NER and Transcription

CSB promotes forward translocation TFIIH loads onto forward edge of bubble 

XPA/RPA, ERCC1/XPF bind incisions, post-incision events 

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Photosensitive trichothiodystrophy (TTD) patients have defects in the XPD or XPB gene and cannot repair cyclobutane dimers (CPD). The phenotype is characterized by many of the symptoms common to the CS patients but with the additional characteristics of brittle hair and nails, and scaly skin. Why mutations in XPD and XPB can give rise to both XP and TTD is explained by the dual functions of the proteins in NER and transcription. The special hallmarks of TTD are thus due to reduced transcription and expression of matrix proteins [76]. 

Fig. 2. The two main pathways of nucleotide excision repair (NER), global genome repair (GG-NER) and transcription-coupled repair (TC-NER) (A) and the common NER pathway. The NER mechanism consists of the removal of a short stretch of DNA containing the lesion and the subsequent restoration of this lesion using the non-damaged DNA strand as a template. GG-NER removes lesions in non-transcribed domains of the genome or non-transcribed strands in the transcribed domains TC-NER removes lesions from the transcribed strand of active genes (modified from Fousteri and Mullenders, 2008).

The NER pathway consists of two different sub-pathways known as global genome repair (GGR) and transcription-coupled repair (TCR). Most genes involved contribute to both sub-pathways. 

The two subpathways of NER, global genome (GG)-NER [8] and transcription-coupled (TC)-NER [9], employ a common set of proteins including XPC/HR23B (also known as XPC-RAD23B Chapter 11), TFIIH, XPA, RPA (replication protein A), XPG, and ERCC1 (excision repair cross-complementation group 1)/XPF. The... 

While defects in protein XPD often cause typical XP symptoms, some defects in the same protein lead to trichothiodystrophy (TTD, brittle hair disease). The hair is sulfur deficient, and scaly skin (ichthyosis, Box 8-F), mental retardation, and other symptoms are observed.0 Like their yeast counterparts (proteins RAD3 and RAD25), XPB and XPD are both DNA helicases.0 They also constitute distinct subunits of the human transcription factor TFIIHP, which is discussed in Chapter 28. It seems likely that XPD is involved in transcription-coupled repair (TCR) of DNA.° °i-s This is a subpathway of the nucleotide excision repair (NER) pathway, which allows for rapid repair of the transcribed strand of DNA. This is important in tissues such as skin, where the global NER process may be too slow to keep up with the need for rapid protein synthesis. Transcription-coupled repair also appears to depend upon proteins CSA and CSB, defects which may result in the rare cockayne syndrome.13 0 4 11 Patients are not only photosensitive but have severe mental and physical retardation including skeletal defects and a wizened appearance. 

TFIIH also partidpates in another important cellular function, namely nucleotide excision repair of damaged DNA. This function accounts for the observation that transcription and the removal of bulky base adducts by nucleotide excision repair (NER) are coupled. An increased repair of DNA damage by NER is observed while a gene is being transcribed. During transcription-coupled repair, TFIIH assembles with other repair proteins into a large repair complex, allowing for the removal of DNA adducts. 

By contrast, deficiencies in GG-NER (see Section 11.3) lead to the inherited disorder xeroderma pigmentosum (XP), which can be viewed as the prototypical DNA repair disorder [7-9]. XP patients are unable to repair UV lesions, and as a consequence suffer from an extreme sensitivity to UV light and an over 1000-fold increased incidence of skin cancer. Severely affected XP patients additionally suffer from neurological abnormalities. The phenotypes of two additional symptoms associated with NER genes, Cockayne syndrome (CS) and trichothiodystro-phy (TTD), are more complex as they are due to defects in transcription as well as defects in DNA repair [10]. 

Damaged bases in DNA that arise from ROS or by the deamination of cytosine to uracil are usually removed by BER however, there is no evidence for the existence ofTC-BER that would be analogous to TC-NER [11, 32]. Some oxidized bases may be repaired by TC-NER when they interfere with transcription elongation. In any case, oxidized bases that alter base incorporation events in nascent RNA could contribute significantly to the pool of altered proteins in cells. In fact, 8-oxo-G has been shown to be subject to TC-NER in E. coli and to induce altered proteins via transcriptional mutagenesis [62]. Furthermore, in a recent publication, Saxowsky et al. report that 8-oxo-G induces a change in the activity of the Ras protein in mammalian cells via transcriptional mutagenesis and that downstream phosphorylation events are dependent on Ras [117]. 

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