Fig. 4
From: i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks
G4-related genome instability. a Schematic representation of G4 structure. b,c Averaged i-BLESS signal in a 200 bp window centered on G4s, calculated by aligning all G4 centers and using 10 bp bins for wild type and pif1-m2 cells. Mean values (solid line) and standard deviation (color shade) for three biological replicates are shown. d DSB densities inside G4 sequences for wild type (blue, wt) and pif1-m2 (purple) cells. DSB density was defined as a number of i-BLESS reads mapped to a given region, divided by region length. Median (center line), lower/upper quartiles (box limits), and lower/upper adjacent (whiskers) are shown. P value was calculated by paired Wilcoxon signed-rank test, ***P < 0.001. e DSB densities inside and outside of G4s containing loops of the indicated length. G4: canonical G-quadruplex structures identified by AllQuad software (see Methods). Flanks: left and right adjacent regions half of the length of their corresponding G4. G4 sequences are classified into: G4 L1–4: all loops ≤ 4 nt; G4 L5–7: all loops ≤ 7 nt, but at least one loop > 4 nt; G4 L8–16: all loops ≤ 16 nt, but at least one loop > 7 nt. Median (center line), lower/upper quartiles (box limits), and lower/upper adjacent (whiskers) are shown. P values were calculated by two-sided Kolmogorov-Smirnov test, ***P < 0.001. f Average DSB densities for G4 loops of length varying from 1 to 7 nucleotides and control genomic regions of the same length. The 1–7 nt-long control genomic regions were randomly selected. Mean values and standard deviation for three biological replicates are shown. The number of reads were normalized to the total mapped reads to compare DSB densities between replicates
