Fig. 6: TRABI-seq detects divergent transcription and provides evidence for XPF sequence preference. | Nature Communications

Fig. 6: TRABI-seq detects divergent transcription and provides evidence for XPF sequence preference.

From: Trabectedin derails transcription-coupled nucleotide excision repair to induce DNA breaks in highly transcribed genes

Fig. 6

Strand-specific profile of the mean DNA break count and its 95% c.i. (shade) throughout the gene body and adjacent regions in U2OS WT (a), CSB-KO (b), XPC-KO (c) and XPA-KO (d) after 2h exposure to trabectedin and subsequent 2h recovery. n = 4425 protein-coding genes (top 30% expressed in unexposed U2OS WT) are considered to compute the means and c.i. Solid, dashed, and dotted curves: means of different biological replicates. Strand- and gene-length-specific profile of the mean DNA break count and its 95% c.i. (shade) in the ±5 kilobase (Kb) proximity of TSS in TC-NER proficient cell lines U2OS WT (e) and XPC-KO (f), zooming out (left panel) and in (right). The same gene set as in a–d. Methods provide gene numbers per gene-length group. DNA break count in two branches of divergent transcription in U2OS WT (g) and XPC-KO (h) versus gene expression. +5 Kb: within 5 Kb downstream of; −5 Kb: within 5 Kb upstream of. The plots are built analogously to Fig. 4a–d (lower panels). Supplementary Fig. 6g–h presents respective correlation analysis for all replicates. Gray band: endogenous DNA breaks not caused by trabectedin treatment (upper quartile of DNA break count in unexpressed genes); this threshold shows that around 25% (lower boundary of boxes) of highly expressed genes may not have trabectedin-induced breaks upstream of the TSS. Sequence logos around DNA breaks in U2OS WT (i) and XPC-KO (j). We considered DNA breaks located in the indicated regions of the gene set used in a–f. The percentage of G at position 1 (+2 relative to the break) is shown. Data: all biological replicates united per cell line. Supplementary Fig. 6i–j: analogous analysis for TC-NER-deficient cell lines. a–f: bin sizes are absolute (a base number) or relative (a percentage of gene length; the corresponding average base number indicated in parentheses). a–h: arb. unit: Methods describe DNA break count normalization. a–j TSS and TES: transcription start and end sites; Kb: kilobase; b: base. Source data are provided as a Source Data file.

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