SMART MODE:

NORMAL GENOMIC

• Hanawalt PC
• Controlling the efficiency of excision repair.
• Mutat Res. 2001; 485: 3-13
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• The early studies are recounted, that led to the discovery of the ubiquitous process of DNA excision repair, followed by a review of the pathways of transcription-coupled repair (TCR) and global genomic nucleotide excision repair (GGR). Repair replication of damaged DNA in UV-irradiated bacteria was discovered through the use of 5-bromouracil to density-label newly synthesized DNA. This assay was then used in human cells to validate the phenomenon of unscheduled DNA synthesis as a measure of excision repair and to elucidate the first example of a DNA repair disorder, xeroderma pigmentosum. Features of the TCR pathway (that is defective in Cockayne syndrome (CS)) include the possibility of "gratuitous TCR" at transcription pause sites in undamaged DNA. The GGR pathway is shown to be controlled through the SOS stress response in E. coli and through the activated product of the p53 tumor suppressor gene in human cells. These regulatory systems particularly affect the efficiency of repair of the predominant UV-induced photoproduct, the cyclobutane pyrimidine dimer, as well as that of chemical carcinogen adducts, such as benzo(a)pyrene diol-epoxide. Rodent cells (typically lacking the p53-controlled GGR pathway) and tumor virus infected human cells (in which p53 function is abrogated) are unable to carry out efficient GGR of some lesions. Therefore, caution should be exercised in the interpretation of results from such systems for risk assessment in genetic toxicology. Many problems in excision repair remain to be solved, including the mechanism of scanning the DNA for lesions and the subcellular localization of the repair factories. Also there are persisting questions regarding the multiple options of repair, recombination, and translesion synthesis when replication forks encounter lesions in the template DNA. That is where the field of DNA excision repair began four decades ago with studies on the recovery of DNA synthesis in UV-irradiated bacteria.

• Takebayashi Y et al.
• Antiproliferative activity of ecteinascidin 743 is dependent upon transcription-coupled nucleotide-excision repair.
• Nat Med. 2001; 7: 961-6
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• While investigating the novel anticancer drug ecteinascidin 743 (Et743), a natural marine product isolated from the Caribbean sea squirt, we discovered a new cell-killing mechanism mediated by DNA nucleotide excision repair (NER). A cancer cell line selected for resistance to Et743 had chromosome alterations in a region that included the gene implicated in the hereditary disease xeroderma pigmentosum (XPG, also known as Ercc5). Complementation with wild-type XPG restored the drug sensitivity. Xeroderma pigmentosum cells deficient in the NER genes XPG, XPA, XPD or XPF were resistant to Et743, and sensitivity was restored by complementation with wild-type genes. Moreover, studies of cells deficient in XPC or in the genes implicated in Cockayne syndrome (CSA and CSB) indicated that the drug sensitivity is specifically dependent on the transcription-coupled pathway of NER. We found that Et743 interacts with the transcription-coupled NER machinery to induce lethal DNA strand breaks.

• Wijnhoven SW, Kool HJ, Mullenders LH, Slater R, van Zeeland AA, Vrieling H
• DMBA-induced toxic and mutagenic responses vary dramatically between NER-deficient Xpa, Xpc and Csb mice.
• Carcinogenesis. 2001; 22: 1099-106
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• Heterogeneity in cancer susceptibility exists between patients with an inherited defect in nucleotide excision repair (NER). While xeroderma pigmentosum (XP) patients have elevated skin cancer rates, Cockayne syndrome (CS) patients do not appear to have increased cancer susceptibility. To investigate whether differences in mutagenesis are the basis for the variability in cancer proneness, we studied mutagenesis at the X-chromosomal Hprt gene and the autosomal Aprt gene in splenic T-lymphocytes after 7,12-dimethyl-1,2-benz[a]anthracene (DMBA) exposure in total NER-deficient Xpa mice, global genome repair (GGR)-deficient Xpc mice and transcription coupled repair (TCR)-deficient Csb mice. Surprisingly, while all intraperitoneally-treated Xpc(-/-) mice survived a dose of 40 mg/kg DMBA, a substantial fraction of the treated Xpa(-/-) and Csb(-/-) mice died a few days after treatment with a 20-fold lower dose. Functional TCR of DMBA adducts in Xpc(-/-) mice thus appears to alleviate DMBA toxicity. However, the mutagenic response in Xpc(-/-) mice was +/- 2-fold enhanced at both the Hprt and the Aprt gene compared to heterozygous controls, indicating that GGR at least partially removes DMBA adducts from the genome overall. DMBA-induced SCE frequencies in mouse dermal fibroblasts were significantly enhanced in Xpa- and Csb-, but not in Xpc-deficient background compared to the frequency in normal fibroblasts. These results indicate that both damage-induced cytotoxicity as well as intra-chromosomal recombinational events were not correlated to differences in cancer susceptibility in human NER syndrome patients.

• Lehmann AR
• The xeroderma pigmentosum group D (XPD) gene: one gene, two functions, three diseases.
• Genes Dev. 2001; 15: 15-23

• Zafeiriou DI et al.
• Xeroderma pigmentosum group G with severe neurological involvement and features of Cockayne syndrome in infancy.
• Pediatr Res. 2001; 49: 407-12
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• We describe a premature, small for gestational age infant girl with micropthalmia, bilateral congenital cataracts, hearing impairment, progressive somatic and neurodevelopmental arrest, and infantile spasms. She presented a massive photosensitive reaction with erythema and blistering after minimal sun exposure, which slowly gave place to small skin cancers. Her skin fibroblasts were 10-fold more sensitive than normal to UV exposure due to a severe deficiency in nucleotide excision repair. By complementation analysis, the patient XPCS4RO was assigned to the very rare xeroderma pigmentosum (XP) group G (XP-G). One allele of her XPG gene contained a 526C-->T transition that changed Gln-176 to a premature UAG stop codon. Only a minor fraction of XPG mRNA was encoded by this allele. The second, more significantly expressed XPG allele contained a 215C-->A transversion. This changed the highly conserved Pro-72 to a histidine, a substitution that would be expected to seriously impair the 3' endonuclease function of XPG in nucleotide excision repair. In cases suspected of having XP and/or early-onset Cockayne syndrome, extensive DNA repair studies should be performed to reach a correct diagnosis, thereby allowing reliable genetic counseling and prenatal diagnosis.

• Bootsma D
• The "Dutch DNA Repair Group", in retrospect.
• Mutat Res. 2001; 485: 37-41
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• The "Dutch DNA Repair Group" was established about 35 years ago. In this brief historical review some of the crucial decisions are described that have contributed to the relative success of the research of this group. The emphasis of the work of this group has been for many years on the genetic analysis of nucleotide excision repair (NER) and genetic diseases based on defects in this repair process: xeroderma pigmentosum (XP), Cockayne syndrome and trichothiodystrophy.

• Berneburg M, Lehmann AR
• Xeroderma pigmentosum and related disorders: defects in DNA repair and transcription.
• Adv Genet. 2001; 43: 71-102
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• The genetic disorders xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD) are all associated with defects in nucleotide excision repair (NER) of DNA damage. Their clinical features are very different, however, XP being a highly cancer-prone skin disorder, whereas CS and TTD are cancer-free multisystem disorders. All three are genetically complex, with at least eight complementation groups for XP (XP-A to -G and variant), five for CS (CS-A, CS-B, XP-B, XP-D, and XP-G), and three for TTD (XP-B, XP-D, and TTD-A). With the exception of the variant, the products of the XP genes are proteins involved in the different steps of NER, and comprise three damage-recognition proteins, two helicases, and two nucleases. The two helicases, XPB and XPD, are components of the basal transcription factor TFIIH, which has a dual role in NER and initiation of transcription. Different mutations in these genes can affect NER and transcription differentially, and this accounts for the different clinical phenotypes. Mutations resulting in defective repair without affecting transcription result in XP, whereas if transcription is also affected, TTD is the outcome. CS proteins are only involved in transcription-coupled repair, a subpathway of NER in which damage in the transcribed strands of active genes is rapidly and preferentially repaired. Current evidence suggests that they also have an important but not essential role in transcription. The variant form of XP is defective in a novel DNA polymerase, which is able to synthesise DNA past UV-damaged sites.

