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Martínez-López W, Moreno-Ortega D, Valencia-Payan J, Sammader P, Meschini R, Palitti F. Influence of chromatin remodeling in the removal of UVC-induced damage in TCR proficient and deficient Chinese hamster cells. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 836:124-131. [DOI: 10.1016/j.mrgentox.2018.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 01/12/2023]
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Enhanced Repair of UV-Induced DNA Damage by 1,25-Dihydroxyvitamin D 3 in Skin Is Linked to Pathways that Control Cellular Energy. J Invest Dermatol 2017; 138:1146-1156. [PMID: 29258892 DOI: 10.1016/j.jid.2017.11.037] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/03/2017] [Accepted: 11/13/2017] [Indexed: 01/22/2023]
Abstract
Inadequately repaired post-UV DNA damage results in skin cancers. DNA repair requires energy but skin cells have limited capacity to produce energy after UV insult. We examined whether energy supply is important for DNA repair after UV exposure, in the presence of 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3), which reduces UV-induced DNA damage and photocarcinogenesis in a variety of models. After UV exposure of primary human keratinocytes, the addition of 1,25(OH)2D3 increased unscheduled DNA synthesis, a measure of DNA repair. Oxidative phosphorylation was depleted in UV-irradiated keratinocytes to undetectable levels within an hour of UV irradiation. Treatment with 1,25(OH)2D3 but not vehicle increased glycolysis after UV. 2-Deoxyglucose-dependent inhibition of glycolysis abolished the reduction in cyclobutane pyrimidine dimers by 1,25(OH)2D3, whereas inhibition of oxidative phosphorylation had no effect. 1,25(OH)2D3 increased autophagy and modulated PINK1/Parkin consistent with enhanced mitophagy. These data confirm that energy availability is limited in keratinocytes after exposure to UV. In the presence of 1,25(OH)2D3, glycolysis is enhanced along with energy-conserving processes such as autophagy and mitophagy, resulting in increased repair of cyclobutane pyrimidine dimers and decreased oxidative DNA damage. Increased energy availability in the presence of 1,25(OH)2D3 is an important contributor to DNA repair in skin after UV exposure.
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Balliano A, Hao F, Njeri C, Balakrishnan L, Hayes JJ. HMGB1 Stimulates Activity of Polymerase β on Nucleosome Substrates. Biochemistry 2017; 56:647-656. [PMID: 28098985 PMCID: PMC5679249 DOI: 10.1021/acs.biochem.6b00569] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The process of base excision repair (BER) recognizes and repairs small lesions or inappropriate bases on DNA through either a short-patch or long-patch pathway. The enzymes involved in BER have been well-characterized on DNA substrates, and, somewhat surprisingly, many of these enzymes, including several DNA glycosylases, AP endonuclease (APE), FEN1 endonuclease, and DNA ligases, have been shown to have activity on DNA substrates within nucleosomes. DNA polymerase β (Pol β), however, exhibits drastically reduced or no activity on nucleosomal DNA. Interestingly, acetylation of Pol β, by the acetyltransferase p300, inhibits its 5' dRP-lyase activity and presumably pushes repair of DNA substrates through the long-patch base excision repair (LP-BER) pathway. In addition to the major enzymes involved in BER, a chromatin architectural factor, HMGB1, was found to directly interact with and enhance the activity of APE1 and FEN1, and thus may aid in altering the structure of the nucleosome to be more accessible to BER factors. In this work, we investigated whether acetylation of Pol β, either alone or in conjunction with HMGB1, facilitates its activity on nucleosome substrates. We find acetylated Pol β exhibits enhanced strand displacement synthesis activity on DNA substrates, but, similar to the unmodified enzyme, has little or no activity on nucleosomes. Preincubation of DNA templates with HMGB1 has little or no stimulatory effect on Pol β and even is inhibitory at higher concentrations. In contrast, preincubation of nucleosomes with HMGB1 rescues Pol β gap-filling activity in nucleosomes, suggesting that this factor may help overcome the repressive effects of chromatin.
