TFIIH
The specific recognition of substrate sites for NER DNA repair system is followed by the stepwise assembly of the rest of the NER machinery.
Among these is a subcomplex called core transcription factor IIH (TFIIH), which is composed of six subunits.
These six subunits (together with additional proteins) constitute one of several RNA polymerase II basal transcription factors, which are required for the initiation of transcription by the RNA polymerase II transcription machinery.
TFIIH facilitates partial unwinding of the DNA duplex. Central to this process are the two DNA helicases (unwinding proteins) XPB and XPD, subunits of TFIIH, that are thought to subserve this function during both transcription and NER.
During transcription, the unwinding process (bubble formation) facilitates the initiation of new messenger RNA transcripts.
In contrast, unwinding of DNA during NER by TFIIH generates discrete junctions between double-stranded and single-stranded DNA at the edges of the bubble structures. These junctions are fundamental to the correct incision of DNA during NER.
Three other subunits of the NER complex comprise two endonucleases that cut the junctions of double-stranded and single-stranded DNA with defined polarity.
The endonuclease activity of XPG cuts the damaged DNA strand 3’ to sites of base damage, whereas the endonuclease activity of the ERCC1-XPF heterodimeric protein cuts the damaged strand 5’ to such sites.
The distance between these incisions in the damaged DNA strand is 30 nucleotides. The damaged base is always located closer to the 3’ incision than to the 5’ incision. However, the precise distance between the incisions varies from one type of base damage to another, as does the precise location of the damaged base with respect to each incision.
The presence of DNA incisions flanking damaged bases generates an oligonucleotide fragment that is excised from the DNA. The precise mechanism of this excision is not yet established.
It almost certainly is not a passive process, as simple base pairing over a distance of 27-30 nucleotides would preclude this.
It is also likely that oligonucleotide excision is temporally, and possibly mechanistically, linked to repair synthesis of DNA, such that the formation of large single-stranded gaps (which might be susceptible to attack by nucleases, thus effectively severing the genome) is avoided during oligonucleotide excision.
See also
xeroderma pigmentosum
DNA repair
- nucleotide excision repair (NER)