• Graham JM Jr et al.
• Cerebro-oculo-facio-skeletal syndrome with a nucleotide excision-repair defect and a mutated XPD gene, with prenatal diagnosis in a triplet pregnancy.
• Am J Hum Genet. 2001; 69: 291-300
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• Cerebro-oculo-facio-skeletal (COFS) syndrome is a recessively inherited rapidly progressive neurologic disorder leading to brain atrophy, with calcifications, cataracts, microcornea, optic atrophy, progressive joint contractures, and growth failure. Cockayne syndrome (CS) is a recessively inherited neurodegenerative disorder characterized by low to normal birth weight, growth failure, brain dysmyelination with calcium deposits, cutaneous photosensitivity, pigmentary retinopathy and/or cataracts, and sensorineural hearing loss. Cultured CS cells are hypersensitive to UV radiation, because of impaired nucleotide-excision repair (NER) of UV-induced damage in actively transcribed DNA, whereas global genome NER is unaffected. The abnormalities in CS are caused by mutated CSA or CSB genes. Another class of patients with CS symptoms have mutations in the XPB, XPD, or XPG genes, which result in UV hypersensitivity as well as defective global NER; such patients may concurrently have clinical features of another NER syndrome, xeroderma pigmentosum (XP). Clinically observed similarities between COFS syndrome and CS have been followed by discoveries of cases of COFS syndrome that are associated with mutations in the XPG and CSB genes. Here we report the first involvement of the XPD gene in a new case of UV-sensitive COFS syndrome, with heterozygous substitutions-a R616W null mutation (previously seen in patients in XP complementation group D) and a unique D681N mutation-demonstrating that a third gene can be involved in COFS syndrome. We propose that COFS syndrome be included within the already known spectrum of NER disorders: XP, CS, and trichothiodystrophy. We predict that future patients with COFS syndrome will be found to have mutations in the CSA or XPB genes, and we document successful use of DNA repair for prenatal diagnosis in triplet and singleton pregnancies at risk for COFS syndrome. This result strongly underlines the need for screening of patients with COFS syndrome, for either UV sensitivity or DNA-repair abnormalities.

• Rapin I, Lindenbaum Y, Dickson DW, Kraemer KH, Robbins JH
• Cockayne syndrome and xeroderma pigmentosum.
• Neurology. 2000; 55: 1442-9
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• OBJECTIVES: To review genetic variants of Cockayne syndrome (CS) and xeroderma pigmentosum (XP), autosomal recessive disorders of DNA repair that affect the nervous system, and to illustrate them by the first case of xeroderma pigmentosum-Cockayne syndrome (XP-CS) complex to undergo neuropathologic examination. METHODS: Published reports of clinical, pathologic, and molecular studies of CS, XP neurologic disease, and the XP-CS complex were reviewed, and a ninth case of XP-CS is summarized. RESULTS: CS is a multisystem disorder that causes both profound growth failure of the soma and brain and progressive cachexia, retinal, cochlear, and neurologic degeneration, with a leukodystrophy and demyelinating neuropathy without an increase in cancer. XP presents as extreme photosensitivity of the skin and eyes with a 1000-fold increased frequency of cutaneous basal and squamous cell carcinomas and melanomas and a small increase in nervous system neoplasms. Some 20% of patients with XP incur progressive degeneration of previously normally developed neurons resulting in cortical, basal ganglia, cerebellar, and spinal atrophy, cochlear degeneration, and a mixed distal axonal neuropathy. Cultured cells from patients with CS or XP are hypersensitive to killing by ultraviolet (UV) radiation. Both CS and most XP cells have defective DNA nucleotide excision repair of actively transcribing genes; in addition, XP cells have defective repair of the global genome. There are two complementation groups in CS and seven in XP. Patients with the XP-CS complex fall into three XP complementation groups. Despite their XP genotype, six of nine individuals with the XP-CS complex, including the boy we followed up to his death at age 6, had the typical clinically and pathologically severe CS phenotype. Cultured skin and blood cells had extreme sensitivity to killing by UV radiation, DNA repair was severely deficient, post-UV unscheduled DNA synthesis was reduced to less than 5%, and post-UV plasmid mutation frequency was increased. CONCLUSIONS: The paradoxical lack of parallelism of phenotype to genotype is unexplained in these disorders. Perhaps diverse mutations responsible for UV sensitivity and deficient DNA repair may also produce profound failure of brain and somatic growth, progressive cachexia and premature aging, and tissue-selective neurologic deterioration by their roles in regulation of transcription and repair of endogenous oxidative DNA damage.

• Takeuchi S
• [Xeroderma pigmentosum]
• Nippon Rinsho. 2000; 58: 1496-500
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• Xeroderma pigmentosum(XP) is an autosomal recessive disease that is characterized by hypersensitivity to sunlight with high incidence of skin cancer and that exhibit variable neurological abnormalities in some groups. There are eight different complementation groups in XP; groups A through G and a variant(XP-V). XP-A through XP-G have a defect in nucleotide excision repair(NER), while XP-V has a defect in translesion DNA synthesis. Almost all of genes for XP have been cloned and their functions in the NER mechanism have been progressively unveiled. In this review, the present knowledge of the pathological features and genetic defects in XP has been discussed.

• Itoh T, Linn S, Ono T, Yamaizumi M
• Reinvestigation of the classification of five cell strains of xeroderma pigmentosum group E with reclassification of three of them.
• J Invest Dermatol. 2000; 114: 1022-9
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• Xeroderma pigmentosum is a photosensitive syndrome caused by a defect in nucleotide excision repair or postreplication repair. Individuals of xeroderma pigmentosum group E (xeroderma pigmentosum E) have a mild clinical form of the disease and their cells exhibit a high level of nucleotide excision repair as measured by unscheduled DNA synthesis, as well as biochemical heterogeneity. Cell strains from one group of xeroderma pigmentosum E patients have normal damage-specific DNA binding activity (Ddb+), whereas others do not (Ddb-). Using a refinement of a previously reported cell fusion complementation assay, the previously assigned Ddb+ xeroderma pigmentosum E strains, XP89TO, XP43TO, and XP24KO, with various phenotypes in DNA repair markers, were reassigned to xeroderma pigmentosum group F, xeroderma pigmentosum variant, and ultraviolet-sensitive syndrome, respectively. The Ddb- xeroderma pigmentosum E strains, XP82TO, and GM02415B, which showed almost normal cellular phenotypes in DNA repair markers, however, remained assigned to xeroderma pigmentosum group E. With the exception of the Ddb+ strain XP89TO, which demonstrated defective nucleotide excision repair, both Ddb- and Ddb+ xeroderma pigmentosum E cells exhibited the same levels of variation in unscheduled DNA synthesis that were seen in normal control cells. By genome DNA sequencing, the two Ddb- xeroderma pigmentosum E strains were shown to have mutations in the DDB2 gene, confirming previous reports for XP82TO and GM02415B, and validating the classification of both cells. As only the Ddb- strains investigated remain classified in the xeroderma pigmentosum E complementation group, it is feasible that only Ddb- cells are xeroderma pigmentosum E and that mutations in the DDB2 gene are solely responsible for the xeroderma pigmentosum E group.

• Rodrigo G, Roumagnac S, Wold MS, Salles B, Calsou P
• DNA replication but not nucleotide excision repair is required for UVC-induced replication protein A phosphorylation in mammalian cells.
• Mol Cell Biol. 2000; 20: 2696-705
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• Exposure of mammalian cells to short-wavelength light (UVC) triggers a global response which can either counteract the deleterious effect of DNA damage by enabling DNA repair or lead to apoptosis. Several stress-activated protein kinases participate in this response, making phosphorylation a strong candidate for being involved in regulating the cellular damage response. One factor that is phosphorylated in a UVC-dependent manner is the 32-kDa subunit of the single-stranded DNA-binding replication protein A (RPA32). RPA is required for major cellular processes like DNA replication, and removal of DNA damage by nucleotide excision repair (NER). In this study we examined the signal which triggers RPA32 hyperphosphorylation following UVC irradiation in human cells. Hyperphosphorylation of RPA was observed in cells from patients with either NER or transcription-coupled repair (TCR) deficiency (A, C, and G complementation groups of xeroderma pigmentosum and A and B groups of Cockayne syndrome, respectively). This exclude both NER intermediates and TCR as essential signals for RPA hyperphosphorylation. However, we have observed that UV-sensitive cells deficient in NER and TCR require lower doses of UV irradiation to induce RPA32 hyperphosphorylation than normal cells, indicating that persistent unrepaired lesions contribute to RPA phosphorylation. Finally, the results of UVC irradiation experiments on nonreplicating cells and S-phase-synchronized cells emphasize a major role for DNA replication arrest in the presence of UVC lesions in RPA UVC-induced hyperphosphorylation in mammalian cells.

• Balajee AS, Bohr VA
• Genomic heterogeneity of nucleotide excision repair.
• Gene. 2000; 250: 15-30
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• Nucleotide excision repair (NER) is one of the major cellular pathways that removes bulky DNA adducts and helix-distorting lesions. The biological consequences of defective NER in humans include UV-light-induced skin carcinogenesis and extensive neurodegeneration. Understanding the mechanism of the NER process is of great importance as the number of individuals diagnosed with skin cancer has increased considerably in recent years, particularly in the United States. Rapid progress made in the DNA repair field since the early 1980s has revealed the complexity of NER, which operates differently in different genomic regions. The genomic heterogeneity of repair seems to be governed by the functional compartmentalization of chromatin into transcriptionally active and inactive domains in the nucleus. Two sub-pathways of NER remove UV-induced photolesions: (I) Global Genome Repair (GGR) and (II) Transcription Coupled Repair (TCR). GGR is a random process that occurs slowly, while the TCR, which is tightly linked to RNA polymerase II transcription, is highly specific and efficient. The efficiency of these pathways is important in avoiding cancer and genomic instability. Studies with cell lines derived from Cockayne syndrome (CS) and Xeroderma pigmentosum (XP) group C patients, that are defective in the NER sub-pathways, have yielded valuable information regarding the genomic heterogeneity of DNA repair. This review deals with the complexity of repair heterogeneity, its mechanism and interacting molecular pathways as well as its relevance in the maintenance of genomic integrity.

