Nucleotide Excision Repair (NER) in Eukaryotes

DNA-reactive chemicals such as free radicals and redox agents, and radiation such as UV light and X-rays, can all damage genomic DNA. Nucleotide excision repair (NER) recognizes localized, single-strand DNA damage based on abnormal structure and chemistry, then excises and replaces such lesions. In humans, excision repair is the only known mechanism for the removal of UV-induced damage. Impairment of NER activity is associated with at least three human autosomal recessive genetic disorders, xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. Mammalian NER consists of two sub-pathways, global genome NER (GG-NER), which operates throughout the genome, and transcription-coupled NER (TC-NER), which is specialized for the elimination of lesions from the transcribed strand of active genes.In the case of GG-NER, the UV-damaged DNA-binding (UV-DDB) and XPC-RAD23B-CETN2 complexes are the initial sensors of lesions. XPC is essential for the recruitment of downstream NER factors including TFIIH. XPB and XPD subunits of TFIIH unwind the duplex at the damage site to form a repair bubble of about 20 nucleotides. Binding of XPA facilitates the binding of RPA, a heterotrimer that binds to and protects both of the separated strands in the open complex. XPG, a structure specific nuclease is then recruited followed by another structure-specific endonuclease, the XPF-ERCC1 complex. XPG makes the 3' incision, followed by the 5' incision made by XPF-ERCC1 heterodimer. The excised oligomer and most of the repair factors dissociate from the duplex, but RPA and XPG remain in the gap and recruit RFC/PCNA and DNA polymerase(s) to repair the DNA strand. In replicating cells, gap-filling DNA synthesis is conducted by Pol ε, while in non-replicating cells this function is fulfilled by Pol δ and Pol κ. The NER reaction is completed through sealing the final nick by DNA ligase 1 or XRCC1/DNA ligase 3 complex, depending on the proliferative status of the cell.DNA damage detected within the transcribed strands of genes by a stalled DNA polymerase is repaired by TC-NER. CSA and CSB are necessary to recruit TFIIH to the damaged site and to encourage RNA polymerase to either back up, dissociate, or disassemble so that TFIIH can access the damaged region. Following the recruitment of TFIIH, TC-NER is identical to the GG-NER pathway. In both pathways, protein modifications such as ubiquitylation, sumoylation, and neddylation play a significant role in detailed regulation and direction of events. For example, XPC after interacting with DDB2 and XPA is sumoylated by UBE2I, and later ubiquitinylated by RNF111. The former enhances its binding to UV lesions and protects it from degradation, while the latter encourages its dissociation to let other steps occur, but does not lead to degradation.