in normal and tumour breast tissues. For T47D and hESC, each point corresponds to one replicate experiment. For MCF-7, each point corresponds to a sample with different MNase digestion level. For breast tissues, each point corresponds to one sample from this work, in a subset of genomic regions enriched with DNA fragment sizes in one of the following ranges [100–120 bp], [120–140 bp], [140–160 bp], [160–180 bp], [180–200 bp]