2.1. The two subpathways in NER
NER has two subpathways – global genome (GG-NER) and transcription coupled NER (TC-NER) (Schärer, 2013; Spivak, 2015). GG-NER utilizes surveillance proteins such as XPC and UV-DDB to recognize DNA damage. Therefore, it repairs damage across the whole genome, including transcribed and untranscribed regions (Kusakabe et al., 2019). In contrast, TC-NER is specific for repair on the transcribed strand of active genes, when elongating RNA Pol II is stalled by the damage. While TC-NER only repairs a small fraction of the human genome, it is more efficient than GG-NER and can rapidly respond to Pol II stalling for repair (Duan et al., 2021; Fousteri & Mullenders, 2008). There are four main steps in NER: damage recognition, DNA unwinding, dual incision, and repair synthesis. Although there is a key difference in the damage recognition step between the two subpathways, the damage recognition is followed by the recruitment of TFIIH in both of them, and the steps after TFIIH are believed to be the same as well (Okuda et al., 2017; Tsutakawa et al., 2020). As GG- and TC-NER are initiated by XPC/UV-DDB and RNA Pol II, respectively, the mechanism for TFIIH recruitment in the two subpathways is found to be significantly different (see below for more details).
Once TFIIH is recruited, it functions as a DNA helicase to promote pre-incision complex formation together with other NER factors, such as XPA and RPA (Coin et al., 2008; Kuper et al., 2014; Topolska-Woś et al., 2020). After the DNA strands have been unwound, TFIIH retains the open DNA conformation (Kokic et al., 2019). ERCC1-XPF and XPG, two repair endonucleases, nick the damaged strand on the 5’ and 3’ side, respectively. XPF and XPG cut the DNA strand asymmetrically relative to the lesion. ERCC1-XPF cleaves DNA 20 nt ± 5 nt upstream of the damage site, whereas XPG cleaves DNA 6 nt ± 3 nt downstream of the lesion (Hu et al., 2015), evicting an oligonucleotide of ~30nt containing the damage. A recent study shows that the Rad5-related DNA translocase HLTF facilitates release of the incised DNA fragment (van Toorn et al., 2022). Once the damage has been excised, DNA polymerase can synthesize new nucleotides, followed by ligation into the DNA strand. This restores the nucleotide sequence for transcription and replication, and the factors then disassociate from the strand (Schärer, 2013).
As NER plays a critical role in the repair of a variety of DNA damage, genetic defects and mutations that occur in TFIIH and other NER proteins are associated with a variety of human disorders (Coin et al., 1998; Lehmann, 2001). These will be discussed more in detail later in this paper.