Fig. 7: CSB is required for the repair of DPCs at transcriptionally active loci.

a, DPC-seq coverage per gene in WT RPE1 cells versus CSB^−/− cells 6 h after formaldehyde treatment. Blue highlights genes with significantly higher DPC coverage in CSB^−/− cells, indicating they undergo CSB-dependent DPC repair. b, Metagene profile of DPC-seq coverage in WT versus CSB^−/− RPE1 cells treated with formaldehyde and with or without 6 h recovery. Metagene specifically shows CSB-dependent genes from a. c, The same as b but showing log₂-fold change coverage for CSB^−/−/WT RPE1 cells with or without 6 h recovery after formaldehyde treatment. d, The level of different genomic features in CSB-dependent genes from a and transcription-dependent genes relative to the non-changing group. rRNA, ribosomal RNA; tRNA, transfer RNA. e, Per gene RNAPII occupancy versus DNA accessibility, as determined via ATAC-seq in RPE1 cells (GEO: GSE209659) showing CSB-dependent genes from a and non-changing genes, including the percentage of each group that are present in the shown quadrants. f, Log₂-fold change of DPC-seq coverage per gene 6 h/0 h after FA treatment in WT RPE1 cells versus CSB^−/− cells, in genes grouped according to whether they show transcription-dependent DPC repair. Statistics via paired two-sided Wilcoxon test. ***P < 0.001; P values are 0.109 and <2.2 × 10⁻¹⁶ for comparisons in no change and transcription-dependent gene sets, respectively. The box plot shows the upper (Q3) and lower (Q1) quartile boundaries and line at the median. Lower whisker (minimum) is Q1 – 1.5 × IQR and upper whisker (maximum) is Q3 + 1.5 × IQR. For all DPC-seq analyses, n = 3 biological replicates. Source numerical data are available in Source data.