Extended Data Fig. 5: CSA and CSB are required for transcription-coupled DPC repair.
From: Transcription-coupled DNA–protein crosslink repair by CSB and CRL4CSA-mediated degradation
a: Representative images of DPC-Seq at 0 hr (blue) and 4 hr (red) after a 1 mM FA pulse of 30 min in MRC-5 WT, CSA and CSB KO cells. Repair is calculated by subtracting 4 hr from 0 hr. Expressed genes were identified by nascent RNA-Seq. b: Violin plots showing DPC repair in MRC-5 WT, CSA and CSB KO cells in expressed genes, sorted into indicated bin based on their expression levels. In the violin plots are normalized to non-expressed genes. In the plots, the median and Q1 and Q3 quartiles are plotted. c: Immunoblot for the indicated proteins in various MRC-5 GFP-RPB1 KI cells with KO of NER factors. This experiment was performed twice with similar results. d: Schematic representation of MRC-5 GFP-RPB1 KI UVSSA KO cells. e: Sequencing of HCT116 CSB-LL1427-28GG knock-in clone, which disrupts the ubiquitin binding domain (UBD). f: Sequencing of HCT116 CSB-K538R knock-in clone, which disrupts the ATPase activity of CSB. g: Schematic depiction of the csb-1 locus (top) and uvs-1 locus (bottom) under which the knockout alleles emc79 and emc80 showing full removal of both genes are indicated. h: Predicted peptide sequences encoded by alleles emc79 (top) and emc80 (bottom) are shown as compared to the N- and C-terminal protein sequences of the wild type CSB-1 and UVS-1 proteins. Red color indicated nonsense sequence. Unprocessed blots are available in source data.
