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.