Fig. 3: Trabectedin-induced DNA breaks are mapped genome-wide with upgraded GLOE-Seq.

a Principle of GLOE-Seq that maps DNA breaks in a genome-wide and strand-specific fashion and provides an estimate of the frequency of individual breaks in a population of cells. The distal adapter with a unique molecular identifier (UMI) is an upgrade from the original GLOE-Seq protocol²⁹. Pos: position, chr: chromosome, OH: free 3’ hydroxyl. b DNA break count along chromosome 19 in 4 cell lines after 2h exposure to trabectedin or vehicle (DMSO) and subsequent 2 h recovery. Solid lines: individual biological replicates, 2 for 50 and 0 nM drug in WT, 50 nM in CSB-KO; 1 for 0 nM in CSB-KO; 3 for 50 and 0 nM in XPC-KO and XPA-KO. Vertical bar heatmap: gene expression level in unexposed U2OS WT. All data are shown per 100-Kb bin. We summed DNA-break counts within this chromosome and provided the min-max range of this value across replicates for either treatment condition (shown also in Supplementary Fig. 4d). P-value: Mann-Whitney U test with the one-sided alternative hypothesis that the trabectedin-treatment-related distribution is stochastically greater than the control distribution (see more details in Supplementary Fig. 4e). TPM, transcripts per million transcripts. Arb. unit, arbitrary unit: Methods describe DNA break count normalization. c Genome-wide correlation of DNA break count with the abundance of DNase I hypersensitivity (HS) sites (transcriptional activity), H3K4me3 (active gene promoters), H3K4me1 (active enhancers) and H3K27ac (active promoters and enhancer) as well as gene expression. Bars: mean, markers: biological replicates (n = 2) of break mapping. N = 28,513 genomic bins to compute the correlation. Source data are provided as a Source Data file.