True lies: the double life of the nucleotide excision repair factors in transcription and DNA repair

Abstract

Nucleotide excision repair (NER) is a major DNA repair pathway in eukaryotic cells. NER removes structurally diverse lesions such as pyrimidine dimers, arising upon UV irradiation or bulky chemical adducts, arising upon exposure to carcinogens and some chemotherapeutic drugs. NER defects lead to three genetic disorders that result in predisposition to cancers, accelerated aging, neurological and developmental defects. During NER, more than 30 polypeptides cooperate to recognize, incise, and excise a damaged oligonucleotide from the genomic DNA. Recent papers reveal an additional and unexpected role for the NER factors. In the absence of a genotoxic attack, the promoters of RNA polymerases I- and II-dependent genes recruit XPA, XPC, XPG, and XPF to initiate gene expression. A model that includes the growth arrest and DNA damage 45alpha protein (Gadd45alpha) and the NER factors, in order to maintain the promoter of active genes under a hypomethylated state, has been proposed but remains controversial. This paper focuses on the double life of the NER factors in DNA repair and transcription and describes the possible roles of these factors in the RNA synthesis process.

Figure 1

Three disorders for nine genes. Mutations in ten genes are responsible for the xeroderma pigmentosum (XP), the trichothyodystrophy (TTD) or the Cockayne syndrome (CS). XPA, XPC, XPE and XPF are only involved in XP; CSA and CSB are only involved in CS; XPG is involved in pure XP or in an combined XP/CS syndrome; XPB and XPD are involved in TTD, XP, or in a combined XP/CS syndrome. TTDA is only involved in TTD.

Figure 2

The two subpathways of mammalian NER. Physical or chemical agents like UV, cis-platin, or benzopyrene can damage DNA and induce damage-mediated helix distortions anywhere in the genome (GG-NER in green, bottom panel) or on the transcribed strand of a gene (TC-NER in red, top panel). Bottom panel: (I) XPC-RAD23B recognizes and binds to DNA damage-mediated helix distortion to initiate GG-NER. (II) TFIIH is recruited in an ATP-dependent manner, followed by XPA and RPA, which verify the presence of the lesion. During this step, the CAK module of TFIIH is released from the preincision complex [29]. (III) Within the preincision complex, ERCC1-XPF and XPG structure-specific endonucleases incise the damaged strand on the 5′ and 3′ sides of the lesion, respectively. Following incision, NER factors are released from the DNA, except XPG and RPA that favour the recruitment of the replication machinery composed of PCNA, RFC, and the DNA Polymerases δ, ε, or κ (ref). (IV) Following replication of the gap, the DNA is sealed by the ligase 1 (or the ligase III-XRCC1 complex in nondividing cells). Top Panel: (I) TC-NER is triggered by DNA damage-mediated blockage of RNA-Pol II (Top panel). (II) CSB is then recruited to the stalled RNA-Pol II enzyme and triggers the recruitment of the NER factors TFIIH, XPA, RPA, ERCC1-XPF, and XPG together with the CSA-CNS complex (III). (IV) Following the excision of the damaged oligonucleotide, the same DNA replication machinery of the GG-NER subpathway fills the gap created by the incision/excision step.

Figure 3

NER factors and gene transcription. Upon gene activation, the formation of preinitiation complex (PIC) precedes the recruitment of XPC, which allows the sequential arrival of the other NER factors in the following order CSB, XPA/RPA, XPG/ERCC1-XPF, and Gadd45α. The association of NER factors and Gadd45α with the transcription machinery leads to a cascade of histone PTMs. Concomitantly, an active demethylation of 5′CpG islands occurs.

Figure 4

Potential mechanisms of cytosine demethylation. (a) The NER machinery, recruited to the preinitiation complex, can recognize the 5-methyl cytosine (meC) as a NER-specific substrate, in the presence of Gadd45α, and eliminate it in a process closely related to the canonical NER process with the incision/excision of the oligonucleotide containing the meC. (b) Another pathway involves two steps; first, the deamination of 5-methylcytosine (meC) to thymine, which involves proteins from Apobec family such as AID or APOBEC1. A role in deamination has been also suggested for DNMTs proteins. Consequently, the impairment of the thymine with the guanine in the opposite strand induces the recruitment of DNA glycosylases such as Mbd4 or TDG that remove thymine through cleavage of the glycosidic bond. Following the action of DNA glycosylases, it remains an apyrimidinic site, which is cleaved by an AP endonuclease such as APE1 and repaired through the polymerase β and DNA ligases. NER factors and Gadd45α are involved in this mechanism but their roles are not determined. (c) We propose that NER factors control the epigenetic environment of the promoter favouring the demethylation of H3K9 and the methylation of H3K4. Following the action of the NER factors, Apobec proteins and BER factors demethylate the meC in a process similar to (b).