Fig. 1: Base-resolution quantitative UV damage footprinting by sequencing.

a Quantification of UV damage (CPD) formation propensity at single-base resolution can reveal changes in local UV damage patterns induced by proteins binding to DNA inside of living cultured cells. b Capture CPD-seq enables deep sampling of UV damage formation at regions of interest through enzymatic digestion at CPDs (T4 endonuclease V) combined with hybridization of complementary capture oligonucleotides. c Targeted regions (positions are relative gene TSSs). d Nine independent cellular samples including serum starved and stimulated and nine naked DNA samples were UV-exposed and assayed, in addition to three non-UV-exposed controls. e Number of CPDs detected per dinucleotide in the assayed regions, based on the combined cellular, naked or unexposed samples. f Number of CPDs detected per individual diPy in each of the targeted sequences, based on the combined cellular or naked samples. g CPD detections in the FOS promoter region in genome-wide non-enriched CPD-seq data¹⁰ (left) compared to Capture CPD-seq (right), illustrating the per-base quantitative nature of the data (total detections in cellular samples shown). h PCA analysis of EGR1 CPD count vectors from the 18 UV-exposed samples reveals that samples cluster based on experimental condition. i Quantile-quantile plot (expected vs. observed uncorrected P-values, two-sided negative binomial test) showing changes in CPD formation at some positions in the EGR1 promoter in serum-stimulated compared to starved cells. CPD Cyclobutane pyrimidine dimer, TSS Transcriptome start site, diPy dipyrimidine. Source data are provided as a Source Data file.