• Winkler GS et al.
• TFIIH with inactive XPD helicase functions in transcription initiation but is defective in DNA repair.
• J Biol Chem. 2000; 275: 4258-66
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• TFIIH is a multisubunit protein complex involved in RNA polymerase II transcription and nucleotide excision repair, which removes a wide variety of DNA lesions including UV-induced photoproducts. Mutations in the DNA-dependent ATPase/helicase subunits of TFIIH, XPB and XPD, are associated with three inherited syndromes as follows: xeroderma pigmentosum with or without Cockayne syndrome and trichothiodystrophy. By using epitope-tagged XPD we purified mammalian TFIIH carrying a wild type or an active-site mutant XPD subunit. Contrary to XPB, XPD helicase activity was dispensable for in vitro transcription, catalytic formation of trinucleotide transcripts, and promoter opening. Moreover, in contrast to XPB, microinjection of mutant XPD cDNA did not interfere with in vivo transcription. These data show directly that XPD activity is not required for transcription. However, during DNA repair, neither 5' nor 3' incisions in defined positions around a DNA adduct were detected in the presence of TFIIH containing inactive XPD, although substantial damage-dependent DNA synthesis was induced by the presence of mutant XPD both in cells and cell extracts. The aberrant damage-dependent DNA synthesis caused by the mutant XPD does not lead to effective repair, consistent with the discrepancy between repair synthesis and survival in cells from a number of XP-D patients.

• Sansom C
• Immunomodulation in DNA damage and repair.
• Mol Med Today. 2000; 6: 411-2

• de Boer J, Hoeijmakers JH
• Nucleotide excision repair and human syndromes.
• Carcinogenesis. 2000; 21: 453-60
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• DNA damage is implicated in cancer and aging, and several DNA repair mechanisms exist that safeguard the genome from these deleterious consequences. Nucleotide excision repair (NER) removes a wide diversity of lesions, the main of which include UV-induced lesions, bulky chemical adducts and some forms of oxidative damage. The NER process involves the action of at least 30 proteins in a 'cut-and-paste'-like mechanism. The consequences of a defect in one of the NER proteins are apparent from three rare recessive syndromes: xeroderma pigmentosum (XP), Cockayne syndrome (CS) and the photosensitive form of the brittle hair disorder trichothiodystrophy (TTD). Sun-sensitive skin is associated with skin cancer predisposition in the case of XP, but remarkably not in CS and TTD. Moreover, the spectrum of clinical symptoms differs considerably between the three syndromes. CS and TTD patients exhibit a spectrum of neurodevelopmental abnormalities and, in addition, TTD is associated with ichthyosis and brittle hair. These typical CS and TTD abnormalities are difficult to comprehend as a consequence of defective NER. This review briefly describes the biochemistry of the NER process, summarizes the clinical features of the NER disorders and speculates on the molecular basis underlying these pleitropic syndromes.

• de Laat WL, Jaspers NG, Hoeijmakers JH
• Molecular mechanism of nucleotide excision repair.
• Genes Dev. 1999; 13: 768-85

• McKay BC, Ljungman M, Rainbow AJ
• Potential roles for p53 in nucleotide excision repair.
• Carcinogenesis. 1999; 20: 1389-96
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• Ultraviolet (UV) light-induced DNA damage is repaired by the nucleotide excision repair pathway, which can be subdivided into transcription-coupled repair (TCR) and global genome repair (GGR). Treatment of cells with a priming dose of UV light appears to stimulate both GGR and TCR, suggesting that these processes are inducible. GGR appears to be disrupted in p53-deficient fibroblasts, whereas the effect of p53 disruption on TCR remains somewhat controversial. Normal recovery of mRNA synthesis following UV irradiation is thought to depend on TCR. We have found that the recovery of mRNA synthesis following exposure to UV light is severely attenuated in p53-deficient human fibroblasts. Therefore, p53 disruption may lead to a defect in TCR or a post-repair process required for the recovery of mRNA synthesis. Several different functions of p53 have been proposed which could contribute to these cellular processes. We suggest that p53 could participate in GGR and the recovery of mRNA synthesis following UV exposure through the regulation of steady-state levels of one or more p53-regulated gene products important for these processes. Furthermore, we suggest that the role of p53 in the recovery of mRNA synthesis is important for resistance to UV-induced apoptosis.

• Hwang BJ, Ford JM, Hanawalt PC, Chu G
• Expression of the p48 xeroderma pigmentosum gene is p53-dependent and is involved in global genomic repair.
• Proc Natl Acad Sci U S A. 1999; 96: 424-8
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• In human cells, efficient global genomic repair of DNA damage induced by ultraviolet radiation requires the p53 tumor suppressor, but the mechanism has been unclear. The p48 gene is required for expression of an ultraviolet radiation-damaged DNA binding activity and is disrupted by mutations in the subset of xeroderma pigmentosum group E cells that lack this activity. Here, we show that p48 mRNA levels strongly depend on basal p53 expression and increase further after DNA damage in a p53-dependent manner. Furthermore, like p53(-/-) cells, xeroderma pigmentosum group E cells are deficient in global genomic repair. These results identify p48 as the link between p53 and the nucleotide excision repair apparatus.

• Araki M, Masutani C, Hanaoka F
• [Molecular mechanism of nucleotide excision repair in mammalian cells]
• Tanpakushitsu Kakusan Koso. 1999; 44: 1845-51

• van Steeg H, Kraemer KH
• Xeroderma pigmentosum and the role of UV-induced DNA damage in skin cancer.
• Mol Med Today. 1999; 5: 86-94
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• Xeroderma pigmentosum (XP) is a rare, autosomal recessive disease that is characterized by the extreme sensitivity of the skin to sunlight. Compared to normal individuals, XP patients have a more than 1000-fold increased risk of developing cancer on sun-exposed areas of the skin. Genetic and molecular analyses have revealed that the repair of ultraviolet (UV)-induced DNA damage is impaired in XP patients owing to mutations in genes that form part of a DNA-repair pathway known as nucleotide excision repair (NER). Two other diseases, Cockayne syndrome (CS) and the photosensitive form of trichothiodystrophy (TTD), are linked to a defect in the NER pathway. Strikingly, although CS and TTD patients are UV-sensitive, they do not develop skin cancer. The recently developed animal models that mimic the human phenotypes of XP, CS and TTD will contribute to a better understanding of the etiology of these diseases and the role of UV-induced DNA damage in the development of skin cancer.

• Leadon SA
• Transcription-coupled repair of DNA damage: unanticipated players, unexpected complexities.
• Am J Hum Genet. 1999; 64: 1259-63

• Coin F, Bergmann E, Tremeau-Bravard A, Egly JM
• Mutations in XPB and XPD helicases found in xeroderma pigmentosum patients impair the transcription function of TFIIH.
• EMBO J. 1999; 18: 1357-66
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• As part of TFIIH, XPB and XPD helicases have been shown to play a role in nucleotide excision repair (NER). Mutations in these subunits are associated with three genetic disorders: xeroderma pigmentosum (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD). The strong heterogeneous clinical features observed in these patients cannot be explained by defects in NER alone. We decided to look at the transcriptional activity of TFIIH from cell lines of XP individuals. We set up an immunopurification procedure to isolate purified TFIIH from patient cell extracts. We demonstrated that mutations in two XP-B/CS patients decrease the transcriptional activity of the corresponding TFIIH by preventing promoter opening. The defect of XPB in transcription can be circumvented by artificial opening of the promoter. Western blot analysis and enzymatic assays indicate that XPD mutations affect the stoichiometric composition of TFIIH due to a weakness in the interaction between XPD-CAK complex and the core TFIIH, resulting in a partial reduction of transcription activity. This work, in addition to clarifying the role of the various TFIIH subunits, supports the current hypothesis that XP-B/D patients are more likely to suffer from transcription repair syndromes rather than DNA repair disorders alone.

• Zeng L, Sarasin A, Mezzina M
• Retrovirus-mediated DNA repair gene transfer into xeroderma pigmentosum cells: perspectives for a gene therapy.
• Cell Biol Toxicol. 1998; 14: 105-10
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• The rare hereditary disease xeroderma pigmentosum (XP) is clinically characterized by extreme sun sensitivity and an increased predisposition for developing skin cancer. Cultured cells from XP patients exhibit hypersensitivity to ultraviolet (UV) radiation due to the defect in nucleotide excision repair (NER), and other cellular abnormalities. Seven genes identified in the classical XP forms, XPA to XPG, are involved in the NER pathway. In view of developing a strategy of gene therapy for XP, we devised recombinant retrovirus-carrying DNA repair genes for transfer and stable expression of these genes in cells from XP patients. Results showed that these retroviruses are efficient tools for transducing XP fibroblasts and correcting repair-defective cellular phenotypes by recovering normal UV survival, unscheduled DNA synthesis, and RNA synthesis after UV irradiation, and also other cellular abnormalities resulting from NER defects. These results imply that the first step of cellular gene therapy might be accomplished successfully.