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Affiliation(s)
- Angela Balliano
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642
| | - Fanfan Hao
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642
- Department of Biology, Indiana University Purdue University Indianapolis 723 W. Michigan St., Indianapolis, IN 46202-5132
| | - Catherine Njeri
- Department of Biology, Indiana University Purdue University Indianapolis 723 W. Michigan St., Indianapolis, IN 46202-5132
| | - Lata Balakrishnan
- Department of Biology, Indiana University Purdue University Indianapolis 723 W. Michigan St., Indianapolis, IN 46202-5132
| | - Jeffrey J. Hayes
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642
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Balliano AJ, Hayes JJ. Base excision repair in chromatin: Insights from reconstituted systems. DNA Repair (Amst) 2015; 36:77-85. [PMID: 26411876 DOI: 10.1016/j.dnarep.2015.09.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The process of base excision repair has been completely reconstituted in vitro and structural and biochemical properties of the component enzymes thoroughly studied on naked DNA templates. More recent work in this field aims to understand how BER operates on the natural substrate, chromatin [1,2]. Toward this end, a number of researchers, including the Smerdon group, have focused attention to understand how individual enzymes and reconstituted BER operate on nucleosome substrates. While nucleosomes were once thought to completely restrict access of DNA-dependent factors, the surprising finding from these studies suggests that at least some BER components can utilize target DNA bound within nucleosomes as substrates for their enzymatic processes. This data correlates well with both structural studies of these enzymes and our developing understanding of nucleosome conformation and dynamics. While more needs to be learned, these studies highlight the utility of reconstituted BER and chromatin systems to inform our understanding of in vivo biological processes.
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Affiliation(s)
- Angela J Balliano
- University of Rochester Medical Center, 601 Elmwood Ave., Box 712, Rochester, NY 14642, United States
| | - Jeffrey J Hayes
- University of Rochester Medical Center, 601 Elmwood Ave., Box 712, Rochester, NY 14642, United States.
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Lu X, Xiao S, Jin C, van der Straaten T, Li X. ERCC1 and XPD/ERCC2 polymorphisms' predictive value of oxaliplatin-based chemotherapies in advanced colorectal cancer has an ethnic discrepancy: a meta-analysis. J Clin Lab Anal 2014; 26:10-5. [PMID: 24833529 DOI: 10.1002/jcla.20494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 08/31/2011] [Indexed: 01/14/2023] Open
Abstract
Our purpose is to evaluate the predictive value of the genetic polymorphisms of Excision repair cross-complementing group 1 (ERCC1) and xeroderma pigmentosum group D/excision repair cross-complementing group 2 (XPD/ERCC2) in patients with advanced colorectal cancer receiving oxaliplatin-based chemotherapy, and we performed a meta-analysis in order to obtain a more precise estimation for a more optimizing individual chemotherapy. The relevant cohort studies were identified by searching the electronic databases of MEDLINE, EMBASE, and CNKI. We used ''colorectal,'' ''cancer,'' ''carcinoma,'' ''ERCC1,'' ''XPD or ERCC2,'' ''polymorphism,'' ''oxaliplatin,'' ''treatment,'' or ''chemotherapy'' as key words. Inclusion criteria were patients with advanced colorectal cancer receiving oxaliplatin-based chemotherapy, evaluation of polymorphism of ERCC1 and XPD/ ERCC2, and overall response rate (ORR). In this meta-analysis, a total of seven studies were selected according to the inclusion criteria. Five studies investigated ERCC1 codon 118 polymorphisms and three studies evaluated XPD/ERCC2 codon 751 polymorphisms. For ERCC1 codon C118T polymorphism, the ORR to oxaliplatin-based chemotherapy in patients with C/C wild genotype was 77.27% and it was 69.30% for C/T and T/T variant genotype. The pooled odds ratio (OR) for C/C wild-type vs. C/T and T/T genotype was 1.11 (95% CI, 0.86-1.42; P = 0.42). For XPD/ERCC2 Lys751Gln polymorphism, the response rate was 86.58 and 67.57% in patients with the A/A and either one or two C alleles (A/C or C/C) respectively, and the pooled OR was 1.15 (95% CI, 1.01-1.30; P = 0.03). Furthermore, we chose subgroup analysis in order to find the difference between the Caucasian and Asian ethnicity. The results indicated that Oxaliplatin sensitivity was significantly associated with ERCC1 C118T polymorphism in Asian people. XPD/ERCC2 Lys751Gln polymorphism had the predictive value especially for the patients from the America and Europe.
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Affiliation(s)
- Xiaobo Lu
- Department of Hygiene Toxicology, China Medical University, Shenyang, People's Republic of China.
