Nucleotide excision repair in Human cell lines lacking both XPC and CSB proteins

Nucleotide excision repair removes UV-induced DNA damage through two distinct sub-pathways, global repair and transcription-coupled repair (TCR). Numerous studies have shown that in human and other mammalian cell lines that the XPC protein is required for repair of DNA damage from nontranscribed DNA via global repair and the CSB protein is required for repair of lesions from transcribed DNA via TCR. Therefore, it is generally assumed that abrogating both sub-pathways with an XPC(−/−)/CSB(−/−) double mutant would eliminate all nucleotide excision repair. Here we describe the construction of three different XPC(−/−)/CSB(−/−) human cell lines that, contrary to expectations, perform TCR. The XPC and CSB genes were mutated in cell lines derived from Xeroderma Pigmentosum patients as well as from normal human fibroblasts and repair was analyzed at the whole genome level using the very sensitive XR-seq method. As predicted, XPC(−/−) cells exhibited only TCR and CSB(−/−) cells exhibited only global repair. However, the XPC(−/−)/CSB(−/−) double mutant cell lines, although having greatly reduced repair, exhibited TCR. Mutating the CSA gene to generate a triple mutant XPC(−/−)/CSB(−/−)/CSA(−/−) cell line eliminated all residual TCR activity. Together, these findings provide new insights into the mechanistic features of mammalian nucleotide excision repair.