• Tantin D
• RNA polymerase II elongation complexes containing the Cockayne syndrome group B protein interact with a molecular complex containing the transcription factor IIH components xeroderma pigmentosum B and p62.
• J Biol Chem. 1998; 273: 27794-9
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• Transcription factor IIH (TFIIH) is involved both in transcription initiation by RNA polymerase II and in nucleotide excision-repair. Nucleotide excision-repair occurs at higher rates in transcriptionally active regions of the genome. Genetic studies indicate that this transcription-coupled repair is dependent on the Cockayne syndrome group A and B proteins, as well as TFIIH subunits. Previous work indicated that Cockayne syndrome group B interacts with RNA polymerase II molecules engaged in ternary complexes containing DNA and RNA. Evidence presented here indicates that this complex can interact with a factor containing the TFIIH core subunits p62 and xeroderma pigmentosum subunit B/excision repair cross-complementing 3. The targeting of TFIIH or a TFIIH-like repair factor to transcriptionally active DNA indicates a potential mechanism for transcription-coupled repair in human cells.

• Karmarkar P, Leer-van Hoffen A, Natarajan AT, van Zeeland AA, Mullenders LH
• UV-induced alterations in the spatial distribution of the basal transcription factor TFIIH: an early event in nucleotide excision repair.
• Mutat Res. 1998; 404: 129-31
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• New findings concerning the molecular mechanisms of nucleotide excision repair (NER) are discussed.

• Lehmann AR
• Dual functions of DNA repair genes: molecular, cellular, and clinical implications.
• Bioessays. 1998; 20: 146-55
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• The complex series of DNA repair pathways that are used to repair damage to cellular DNA employ many different proteins. A substantial number of these have second functions. Defects in these multifunctional proteins in man can lead to widely differing clinical phenotypes depending on which of the functions is affected. This is illustrated most clearly in the transcription factor TFIIH, which is involved in both basal transcription and nucleotide excision repair. Different mutations in genes encoding TFIIH subunits can result in the highly cancer-prone repair disorder xeroderma pigmentosum, or the noncancer-prone multisystem disorder trichothiodystrophy, the features of which are probably a consequence of abnormalities in transcription. The involvement of repair proteins in other processes also poses interesting evolutionary questions.

• Sugasawa K et al.
• Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair.
• Mol Cell. 1998; 2: 223-32
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• The XPC-HR23B complex is specifically involved in global genome but not transcription-coupled nucleotide excision repair (NER). Its function is unknown. Using a novel DNA damage recognition-competition assay, we identified XPC-HR23B as the earliest damage detector to initiate NER: it acts before the known damage-binding protein XPA. Coimmunoprecipitation and DNase I footprinting show that XPC-HR23B binds to a variety of NER lesions. These results resolve the function of XPC-HR23B, define the first NER stages, and suggest a two-step mechanism of damage recognition involving damage detection by XPC-HR23B followed by damage verification by XPA. This provides a plausible explanation for the extreme damage specificity exhibited by global genome repair. In analogy, in the transcription-coupled NER subpathway, RNA polymerase II may take the role of XPC. After this subpathway-specific initial lesion detection, XPA may function as a common damage verifier and adaptor to the core of the NER apparatus.

• Ford JM, Hanawalt PC
• Role of DNA excision repair gene defects in the etiology of cancer.
• Curr Top Microbiol Immunol. 1997; 221: 47-70

• Quilliet X et al.
• Retroviral-mediated correction of DNA repair defect in xeroderma pigmentosum cells is associated with recovery of catalase activity.
• Mutat Res. 1997; 385: 235-42
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• Xeroderma pigmentosum (XP) is a rare inherited disease associated with photosensitivity, a very high susceptibility to develop neoplasm on sun-exposed skin and neurological abnormalities for some patients. We previously reported that diploid cell lines established from XP skin biopsies present an abnormal low level of catalase activity, which is involved in the defense against oxygen free radicals. This biochemical dysfunction, probably involved in the skin cancer formation, has been difficult to be directly related to the nucleotide excision repair (NER) defect in XP. In this paper we report that the retroviral-mediated transduction of XP diploid cells by the XPC and XPD/ERCC2 cDNAs fully and stably corrects the NER defect in terms of survival and unscheduled DNA synthesis (UDS) after ultraviolet (UV) irradiation. The catalase activity in transduced cells was recovered up to normal levels only in cells transduced with repair genes correcting the repair defect. These results imply that: (i) the reduced catalase activity in XP, which might result from cellular depletion of its NADPH cofactor, is directly related to impaired DNA repair, and (ii) this depletion might be one of the multiple cellular consequences of XP inborn defect.

• Taylor EM et al.
• Xeroderma pigmentosum and trichothiodystrophy are associated with different mutations in the XPD (ERCC2) repair/transcription gene.
• Proc Natl Acad Sci U S A. 1997; 94: 8658-63
• Display abstract

• The xeroderma pigmentosum group D (XPD) protein has a dual function, both in nucleotide excision repair of DNA damage and in basal transcription. Mutations in the XPD gene can result in three distinct clinical phenotypes, XP, trichothiodystrophy (TTD), and XP with Cockayne syndrome. To determine if the clinical phenotypes of XP and TTD can be attributed to the sites of the mutations, we have identified the mutations in a large group of TTD and XP-D patients. Most sites of mutations differed between XP and TTD, but there are three sites at which the same mutation is found in XP and TTD patients. Since the corresponding patients were all compound heterozygotes with different mutations in the two alleles, the alleles were tested separately in a yeast complementation assay. The mutations which are found in both XP and TTD patients behaved as null alleles, suggesting that the disease phenotype was determined by the other allele. If we eliminate the null mutations, the remaining mutagenic pattern is consistent with the site of the mutation determining the phenotype.

• Sarasin A, Stary A
• Human cancer and DNA repair-deficient diseases.
• Cancer Detect Prev. 1997; 21: 406-11
• Display abstract

• Cancer development requires the accumulation of numerous genetic changes which are usually believed to occur through the presence of unrepaired DNA lesions. Exogenous or endogenous DNA-damaging agents can lead to mutations in the absence of efficient error-free repair, via replication of DNA damage. Several DNA repair pathways are present in living cells and well conserved from bacteria to human cells. Apart from mismatch repair, photolyases, base excision, and postreplication repair, the nucleotide excision repair (NER), the most versatile of these DNA repair systems, recognizes and eliminates a wide variety of DNA lesions and particularly those induced by ultraviolet (UV) light. The phenotypic consequences of an NER defect in humans are apparent in rare but dramatic diseases characterized by hypersensitivity to UV and a striking clinical and genetic heterogeneity. The xeroderma pigmentosum syndrome (XP), the Cockayne's syndrome (CS), and the photosensitive form of trichothiodystrophy (TTD) are three of these clinically distinct human disorders inherited as an autosomal recessive trait. Persistence of unrepaired DNA damage produced by exposure to UV light is associated, in the XP syndrome, with an extremely high level of skin tumors in sun-exposed sites. But the direct link of defective DNA repair to cancer seems to be complex, since, in contrast to patients with XP, those with TTD or CS do not have an increased frequency of skin cancers. The understanding of the absence of skin tumors in TTD and CS patients may offer a way to better protect normal individuals from the most rapidly increasing cancer: skin cancer.

• Hess MT, Schwitter U, Petretta M, Giese B, Naegeli H
• Bipartite substrate discrimination by human nucleotide excision repair.
• Proc Natl Acad Sci U S A. 1997; 94: 6664-9
• Display abstract

• Mammalian nucleotide excision repair (NER) eliminates carcinogen-DNA adducts by double endonucleolytic cleavage and subsequent release of 24-32 nucleotide-long single-stranded fragments. Here we manipulated the deoxyribose-phosphate backbone of DNA to analyze the mechanism by which damaged strands are discriminated as substrates for dual incision. We found that human NER is completely inactive on DNA duplexes containing single C4'-modified backbone residues. However, the same C4' backbone variants, which by themselves do not perturb complementary hydrogen bonds, induced strong NER reactions when incorporated into short segments of mispaired bases. No oligonucleotide excision was detected when DNA contained abnormal base pairs without concomitant changes in deoxyribose-phosphate composition. Thus, neither C4' backbone lesions nor improper base pairing stimulated human NER, but the combination of these two substrate alterations constituted an extremely potent signal for double DNA incision. In summary, we used C4'-modified backbone residues as molecular tools to dissect DNA damage recognition by human NER into separate components and identified a bipartite discrimination mechanism that requires changes in DNA chemistry with concurrent disruption of Watson-Crick base pairing.

