Fig. 1: Lesion-stalled Pol II is resolved in UVSSA-KO cells by a CSA- and ubiquitination-dependent manner.

a Schematic representation of Damage-seq and PADD-seq. For Damage-seq, genomic DNA extracted from UV-irradiated cells are sonicated and ligated to the first adapter, followed by immunoprecipitation (IP) with the lesion-specific antibody. The precise sites of the lesions are determined by the stalling of primer extension with high-fidelity DNA polymerase. After the ligation of the second adapter, the primer extension products are PCR-amplified and sequenced. For PADD-seq, Pol II-associated DNA are enriched by regular chromatin-immunoprecipitation (ChIP) with an anti-pan-RPB1 antibody. Purified DNA fragments are subjected to Damage-seq. TS, template strand; NTS, non-template strand; TSS, transcription start site; CPD, cyclobutane pyrimidine dimer; kb, kilobase; RPKM: reads per kilobase per million reads mapped. b Diagram of the experimental design for the measurement of TCR (by Damage-seq) and Pol II-CPD interaction (by PADD-seq). c Meta-gene analysis of PADD-seq signals around TSSs and TESs for active genes longer than 50 kb (n = 2790) under indicated conditions. KO, knockout; TES, transcription end site; CRLi, cullin family E3 ligases inhibitor; Ctrl, control (XP-C cells). d Quantification of Pol II retention on damage sites by relative change of PADD-seq signals from 0.5 h to 2 h on each gene. Active genes longer than 20 kb were selected (n = 4488). Pol II, RNA polymerase II. e Meta-gene analysis of Damage-seq signals around TSSs for active genes longer than 50 kb (n = 2790) under indicated conditions. Cells were collected immediately (0 h) or at 8 h after UV irradiation. Fraction CPDs remaining was calculated as the ratio of 8 h to 0 h. f Violin plots of relative Damage-seq signals on each active gene (n = 6406). Log2 value of the ratio of fraction CPDs remaining on TS to that on NTS was calculated. For d and f, the bounds of box represent the interquartile range (IQR, 25%–75%); the white dot in the box indicates the median; the whiskers indicate the range within 1.5 IQR; P value was calculated using two-tailed paired Student’s t-test. See also Supplementary Fig. 1 and 2. Source data are provided as a Source Data file.