UV damage mapping reveals different impacts of yeast XPD mutations on global genomic and transcription-coupled DNA repair.

Two subpathways of nucleotide excision repair (NER), global genomic (GG-NER) and transcription-coupled NER (TC-NER), remove bulky DNA lesions such as cyclobutane pyrimidine dimers (CPDs). Xeroderma pigmentosum protein D (XPD) is a DNA helicase subunit within the transcription factor IIH complex that is important for DNA unwinding and damage verification during NER. Germline mutations in XPD can not only cause the cancer-prone disease xeroderma pigmentosum (XP), but also a combination of XP with Cockayne Syndrome (CS), a syndrome characterized by neurodegeneration and premature aging. While XP and XP/CS mutations in XPD disrupt NER, their specific effects on the NER subpathways are less well understood. In this study, we introduced two pairs of XP and XP/CS mutations into the yeast RAD3 gene, a homolog of human XPD. Our data indicates that yeast XP/CS mutants are more sensitive to UV radiation and have reduced NER capacity relative to the XP mutants. Using a damage mapping method named CPD sequencing (CPD-seq 2.0), we found that the XP/CS mutations abrogated repair by both GG-NER and TC-NER, while XP mutations impaired GG-NER but retained significant TC-NER activity. Consistent with these results, XPD mutant human cell lines established from individuals with XP/CS were sensitivity to Illudin S, an agent that induces damage repaired by TC-NER. Thus, we conclude that XP/CS mutations not only cause a more severe overall NER defect than XP mutations, but specifically disrupt the TC-NER subpathway, with this defect likely underlying the Cockayne Syndrome symptoms.