• Wood RD
• Nucleotide excision repair in mammalian cells.
• J Biol Chem. 1997; 272: 23465-8

• Bowman KK, Smith CA, Hanawalt PC
• Excision-repair patch lengths are similar for transcription-coupled repair and global genome repair in UV-irradiated human cells.
• Mutat Res. 1997; 385: 95-105
• Display abstract

• We have used the buoyant density shift method to measure excision-repair patch lengths in UV-irradiated repair-proficient human cells and in primary fibroblasts belonging to xeroderma pigmentosum complementation group C (XP-C), in which excision repair of UV-induced photoproducts is dependent upon transcription. The patch size was found to be about 30 nucleotides for both cell types. This agrees with the size of the DNA fragments excised in vitro by the dual incisions of the structure-specific nucleases XPG and ERCC1-XPF. We conclude that the XPC protein is not required to target the excision nucleases to sites of DNA cleavage in transcribed strands of expressed genes or to protect the newly incised DNA from further processing by exonucleases.

• Reardon JT, Bessho T, Kung HC, Bolton PH, Sancar A
• In vitro repair of oxidative DNA damage by human nucleotide excision repair system: possible explanation for neurodegeneration in xeroderma pigmentosum patients.
• Proc Natl Acad Sci U S A. 1997; 94: 9463-8
• Display abstract

• Xeroderma pigmentosum (XP) patients fail to remove pyrimidine dimers caused by sunlight and, as a consequence, develop multiple cancers in areas exposed to light. The second most common sign, present in 20-30% of XP patients, is a set of neurological abnormalities caused by neuronal death in the central and peripheral nervous systems. Neural tissue is shielded from sunlight-induced DNA damage, so the cause of neurodegeneration in XP patients remains unexplained. In this study, we show that two major oxidative DNA lesions, 8-oxoguanine and thymine glycol, are excised from DNA in vitro by the same enzyme system responsible for removing pyrimidine dimers and other bulky DNA adducts. Our results suggest that XP neurological disease may be caused by defective repair of lesions that are produced in nerve cells by reactive oxygen species generated as by-products of an active oxidative metabolism.

• Hwang JR et al.
• A 3' --> 5' XPB helicase defect in repair/transcription factor TFIIH of xeroderma pigmentosum group B affects both DNA repair and transcription.
• J Biol Chem. 1996; 271: 15898-904
• Display abstract

• XPB is a subunit of the basal transcription factor TFIIH, which is also involved in nucleotide excision repair (NER) and potentially in cell cycle regulation. A frameshift mutation in the 3'-end of the XPB gene is responsible for a concurrence of two disorders: xeroderma pigmentosum (XP) and Cockayne's syndrome (CS). We have isolated TFIIH from cells derived from a patient (XP11BE) who carries this frameshift mutation (TFIIHmut) and from the mother of this patient (TFIIHwt) to determine the biochemical consequences of the mutation. Although identical in composition and stoichiometry to TFIIHwt, TFIIHmut shows a reduced 3' --> 5' XPB helicase activity. A decrease in helicase and DNA-dependent ATPase activities was also observed with the mutated recombinant XPB protein. The XPB mutation causes a severe NER defect. In addition, we provide evidence for a decrease in basal transcription activity in vitro. The latter defect may provide an explanation for many of the XP and CS symptoms that are difficult to rationalize based solely on an NER defect. Thus, this work presents the first detailed analysis of a naturally occurring mutation in a basal transcription factor and supports the concept that the combined XP/CS clinical entity is actually the result of a combined transcription/repair deficiency.

• Chu G, Mayne L
• Xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy: do the genes explain the diseases?
• Trends Genet. 1996; 12: 187-92
• Display abstract

• Xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy are three distinct human syndromes associated with sensitivity to ultraviolet radiation. We review evidence that these syndromes overlap with each other and arise from mutations in genes involved in nucleotide-excision repair and RNA transcription. Attempts have been made to explain the syndromes in terms of defects in repair and transcription. These two biochemical pathways do not easily account for all the features of the syndromes. Therefore, we propose a third pathway, in which the syndromes are due, in part, to defects in a demethylation mechanism involving the excision of methylated cytosine. Perturbation of demethylation could affect the developmentally regulated expression of some genes.

• Wagner SD, Elvin JG, Norris P, McGregor JM, Neuberger MS
• Somatic hypermutation of Ig genes in patients with xeroderma pigmentosum (XP-D).
• Int Immunol. 1996; 8: 701-5
• Display abstract

• Antibody diversification by somatic hypermutation occurs by the introduction of nucleotide substitutions in and around the rearranged Ig V gene segments. Several characteristics of the process suggest that the introduction of mutations is linked to Ig gene transcription. Since there is a connection between mutation and repair with indications that both processes might show linkage to transcription, we asked whether defects in a component of the transcription factor TFIIH which lead to an inability to carry out nucleotide excision repair also affect somatic hypermutation. A PCR strategy was devised that required small samples of peripheral blood and enabled us to monitor hypermutation of a single, abundantly used VH gene. However, the results showed that in xeroderma pigmentosum patients (complementation group D), somatic hypermutaton appears to take place unaffected as regard both extent and distribution.

• Jaspers NG
• Multiple involvement of nucleotide excision repair enzymes: clinical manifestations of molecular intricacies.
• Cytokines Mol Ther. 1996; 2: 115-9
• Display abstract

• Nucleotide excision repair (NER) is a process required to remove DNA damage inflicted upon our skin by the short-wave bands of natural sunlight. Defective NER may result in a high risk of UV-induced skin tumors, since it occurs in patients with the inherited disorder xeroderma pigmentosum (XP). However, Cockayne's syndrome (CS) and PIBIDS (a photosensitive form of trichothiodystrophy) are also disorders with defective NER, but show no evidence of an elevated risk of cancer. In addition, many of CS and PIBIDS symptoms are difficult to explain on the basis of an NER defect only. Recent new insights into the molecular mechanisms of NER have shown additional involvements of many NER enzymes in other cellular processes. These multiple functions are likely to be the basis of the complex symptomatology of XP, CS and PIBIDS. Specific gene-targeted mouse models will probably help to solve these intricacies.

• Sijbers AM et al.
• Xeroderma pigmentosum group F caused by a defect in a structure-specific DNA repair endonuclease.
• Cell. 1996; 86: 811-22
• Display abstract

• Nucleotide excision repair, which is defective in xeroderma pigmentosum (XP), involves incision of a DNA strand on each side of a lesion. We isolated a human gene homologous to yeast Rad1 and found that it corrects the repair defects of XP group F as well as rodent groups 4 and 11. Causative mutations and strongly reduced levels of encoded protein were identified in XP-F patients. The XPF protein was purified from mammalian cells in a tight complex with ERCC1. This complex is a structure-specific endonuclease responsible for the 5' incision during repair. These results demonstrate that the XPF, ERCC4, and ERCC11 genes are equivalent, complete the isolation of the XP genes that form the core nucleotide excision repair system, and solve the catalytic function of the XPF-containing complex.

• Seroz T, Hwang JR, Moncollin V, Egly JM
• TFIIH: a link between transcription, DNA repair and cell cycle regulation.
• Curr Opin Genet Dev. 1995; 5: 217-21
• Display abstract

• TFIIH is a basal transcription factor for protein-coding genes. It contains ERCC2, ERCC3, MO15 and cyclin H, polypeptides implicated in nucleotide excision repair or cell cycle regulation. The dysfunction of TFIIH could result in a large panel of genetic disorders, such as xeroderma pigmentosum, Cockayne's syndrome and trichothiodystrophy. This link between transcription, DNA repair and cell cycle has highlighted a complex and essential role for TFIIH in the cell and has provided much information on the molecular mechanisms of each of these cellular processes.

• Bohr VA
• DNA repair fine structure and its relations to genomic instability.
• Carcinogenesis. 1995; 16: 2885-92

• Evans DA, Burbach JP, van Leeuwen FW
• Somatic mutations in the brain: relationship to aging?
• Mutat Res. 1995; 338: 173-82
• Display abstract

• Genetic instability is generally thought to underlie the process of aging and is predominantly associated with meiosis and mitosis. This review will discuss DNA damage and repair, somatic mutations and somatic recombination events in non-dividing neurons in relation to aging. In general it can be concluded that mutagenesis operates at high frequency in the brain. Present data do not provide clear evidence for accumulating DNA damage or a change in DNA repair activity in the brain with age. However, a linear age-related increase in frameshift mutations has been shown to occur in vasopressin neurons of the rat, revealing a novel post-mitotic mechanism.

• Wang XW et al.
• p53 modulation of TFIIH-associated nucleotide excision repair activity.
• Nat Genet. 1995; 10: 188-95
• Display abstract

• p53 has pleiotropic functions including control of genomic plasticity and integrity. Here we report that p53 can bind to several transcription factor IIH-associated factors, including transcription-repair factors, XPD (Rad3) and XPB, as well as CSB involved in strand-specific DNA repair, via its C-terminal domain. We also found that wild-type, but not Arg273His mutant p53 inhibits XPD (Rad3) and XPB DNA helicase activities. Moreover, repair of UV-induced dimers is slower in Li-Fraumeni syndrome cells (heterozygote p53 mutant) than in normal human cells. Our findings indicate that p53 may play a direct role in modulating nucleotide excision repair pathways.