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Dhillon VS, Thomas P, Iarmarcovai G, Kirsch-Volders M, Bonassi S, Fenech M. Genetic polymorphisms of genes involved in DNA repair and metabolism influence micronucleus frequencies in human peripheral blood lymphocytes. Mutagenesis 2010; 26:33-42. [DOI: 10.1093/mutage/geq076] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Germann MW, Johnson CN, Spring AM. Recognition of Damaged DNA: Structure and Dynamic Markers. Med Res Rev 2010; 32:659-83. [DOI: 10.1002/med.20226] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Markus W. Germann
- Department of Chemistry; Georgia State University; Atlanta Georgia 30302
- Department of Biology and the Neuroscience Institute; Georgia State University; Atlanta Georgia 30302
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Cole HA, Tabor-Godwin JM, Hayes JJ. Uracil DNA glycosylase activity on nucleosomal DNA depends on rotational orientation of targets. J Biol Chem 2009; 285:2876-85. [PMID: 19933279 DOI: 10.1074/jbc.m109.073544] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The activity of uracil DNA glycosylases (UDGs), which recognize and excise uracil bases from DNA, has been well characterized on naked DNA substrates but less is known about activity in chromatin. We therefore prepared a set of model nucleosome substrates in which single thymidine residues were replaced with uracil at specific locations and a second set of nucleosomes in which uracils were randomly substituted for all thymidines. We found that UDG efficiently removes uracil from internal locations in the nucleosome where the DNA backbone is oriented away from the surface of the histone octamer, without significant disruption of histone-DNA interactions. However, uracils at sites oriented toward the histone octamer surface were excised at much slower rates, consistent with a mechanism requiring spontaneous DNA unwrapping from the nucleosome. In contrast to the nucleosome core, UDG activity on DNA outside the core DNA region was similar to that of naked DNA. Association of linker histone reduced activity of UDG at selected sites near where the globular domain of H1 is proposed to bind to the nucleosome as well as within the extra-core DNA. Our results indicate that some sites within the nucleosome core and the extra-core (linker) DNA regions represent hot spots for repair that could influence critical biological processes.
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Affiliation(s)
- Hope A Cole
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
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Subramanian M, Gonzalez RW, Patil H, Ueda T, Lim JH, Kraemer KH, Bustin M, Bergel M. The nucleosome-binding protein HMGN2 modulates global genome repair. FEBS J 2009; 276:6646-57. [PMID: 19843163 PMCID: PMC3460546 DOI: 10.1111/j.1742-4658.2009.07375.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The HMGN family comprises nuclear proteins that bind to nucleosomes and alter the structure of chromatin. Here, we report that DT40 chicken cells lacking either HMGN2 or HMGN1a, or lacking both HMGN1a and HMGN2, are hypersensitive to killing by UV irradiation. Loss of both HMGN1a and HMGN2 or only HMGN2 increases the extent of UV-induced G(2)-M checkpoint arrest and the rate of apoptosis. HMGN null mutant cells showed slower removal of UV-induced DNA lesions from native chromatin, but the nucleotide excision repair remained intact, as measured by host cell reactivation assays. These results identify HMGN2 as a component of the global genome repair subpathway of the nucleotide excision repair pathway, and may indicate that HMGN2 facilitates the ability of the DNA repair proteins to access and repair UV-induced DNA lesions in chromatin. Our finding that HMGNs play a role in global DNA repair expands the role of these proteins in the maintenance of genome integrity.
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Tremblay M, Toussaint M, D'Amours A, Conconi A. Nucleotide excision repair and photolyase repair of UV photoproducts in nucleosomes: assessing the existence of nucleosome and non-nucleosome rDNA chromatin in vivo. Biochem Cell Biol 2009; 87:337-46. [PMID: 19234545 DOI: 10.1139/o08-128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The genome is organized into nuclear domains, which create microenvironments that favor distinct chromatin structures and functions (e.g., highly repetitive sequences, centromeres, telomeres, noncoding sequences, inactive genes, RNA polymerase II and III transcribed genes, and the nucleolus). Correlations have been drawn between gene silencing and proximity to a heterochromatic compartment. At the other end of the scale are ribosomal genes, which are transcribed at a very high rate by RNA polymerase I (~60% of total transcription), have a loose chromatin structure, and are clustered in the nucleolus. The rDNA sequences have 2 distinct structures: active rRNA genes, which have no nucleosomes; and inactive rRNA genes, which have nucleosomes. Like DNA transcription and replication, DNA repair is modulated by the structure of chromatin, and the kinetics of DNA repair vary among the nuclear domains. Although research on DNA repair in all chromosomal contexts is important to understand the mechanisms of genome maintenance, this review focuses on nucleotide excision repair and photolyase repair of UV photoproducts in the first-order packing of DNA in chromatin: the nucleosome. In addition, it summarizes the studies that have demonstrated the existence of the 2 rDNA chromatins, and the way this feature of the rDNA locus allows for direct comparison of DNA repair in 2 very different structures: nucleosome and non-nucleosome DNA.
