Fig. 2: Altered CPD formation immediately upstream of transcription starts in expressed genes.

a Overview of CPD changes across 20 promoter regions. The heatmap shows, for each 25 bp window and each promoter, the strongest base-specific change in CPD formation in cellular compared to naked samples. The color scale indicates the maximum absolute log₂ fold change, such that both positive and negative changes are equally considered. Regions are ordered by gene expression level based on CCLE⁴⁸ data (grey bars, right). b Strong stimulation as well as inhibition of CPD damage in upstream regions. The bar graph indicates, for each 25 bp window, the strongest stimulatory effect (maximum log₂ fold change; green) and strongest inhibitory effect (minimum log₂ fold change; red) seen across all promoter regions. Bottom bar graph: lack of net damage change or altered CPD coverage in immediate upstream regions. c Per-position cell/naked CPD level change plots for four promoters (remaining are shown in Supplementary Fig. 6). Strong changes in damage (up to ~16-fold, i.e. 4 log₂ transformed) arise preferably in open regulatory regions indicated by DNaseI hypersensitivity (ENCODE³³), and large changes are generally lacking in lowly expressed genes such as TERT. RPKM, read per kilobase and million reads. Source data are provided as a Source Data file.