• Wood RD
• Proteins that participate in nucleotide excision repair of DNA in mammalian cells.
• Philos Trans R Soc Lond B Biol Sci. 1995; 347: 69-74
• Display abstract

• The most versatile strategy for repair of damage to DNA, and the main process for repair of UV-induced damage, is nucleotide excision repair. In mammalian cells, the complete mechanism involves more than 20 polypeptides, and defects in many of these are associated with various forms of inherited disorders in humans. The syndrome xeroderma pigmentosum (XP) is associated with mutagen hypersensitivity and increased cancer frequency, and studies of the nucleotide excision repair defect in this disease have been particularly informative. Many of the XP proteins are now being characterized. XPA binds to DNA, with a preference for damaged base pairs. XPC activity is part of a protein complex with single-stranded DNA binding activity. The XPG protein is a nuclease.

• Bootsma D et al.
• Nucleotide excision repair syndromes: molecular basis and clinical symptoms.
• Philos Trans R Soc Lond B Biol Sci. 1995; 347: 75-81
• Display abstract

• The phenotypic consequences of a nucleotide excision repair (NER) defect in man are apparent from three distinct inborn diseases characterized by hypersensitivity of the skin to ultraviolet light and a remarkable clinical and genetic heterogeneity. These are the prototype repair syndrome, xeroderma pigmentosum (XP) (seven genetic complementation groups, designated XP-A to XP-G), Cockayne's syndrome (two groups: CS-A and CS-B) and PIBIDS, a peculiar photosensitive form of the brittle hair disease trichothiodystrophy (TTD, at least two groups of which one equivalent to XP-D). To investigate the mechanism of NER and to resolve the molecular defect in these NER deficiency diseases we have focused on the cloning and characterization of human DNA repair genes. One of the genes that we cloned is ERCC3. It specifies a chromatin binding helicase. Transfection and microinjection experiments demonstrated that mutations in ERCC3 are responsible for XP complementation group B, a very rare form of XP that is simultaneously associated with Cockayne's syndrome (CS). The ERCC3 protein was found to be part of a multiprotein complex (TFIIH) required for transcription initiation of most structural genes and for NER. This defines the additional, hitherto unknown vital function of the gene. This ERCC3 gene and several other NER genes involved in transcription initiation will be discussed.

• Naegeli H
• Mechanisms of DNA damage recognition in mammalian nucleotide excision repair.
• FASEB J. 1995; 9: 1043-50
• Display abstract

• The ability of nucleotide excision repair (NER) to process multiple forms of DNA damage is highly dependent on the precision by which DNA modifications are located in the genome. Studies of mammalian NER have shown that this system eliminates a wide range of chemically and structurally distinct DNA lesions whereby some types of damage are repaired at higher rates than others. Although the biochemical basis for this broad but heterogeneous response to DNA damage is poorly understood, recent discoveries in closely related areas of DNA metabolism indicate that selectivity for specific sites is achieved through the assembly of nucleoprotein complexes, in which DNA is frequently bent and unwound. In many cases, selectivity may be further enhanced by the action of specialized DNA helicases. These principles in protein-DNA recognition suggest a hypothetical mechanism of damage recognition that accounts for the wide substrate range of mammalian NER and also accommodates its preference for specific DNA lesions.

• Lehmann AR
• Nucleotide excision repair and the link with transcription.
• Trends Biochem Sci. 1995; 20: 402-5
• Display abstract

• Nucleotide excision repair (NER) uses the products of about 30 genes to remove a damage-containing oligonucleotide from cellular DNA. The transcription factor TFIIH is an essential component of NER. In man, defects in NER can result in three distinct genetic disorders, whose features can be ascribed to abnormalities in DNA repair or transcription.

• Takayama K, Salazar EP, Lehmann A, Stefanini M, Thompson LH, Weber CA
• Defects in the DNA repair and transcription gene ERCC2 in the cancer-prone disorder xeroderma pigmentosum group D.
• Cancer Res. 1995; 55: 5656-63
• Display abstract

• Xeroderma pigmentosum (XP) is a sun-sensitive, cancer-prone genetic disorder characterized by a defect in nucleotide excision repair. The human nucleotide excision repair and transcription gene ERCC2 is able to restore survival to normal levels after exposure to UV light in XP complementation group D cells. No enhancement of UV survival is seen in groups C, E, F, or G. XP-CS-2 cells are complemented by ERCC2, confirming the reassignment to group D of this combined XP/Cockayne's syndrome patient. Nucleotide sequence analysis of the ERCC2 cDNA from five XP group D cell strains [XP6BE(SV40), XP17PV, XP102LO, A31-27 (a HeLa/XP102LO hybrid), and XP-CS-2] revealed mutations predominantly affecting previously identified functional domains. The mutations include base substitutions resulting in amino acid substitutions, deletions due to splicing alterations, and defects in expression. XP6BE(SV40), XP17PV, XP102LO, and A31-27 all have one allele with an Arg683 to Trp substitution within the putative nuclear location signal. The genetic disorder trichothiodystrophy (which is not cancer-prone) can also result from mutations in the ERCC2 gene, some of which are the same as those found in XP-D. The various clinical presentations can be correlated with the particular mutations found in the ERCC2 locus.

• Broughton BC et al.
• Molecular and cellular analysis of the DNA repair defect in a patient in xeroderma pigmentosum complementation group D who has the clinical features of xeroderma pigmentosum and Cockayne syndrome.
• Am J Hum Genet. 1995; 56: 167-74
• Display abstract

• Xeroderma pigmentosum (XP) and Cockayne syndrome (CS) are quite distinct genetic disorders that are associated with defects in excision repair of UV-induced DNA damage. A few patients have been described previously with the clinical features of both disorders. In this paper we describe an individual in this category who has unusual cellular responses to UV light. We show that his cultured fibroblasts and lymphocytes are extremely sensitive to irradiation with UV-C, despite a level of nucleotide excision repair that is 30%-40% that of normal cells. The deficiency is assigned to the XP-D complementation group, and we have identified two causative mutations in the XPD gene: a gly-->arg change at amino acid 675 in the allele inherited from the patient's mother and a -1 frameshift at amino acid 669 in the allele inherited from his father. These mutations are in the C-terminal 20% of the 760-amino-acid XPD protein, in a region where we have recently identified several mutations in patients with trichothiodystrophy.

• Sanford KK, Parshad R, Price FM, Tarone RE, Lehmann AR
• G2 phase repair of X-ray-induced chromosomal DNA damage in trichothiodystrophy cells.
• Mutat Res. 1995; 346: 107-14
• Display abstract

• The repair of X-ray-induced DNA damage during G2 cell-cycle phase has been examined in lines of skin fibroblasts from three patients with trichothiodystrophy (TTD), one with apparently normal and two with defective nucleotide excision repair (NER). These responses are compared with those of five lines from clinically normal controls, lines from xeroderma pigmentosum (XP), Cockayne syndrome (CS), Down syndrome (DS), and ataxia telangiectasia (AT) patients. Chromosomal DNA repair was measured as the chromatid aberration frequency (CAF) or total number of chromatid breaks and long gaps per 100 metaphase cells, determined 0.5-1.5 h after X-irradiation (53 rad). Chromatid breaks and gaps (as defined herein) represent unrepaired DNA strand breaks. Only one of the TTD lines, TTD 1BR, showed an abnormally high CAF. This line was shown subsequently to be of a different complementation group, representing a new nucleotide excision repair gene. An abnormally high CAF was also observed, as reported previously, in XP-C, AT and DS but not in CS skin fibroblasts. In addition, cell lines were examined for DNA incision activity by an indirect method in which chromatid aberrations were enumerated with or without ara-C, an inhibitor of repair synthesis, added after X-irradiation. All TTD lines had abnormally low incision activity.

• Shimamoto T et al.
• Expression and functional analyses of the Dxpa gene, the Drosophila homolog of the human excision repair gene XPA.
• J Biol Chem. 1995; 270: 22452-9
• Display abstract

• Xeroderma pigmentosum (XP) is a human hereditary disease characterized by a defect in DNA repair after exposure to ultraviolet light. Among the seven groups of XP, group A (XP-A) patients show the most severe deficiency in excision repair and a wide variety of cutaneous and neurological disorders. We have cloned homologs of the human XPA gene from chicken, Xenopus, and Drosophila, and sequence analysis revealed that these genes are highly conserved throughout evolution. Here, we report characterization of the Drosophila homolog of the human XPA gene (Dxpa). The Dxpa gene product shows DNA repair activities in an in vitro repair system, and Dxpa cDNA has been shown to complement a mutant allele of human XP-A cells by transfection. Polytene chromosome in situ hybridization mapped Dxpa to 3F6-8 on the X chromosome, where no mutant defective in excision repair was reported. Northern blot analysis showed that the gene is continuously expressed in all stages of fly development. Interestingly, the Dxpa protein is strongly expressed in the central nervous system and muscles as revealed by immunohistochemical analysis using anti-Dxpa antibodies, consistent with the results obtained in transgenic flies expressing a Dxpa-beta-galactosidase fusion gene driven by the Dxpa promoter.