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Affiliation(s)
- Maxime Tremblay
- Departement de Microbiologie et Infectiologie, Faculte de Medecine, Universite de Sherbrooke, Sherbrooke, QCJ1H5N4, Canada
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The nucleotide excision repair of DNA in human cells and its association with xeroderma pigmentosum. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 637:113-9. [PMID: 19181116 DOI: 10.1007/978-0-387-09599-8_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Cheng J, Leng S, Dai Y, Huang C, Pan Z, Niu Y, Li B, Zheng Y. Association between nucleotide excision repair gene polymorphisms and chromosomal damage in coke-oven workers. Biomarkers 2008; 12:76-86. [PMID: 17438655 DOI: 10.1080/13547500600950168] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The associations between several genetic polymorphisms of nucleotide excision repair genes (NER) and chromosome damage level were studied among 140 coke-oven workers exposed to a high level of polyaromatic hydrocarbons (PAHs) and 66 non-exposed workers. Seven polymorphisms with functional potential in five NER genes (ERCC1, ERCC2, ERCC4, ERCC5 and ERCC6) were genotyped in the 206 study subjects. Multivariate analysis of covariance revealed that coke-oven workers with the ERCC1 19007 CC genotype had significantly higher cytokinesis-block micronucleus frequency (CBMN) (10.5 +/- 6.8 per thousand) than those with CT (8.1 +/- 6.6 per thousand, p = 0.01) or TT (6.6 +/- 3.7-/ per thousand p = 0.05) or CT+TT genotypes (7.5 +/- 6.3 per thousand, p = 0.004). The ERCC6 A3368G polymorphism was also associated with CBMN frequency among coke-oven workers. Subjects with the AA genotype have a significantly higher CBMN frequency (10.0 +/- 6.9 per thousand) than those with AG (6.7 +/- 4.2 per thousand, p = 0.05) or AG+GG genotypes (6.6 +/- 4.1 per thousand, p = 0.02). Stratification analysis revealed the significant associations between ERCC1 C19007T and ERCC6 A3368G, and the CBMN frequencies were only found among older workers. In addition, a significant association between ERCC2 G23591A polymorphism and CBMN frequencies was also found among older coke-oven workers. The results suggest that polymorphisms of ERCC1 C19007T, ERCC6 A3368G and ERCC2 G23591A are associated with the CBMN frequencies among coke-oven workers.
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Affiliation(s)
- J Cheng
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
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Teng Y, Yu Y, Ferreiro JA, Waters R. Histone acetylation, chromatin remodelling, transcription and nucleotide excision repair in S. cerevisiae: studies with two model genes. DNA Repair (Amst) 2007; 4:870-83. [PMID: 15950549 DOI: 10.1016/j.dnarep.2005.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2005] [Indexed: 11/23/2022]
Abstract
We describe the technology and two model systems in yeast designed to study nucleotide excision repair (NER) in relation to transcription and chromatin modifications. We employed the MFA2 and MET16 genes as models. How transcription-coupled (TCR) and global genome repair (GGR) operate at the transcriptionally active and/or repressed S. cerevisiae MFA2 locus, and how this relates to nucleosome positioning are considered. We discuss the role of the Gcn5p histone acetyltransferase, also associated with MFA2's transcriptional activation, in facilitating efficient NER at the transcriptionally active and inactive genes. The effect of Gcn5p's absence in reducing NER was local and UV stimulates Gcn5p-mediated histone acetylation at the repressed MFA2 promoter. After UV irradiation Swi2p is partly responsible for facilitating access to restriction of DNA in the cores of the nucleosomes at the MFA2 promoter. The data suggest similarities between chromatin remodelling for NER and transcription, yet differences must exist to ensure this gene remains repressed in alpha cells during NER. For MET16, we consider experiments examining chromatin structure, transcription and repair in wild type and cbf1Delta cells under repressing or derepressing conditions. Cbf1p is a sequence specific DNA binding protein required for MET16 chromatin remodelling and transcription.
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Affiliation(s)
- Yumin Teng
- Department of Pathology, University Wales College of Medicine, Heath Park, Cardiff CF14 4XN, UK
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Conconi A. The yeast rDNA locus: a model system to study DNA repair in chromatin. DNA Repair (Amst) 2007; 4:897-908. [PMID: 15996904 DOI: 10.1016/j.dnarep.2005.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2005] [Indexed: 11/23/2022]
Abstract
Most of the studies on the effect of chromatin structure and chromatin remodeling on DNA repair are based on in vitro reconstituted assays. In such experiments individual nucleosomes are either released by nuclease digestion of native chromatin fibers or are assembled from purified histones. Though reconstituted assays are valid approaches to follow NER in chromatin they are of somehow limited physiological relevance since single core particles do not exist in vivo [K. van Holde, J. Zlatanova, The nucleosome core particle: does it have structural and physiological relevance? Bioessays 21 (1999) 776-778]. This is particularly true for studies involving core histones tails, as in their natural chromatin context histones tails participate in interactions that are not necessarily present in vitro [J.C. Hansen, C. Tse, A.P. Wolffe, Structure and function of the core histone N-termini: more than meets the eye, Biochemistry 37 (1998) 17637-17641; J.J. Hayes, J.C. Hansen, Nucleosomes and chromatin fiber, Curr. Opin. Genet. Dev. 11 (2001) 124-129]. Indeed it was found that human DNA ligase I has the capability to ligate a nick on the surface of a 215bp nucleosome but not a nick in a nucleosome lacking linker DNA, possibly because of forced interactions between histone tails and core DNA present in the latter complex [D.R. Chafin, J.M. Vitolo, L.A. Henricksen, B.A. Bambara, J.J. Hayes, Human DNA ligase I efficiently seals nicks in nucleosomes, EMBO J. 19 (2000) 5492-5501]. In addition, chromatin remodeling could also occur in the higher ordered folding of chromatin and involve multiple arrays of nucleosomes [P.J. Horn, C.L. Peterson, Chromatin higher order folding: wrapping up transcription, Science 297 (2002) 1824-1827]. By studying the chromatin structure of ribosomal genes in yeast, our knowledge of the fate of nucleosomes during transcription and DNA replication has improved considerably [R. Lucchini, J.M. Sogo, The dynamic structure of ribosomal RNA gene chromatin, in: M.R. Paule (Ed.), Transcription of Ribosomal RNA Genes by Eukaryotic RNA Polymerase I, Springer-Verlag/R.G. Landes Company, 1998, pp. 254-276]. How nuclear processes such as DNA repair take place in chromatin is still largely unknown, and in this review I discuss how the yeast rDNA locus may be exploited to investigate DNA repair and chromatin modification in vivo.
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Affiliation(s)
- Antonio Conconi
- Department de Microbiologie et Infectiologie, Faculte de Medecine, Universite de Sherbrooke, 3001, 12(e) Avenue Nord, Sherbrooke, Que., Canada J1H 5N4
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Sen SP, De Benedetti A. TLK1B promotes repair of UV-damaged DNA through chromatin remodeling by Asf1. BMC Mol Biol 2006; 7:37. [PMID: 17054786 PMCID: PMC1626478 DOI: 10.1186/1471-2199-7-37] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Accepted: 10/20/2006] [Indexed: 11/21/2022] Open
Abstract
Background The mammalian protein kinase TLK1 is a homologue of Tousled, a gene involved in flower development in Arabidopsis thaliana. The function of TLK1 is not well known, although knockout of the gene in Drosophila, or expression of a dominant negative mutant in mouse mammary cells causes loss of nuclear divisions and chromosome mis-segregation. TLK1B is a splice variant of TLK1 and it confers radioresistance in a normal mammary mouse cell line possibly due to increased chromatin remodeling capacity, but the mechanism of resistance remains to be fully elucidated. Results We now show that TLK1B also affords protection against UV radiation. We find that nuclear extracts isolated from TLK1B-containing mouse cells promote more efficient chromatin assembly than comparable extracts lacking TLK1B. TLK1B-containing extracts are also more efficient in repair of UV-damaged plasmid DNA assembled into nucleosomes. One of the two known substrates of TLK1 (or TLK1B) is the histone chaperone Asf1, and immuno-inactivation experiments suggest that TLK1B increases UV-repair through the action of Asf1 on chromatin assembly/disassembly. Conclusion Our studies provide evidence for TLK1B-mediated phosphorylation of Asf1 triggering DNA repair. We suggest that this occurs via Asf1-mediated chromatin assembly at the sites of UV damage.