• Cleaver JE, Speakman JR, Volpe JP
• Nucleotide excision repair: variations associated with cancer development and speciation.
• Cancer Surv. 1995; 25: 125-42
• Display abstract

• Nucleotide excision repair requires the action of multiple interacting proteins that locate damage in DNA, remove it as a short oligonucleotide and synthesize a replacement patch. Mutations in genes coding for these proteins give rise to a wide range of diseases involving skin carcinogenesis, neuronal decline and developmental disorders of bone and central nervous system. Complex clinical symptoms of more than one clinical disorder may occur because of mutations that influence protein-protein interactions. Significant differences in repair occur between individuals and species for which the molecular basis and phenotypic consequences have yet to be explained.

• Cooper PK, Leadon SA
• Defective repair of ionizing radiation damage in Cockayne's syndrome and xeroderma pigmentosum group G.
• Ann N Y Acad Sci. 1994; 726: 330-2

• Keeney S et al.
• Correction of the DNA repair defect in xeroderma pigmentosum group E by injection of a DNA damage-binding protein.
• Proc Natl Acad Sci U S A. 1994; 91: 4053-6
• Display abstract

• Cells from a subset of patients with the DNA-repair-defective disease xeroderma pigmentosum complementation group E (XP-E) are known to lack a DNA damage-binding (DDB) activity. Purified human DDB protein was injected into XP-E cells to test whether the DNA-repair defect in these cells is caused by a defect in DDB activity. Injected DDB protein stimulated DNA repair to normal levels in those strains that lack the DDB activity but did not stimulate repair in cells from other xeroderma pigmentosum groups or in XP-E cells that contain the activity. These results provide direct evidence that defective DDB activity causes the repair defect in a subset of XP-E patients, which in turn establishes a role for this activity in nucleotide-excision repair in vivo.

• van Vuuren AJ et al.
• Correction of xeroderma pigmentosum repair defect by basal transcription factor BTF2 (TFIIH).
• EMBO J. 1994; 13: 1645-53
• Display abstract

• ERCC3 was initially identified as a gene correcting the nucleotide excision repair (NER) defect of xeroderma pigmentosum complementation group B (XP-B). The recent finding that its gene product is identical to the p89 subunit of basal transcription factor BTF2(TFIIH), opened the possibility that it is not directly involved in NER but that it regulates the transcription of one or more NER genes. Using an in vivo microinjection repair assay and an in vitro NER system based on cell-free extracts we demonstrate that ERCC3 in BTF2 is directly implicated in excision repair. Antibody depletion experiments support the idea that the p62 BTF2 subunit and perhaps the entire transcription factor function in NER. Microinjection experiments suggest that exogenous ERCC3 can exchange with ERCC3 subunits in the complex. Expression of a dominant negative K436-->R ERCC3 mutant, expected to have lost all helicase activity, completely abrogates NER and transcription and concomitantly induces a dramatic chromatin collapse. These findings establish the role of ERCC3 and probably the entire BTF2 complex in transcription in vivo which was hitherto only demonstrated in vitro. The results strongly suggest that transcription itself is a critical component for maintenance of chromatin structure. The remarkable dual role of ERCC3 in NER and transcription provides a clue in understanding the complex clinical features of some inherited repair syndromes.

• Hanawalt PC
• Transcription-coupled repair and human disease.
• Science. 1994; 266: 1957-8

• Habraken Y, Sung P, Prakash L, Prakash S
• Human xeroderma pigmentosum group G gene encodes a DNA endonuclease.
• Nucleic Acids Res. 1994; 22: 3312-6
• Display abstract

• Because of defective nucleotide excision repair of ultraviolet damaged DNA, xeroderma pigmentosum (XP) patients suffer from a high incidence of skin cancers. Cell fusion studies have identified seven XP complementation groups, A to G. Previous studies have implicated the products of these seven XP genes in the recognition of ultraviolet-induced DNA damage and in incision of the damage-containing DNA strand. Here, we express the XPG-encoded protein in Sf9 insect cells and purify it to homogeneity. We demonstrate that XPG is a single-strand specific DNA endonuclease, thus identifying the catalytic role of the protein in nucleotide excision repair. We suggest that XPG nuclease acts on the single-stranded region created as a result of the combined action of the XPB helicase and XPD helicase at the DNA damage site.

• Taylor AM, McConville CM, Byrd PJ
• Cancer and DNA processing disorders.
• Br Med Bull. 1994; 50: 708-17
• Display abstract

• Defects in cloned DNA repair genes are now associated with particular human disorders in which an important feature is a predisposition to cancer. Recently some repair genes have been implicated in other aspects of DNA metabolism such as transcription initiation. In addition mutations in a single gene can give rise to phenotypes recognised clinically as different disorders. These newly appreciated complexities, amongst others, will eventually help us to understand the development of the complete clinical phenotype in a range of 'DNA processing disorders'.

• Shivji MK, Eker AP, Wood RD
• DNA repair defect in xeroderma pigmentosum group C and complementing factor from HeLa cells.
• J Biol Chem. 1994; 269: 22749-57
• Display abstract

• A predominant form of the inherited syndrome xeroderma pigmentosum is genetic complementation group C (XP-C). XP-C cells are defective in DNA nucleotide excision repair in the bulk of the genome but can repair transcribed strands of active genes. An activity that can complement the repair deficiency of extracts from XP-C cells has been purified approximately 2,000-fold from HeLa cells. The factor also increases the unscheduled DNA synthesis of XP-C fibroblasts in vivo after microinjection. Hydrodynamic measurements show that the XP-C complementing factor has a native molecular mass of approximately 160 kDa. The factor binds tightly to single-stranded DNA cellulose, eluting in approximately 1.3 M NaCl. No incision or ATPase activity of the protein alone was detected. XP-C protein is involved in an early stage of repair since its presence was required before the start of gap-filling repair synthesis. In vitro complementation was achieved with naked DNA substrates, and so a primary role in processing chromatin to allow access for repair enzymes seems unlikely. Surprisingly, however, extracts from an XP-C cell line introduced some incisions in UV-irradiated DNA; these were unstable in cell extracts and did not lead to complete repair. The data can be explained by a model in which XP-C factor participates in forming one of the repair incisions flanking DNA damage but not the other. In transcribed DNA, its role is subsumed by RNA polymerase and/or transcription coupling factors.

• Stefanini M et al.
• A new nucleotide-excision-repair gene associated with the disorder trichothiodystrophy.
• Am J Hum Genet. 1993; 53: 817-21
• Display abstract

• The sun-sensitive, cancer-prone genetic disorder xeroderma pigmentosum (XP) is associated in most cases with a defect in the ability to carry out excision repair of UV damage. Seven genetically distinct complementation groups (i.e., A-G) have been identified. A large proportion of patients with the unrelated disorder trichothiodystrophy (TTD), which is characterized by hair-shaft abnormalities, as well as by physical and mental retardation, are also deficient in excision repair of UV damage. In most of these cases the repair deficiency is in the same complementation group as is XP group D. We report here on cells from a patient, TTD1BR, in which the repair defect complements all known XP groups (including XP-D). Furthermore, microinjection of various cloned human repair genes fails to correct the repair defect in this cell strain. The defect in TTD1BR cells is therefore in a new gene involved in excision repair in human cells. The finding of a second DNA repair gene that is associated with the clinical features of TTD argues strongly for an involvement of repair proteins in hair-shaft development.

• Bootsma D, Hoeijmakers JH
• DNA repair. Engagement with transcription.
• Nature. 1993; 363: 114-5

• Satoh MS, Jones CJ, Wood RD, Lindahl T
• DNA excision-repair defect of xeroderma pigmentosum prevents removal of a class of oxygen free radical-induced base lesions.
• Proc Natl Acad Sci U S A. 1993; 90: 6335-9
• Display abstract

• Plasmid DNA was gamma-irradiated or treated with H2O2 in the presence of Cu2+ to generate oxygen free radical-induced lesions. Open circular DNA molecules were removed by ethidium bromide/CsCl density gradient centrifugation. The closed circular DNA fraction was treated with the Escherichia coli reagent enzymes endonuclease III (Nth protein) and Fpg protein. This treatment converted DNA molecules containing the major base lesions pyrimidine hydrates and 8-hydroxyguanine to a nicked form. Remaining closed circular DNA containing other oxygen radical-induced base lesions was used as a substrate for nucleotide excision-repair in a cell-free system. Extracts from normal human cells, but not extracts from xeroderma pigmentosum cells, catalyzed repair synthesis in this DNA. The repair defect in the latter extracts could be specifically corrected by in vitro complementation. The data suggest that accumulation of endogenous oxidative damage in cellular DNA from xeroderma pigmentosum patients contributes to the increased frequency of internal cancers and the neural degeneration occurring in serious cases of the syndrome.