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Affiliation(s)
- Siddhartha P Sen
- Department of Biochemistry and Molecular Biology and the Feist Weiller Cancer Center, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130-3932, USA
| | - Arrigo De Benedetti
- Department of Biochemistry and Molecular Biology and the Feist Weiller Cancer Center, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130-3932, USA
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Jagannathan I, Cole HA, Hayes JJ. Base excision repair in nucleosome substrates. Chromosome Res 2006; 14:27-37. [PMID: 16506094 DOI: 10.1007/s10577-005-1020-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 11/01/2005] [Indexed: 01/29/2023]
Abstract
Eukaryotic cells must repair DNA lesions within the context of chromatin. Much of our current understanding regarding the activity of enzymes involved in DNA repair processes comes from in-vitro studies utilizing naked DNA as a substrate. Here we review current literature investigating how enzymes involved in base excision repair (BER) contend with nucleosome substrates, and discuss the possibility that some of the activities involved in BER are compatible with the organization of DNA within nucleosomes. In addition, we examine evidence for the role of accessory factors, such as histone modification enzymes, and the role of the histone tail domains in moderating the activities of BER factors on nucleosomal substrates.
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Affiliation(s)
- Indu Jagannathan
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Box 712, NY 14642, USA
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Marcus WD, Wang H, Lohr D, Sierks MR, Lindsay SM. Isolation of an scFv targeting BRG1 using phage display with characterization by AFM. Biochem Biophys Res Commun 2006; 342:1123-9. [PMID: 16513088 DOI: 10.1016/j.bbrc.2006.02.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Accepted: 02/13/2006] [Indexed: 11/20/2022]
Abstract
Remodeling of chromatin is a vitally important event in processes such as transcription and replication. Brahma-related gene 1 (BRG1) protein is the major ATPase subunit in the human Swi/Snf complex (hSwi/Snf), an important example of the family of enzymes that carry out such remodeling events. We have used a recently developed technique, recognition imaging, to better understand the role of BRG1 in remodeling chromatin. In such experiments, a specific antibody against BRG1 is needed. However, we have found that the commercially available polyclonal (CAP) antibodies interact non-specifically with nucleosomes, making it impossible to identify hSwi/Snf (BRG1) in their presence. Here antibody phage display technology is employed for development of an antibody specifically targeting BRG1. The Tomlinson I and J single chain variable fragment (scFv) libraries were used for successful isolation of an anti-BRG1 scFv. We demonstrate that the scFv binds more strongly and with less nonspecific interactions than the CAP antibody. This work lays the groundwork for future studies involving chromatin remodeling.
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Affiliation(s)
- W D Marcus
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287, USA.
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Robert J, Morvan VL, Smith D, Pourquier P, Bonnet J. Predicting drug response and toxicity based on gene polymorphisms. Crit Rev Oncol Hematol 2005; 54:171-96. [PMID: 15890268 DOI: 10.1016/j.critrevonc.2005.01.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2004] [Revised: 01/01/2005] [Accepted: 01/28/2005] [Indexed: 12/16/2022] Open
Abstract
The sequencing of the human genome has allowed the identification of thousands of gene polymorphisms, most often single nucleotide polymorphims (SNP), which may play an important role in the expression level and activity of the corresponding proteins. When these polymorphisms occur at the level of drug metabolising enzymes or transporters, the disposition of the drug may be altered and, consequently, its efficacy may be compromised or its toxicity enhanced. Polymorphisms can also occur at the level of proteins directly involved in drug action, either when the protein is the target of the drug or when the protein is involved in the repair of drug-induced lesions. There again, these polymorphisms may lead to alterations in drug efficacy and/or toxicity. The identification of functional polymorphisms in patients undergoing chemotherapy may help the clinician prescribe the optimal drug combination or schedule and predict with more accuracy the response to these prescriptions. We have recorded in this review the polymorphisms that have been identified up till now in genes involved in anticancer drug activity. Some of them appear especially important in predicting drug toxicity and should be determined in routine before drug administration; this is the case of the most common variations of thiopurine methyltransferase for 6-mercaptopurine and of dihydropyrimidine dehydrogenase for fluorouracil. Other appear determinant for drug response, such as the common SNPs found in glutathione S-transferase P1 or xereoderma pigmentosum group D enzyme for the activity of oxaliplatin. However, confusion factors may exist between the role of gene polymorphisms in cancer risk or overall prognosis and their role in drug response.