• Hoeijmakers JH
• Nucleotide excision repair. II: From yeast to mammals.
• Trends Genet. 1993; 9: 211-7
• Display abstract

• An intricate network of repair systems safeguards the integrity of genetic material, by eliminating DNA lesions induced by numerous environmental and endogenous genotoxic agents. Nucleotide excision repair (NER) is one of the most versatile DNA repair systems. Deficiencies in this process give rise to the classical human DNA repair disorders xeroderma pigmentosum (XP) and Cockayne's syndrome (CS), and to a recently recognized disease called PIBIDS, a photosensitive form of the brittle hair disorder trichothiodystrophy. This is the second of a two-part review on NER. Part I (in the previous issue of TIG) concentrated on the main characteristics of the NER pathway of E. coli and yeast. Part II compares the mammalian and yeast systems, and attempts to integrate current knowledge on the eukaryotic pathway to suggest an outline for the reaction mechanism.

• Barnes DE, Lindahl T, Sedgwick B
• DNA repair.
• Curr Opin Cell Biol. 1993; 5: 424-33
• Display abstract

• Multiple DNA repair processes are required to maintain the integrity of the cellular genome. Recent advances, including elucidation of three-dimensional structures of DNA repair enzymes, and the cloning and characterization of DNA repair genes implicated in human inherited disease, have given new insights into the surprising complexity of cellular responses to DNA damage.

• Friedberg EC, Henning KA
• The conundrum of xeroderma pigmentosum--a rare disease with frequent complexities.
• Mutat Res. 1993; 289: 47-53

• Reardon JT, Thompson LH, Sancar A
• Excision repair in man and the molecular basis of xeroderma pigmentosum syndrome.
• Cold Spring Harb Symp Quant Biol. 1993; 58: 605-17

• Mounkes LC, Jones RS, Liang BC, Gelbart W, Fuller MT
• A Drosophila model for xeroderma pigmentosum and Cockayne's syndrome: haywire encodes the fly homolog of ERCC3, a human excision repair gene.
• Cell. 1992; 71: 925-37
• Display abstract

• The haywire gene of Drosophila encodes a protein with 66% identity to the product of the human ERCC3 gene, associated with xeroderma pigmentosum B (XP-B) and Cockayne's syndrome (CS). XP is a human autosomal recessive disease characterized by extreme sensitivity to ultraviolet irradiation and marked susceptibility to skin cancer. In addition, XP and CS patients often exhibit a variety of defects, ranging from central nervous system disorders to hypogonadism. Phenotypes of haywire mutants mimic some of the effects of XP. Many haywire alleles are recessive lethal, viable alleles cause ultraviolet sensitivity, and files expressing marginal levels of haywire display motor defects and reduced life span. Progeny of females carrying a maternal effect allele show central nervous system defects.

• Wood RD, Coverley D
• DNA excision repair in mammalian cell extracts.
• Bioessays. 1991; 13: 447-53
• Display abstract

• The many genetic complementation groups of DNA excision-repair defective mammalian cells indicate the considerable complexity of the excision repair process. The cloning of several repair genes is taking the field a step closer to mechanistic studies of the actions and interactions of repair proteins. Early biochemical studies of mammalian DNA repair in vitro are now at hand. Repair synthesis in damaged DNA can be monitored by following the incorporation of radiolabelled nucleotides. Synthesis is carried out by mammalian cell extracts and is defective in extracts from cell lines derived from individuals with the excision-repair disorder xeroderma pigmentosum. Biochemical complementation of the defective extracts can be used to purify repair proteins. Repair of damage caused by agents including ultraviolet irradiation, psoralens, and platinating compounds has been observed. Neutralising antibodies against the human single-stranded DNA binding protein (HSSB) have demonstrated a requirement for this protein in DNA excision repair as well as in DNA replication.

• Wood RD
• Human diseases associated with defective DNA excision repair.
• J R Coll Physicians Lond. 1991; 25: 300-3
• Display abstract

• DNA excision repair is the process used by cells to remove damage from DNA such as that caused by ultraviolet light and many chemicals. Dysfunction of excision repair in humans can lead to heritable diseases in which individuals are sensitive to mutagens, and have an increased risk of skin cancer. The best studied syndrome of this type is xeroderma pigmentosum. Recent research has revealed the genes which encode several different components of DNA excision repair. Work has begun on the protein products encoded by these genes, with the aim of elucidating the detailed biochemical mechanism of the DNA excision repair pathway.

• Cleaver JE
• DNA repair in man.
• Birth Defects Orig Artic Ser. 1989; 25: 61-82
• Display abstract

• DNA repair in man can be described in general terms, but details are still obscure. Excision repair of base damage has a general similarity to the mechanism of the bacterial uvr ABC exonuclease, but the individual roles of at least 15 genes that regulate mammalian excision repair are as yet unknown. The differential repair of specific regions of DNA and of specific genes is highlighted by the clustered mode of repair characteristic of xeroderma pigmentosum group C and by the rapid repair of the dihydrofolate reductase gene. Cloning of genes that specify repair in man is proceeding slowly, in part, because of confusion by genes that produce only partial correction or nonspecific changes in sensitivity and by phenotypic reversion. In human cells, DNA damage-inducible genes are recognized that may overlap the spectra of other stress-induced proteins, but the relationship of these to any error-prone or recA-like system is unknown and unlikely. Four diseases, xeroderma pigmentosum, ataxia telangiectasia, Cockayne syndrome, and Fanconi anemia, have well-documented and significantly increased sensitivities to DNA-damaging agents, and each has recognizable though complex abnormalities in processing DNA damage. In addition, a wide variety of diseases and cellular processes have been ascribed to an association with DNA damage and repair, but the accuracy and significance of these associations are hard to identify.

• Rubin JS
• The molecular genetics of the incision step in the DNA excision repair process.
• Int J Radiat Biol. 1988; 54: 309-65
• Display abstract

• This review describes the evolution of research into the genetic basis of how different organisms use the process of excision repair to recognize and remove lesions from their cellular DNA. One particular aspect of excision repair, DNA incision, and how it is controlled at the genetic level in bacteriophage, bacteria, S. cerevisae, D. melanogaster, rodent cells and humans is examined. In phage T4, DNA is incised by a DNA glycosylase-AP endonuclease that is coded for by the denV gene. In E. coli, the products of three genes, uvrA, uvrB and uvrC, are required to form the UVRABC excinuclease that cleaves DNA and releases a fragment 12-13 nucleotides long containing the site of damage. In S. cerevisiae, genes complementing five mutants of the RAD3 epistasis group, rad1, rad2, rad3, rad4 and rad10 have been cloned and analyzed. Rodent cells sensitive to a variety of mutagenic agents and deficient in excision repair are being used in molecular studies to identify and clone human repair genes (e.g. ERCC1) capable of complementing mammalian repair defects. Most studies of the human system, however, have been done with cells isolated from patients suffering from the repair defective, cancer-prone disorder, xeroderma pigmentosum, and these cells are now beginning to be characterized at the molecular level. Studies such as these that provide a greater understanding of the genetic basis of DNA repair should also offer new insights into other cellular processes, including genetic recombination, differentiation, mutagenesis, carcinogenesis and aging.

• Kaneko M, Leadon SA
• Production of thymine glycols in DNA by N-hydroxy-2-naphthylamine as detected by a monoclonal antibody.
• Cancer Res. 1986; 46: 71-5
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• We have quantitated the production of thymine glycols in DNA following treatment of cultured human fibroblasts or DNA in solution with the carcinogen N-hydroxy-2-naphthylamine. Thymine glycols, detected by using a monoclonal antibody specific to this base damage, were produced in DNA in a dose dependent manner both in vitro and in vivo. Exposure of DNA to N-hydroxy-2-naphthylamine in the presence of catalase and superoxide dismutase, which break down hydrogen peroxide and superoxide anions, respectively, inhibited the production of this base damage. Thymine glycols were efficiently removed from DNA in both normal human fibroblasts and in cells from a patient with xeroderma pigmentosum complementation group A, which are deficient in nucleotide excision repair.

• Gabrielli F
• Minireview. Roles of turnover and repair of macromolecules and supramolecular structural components.
• Life Sci. 1983; 33: 805-16
• Display abstract

• Macromolecules and supramolecular structural components that are incorrectly synthesized or are damaged by radiation or by reactive chemicals are either repaired or selectively degraded and resynthesized. In addition, turnover rates for macromolecules and supramolecular structures can be elevated by alternation of fasting and feeding periods and can be influenced by metabolic regulatory mechanisms which are governed by steady-state concentrations of labile macromolecules.

• Cleaver JE
• Rapid complementation method for classifying excision repair-defective xeroderma pigmentosum cell strains.
• Somatic Cell Genet. 1982; 8: 801-10
• Display abstract

• A rapid method has been developed that permits demonstration of complementation between different cell strains from ultraviolet-sensitive xeroderma pigmentosum patients. Combining polyethylene glycol-mediated cell fusion with low doses of ultraviolet light to eliminate unfused sensitive cells, the method permits assignment of cell strains to complementation groups by visual inspection, avoiding use of laborious methods involving autoradiography. This method can be augmented by measuring DNA repair synthesis, which shows large quantitative differences between fusions that result in complementation and those that do not.

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