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Affiliation(s)
- Jacques Robert
- Institut Bergonié and Université Victor Segalen Bordeaux 2, 229 cours de l'Argonne, 33076 Bordeaux-Cedex, France.
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20
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Wang H, Bash R, Lindsay SM, Lohr D. Solution AFM studies of human Swi-Snf and its interactions with MMTV DNA and chromatin. Biophys J 2005; 89:3386-98. [PMID: 16100261 PMCID: PMC1366835 DOI: 10.1529/biophysj.105.065391] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ATP-dependent nucleosome remodeling complexes are crucial for relieving nucleosome repression during transcription, DNA replication, recombination, and repair. Remodeling complexes can carry out a variety of reactions on chromatin substrates but precisely how they do so remains a topic of active inquiry. Here, a novel recognition atomic force microscopy (AFM) approach is used to characterize human Swi-Snf (hSwi-Snf) nucleosome remodeling complexes in solution. This information is then used to locate hSwi-Snf complexes bound to mouse mammary tumor virus promoter nucleosomal arrays, a natural target of hSwi-Snf action, in solution topographic AFM images of surface-tethered arrays. By comparing the same individual chromatin arrays before and after hSwi-Snf activation, remodeling events on these arrays can be monitored in relation to the complexes bound to them. Remodeling is observed to be: inherently heterogeneous; nonprocessive; able to occur near and far from bound complexes; often associated with nucleosome height decreases. These height decreases frequently occur near sites of DNA release from chromatin. hSwi-Snf is usually incorporated into nucleosomal arrays, with multiple DNA strands entering into it from various directions, + or - ATP; these DNA paths can change after hSwi-Snf activation. hSwi-Snf appears to interact with naked mouse mammary tumor virus DNA somewhat differently than with chromatin and ATP activation of surface-bound DNA/hSwi-Snf produces no changes detectable by AFM.
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Affiliation(s)
- H Wang
- Arizona Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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21
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Hasegawa K, Saigusa T, Tamai Y. Caenorhabditis elegans opens up new insights into circadian clock mechanisms. Chronobiol Int 2005; 22:1-19. [PMID: 15865318 DOI: 10.1081/cbi-200038149] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The roundworm, Caenorhabditis elegans, is known to carry homologues of clock genes such as per (=period) and tim (=timeless), which constitute the core of the circadian clock in Drosophila and mammals: lin-42 and tim-1. Analyses using WormBase (C. elegans gene database) have identified with relatively high identity analogous of the clock genes recognized in Drosophila and mammals, with the notable exception of cry (=cryptochrome), which is lacking in C. elegans. All of these C. elegans cognates of the clock genes appear to belong to members of the PAS-superfamily and to participate in development or responsiveness to the environment but apparently are not involved in the C. elegans circadian clock. Nevertheless, C. elegans exhibits convincing circadian rhythms in locomotor behavior in the adult stage and in resistance to hyperosmotic stress in starved larvae (L1) after hatching, indicating that it has a circadian clock with a core design entirely different from that of Drosophila and mammals. Here two possibilities are considered. First, the core of the C. elegans circadian clock includes transcriptional/translational feedback loops between genes and their protein products that are entirely different from those of Drosophila and mammals. Second, a more basic principle such as homeostasis governs the circadian cellular physiology, and was established primarily to minimize the accumulation of DNA damage in response to an environment cycling at 24 h intervals.
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Affiliation(s)
- Kenji Hasegawa
- Division of Brain Science, Graduate School of Medicine, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan.
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22
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Reed SH. Nucleotide excision repair in chromatin: The shape of things to come. DNA Repair (Amst) 2005; 4:909-18. [PMID: 15905137 DOI: 10.1016/j.dnarep.2005.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2005] [Indexed: 11/26/2022]
Abstract
Much of our mechanistic understanding of nucleotide excision repair (NER) has been derived from biochemical studies that have analysed the reaction as it occurs on DNA substrates that are not representative of DNA as it exists in the living cell. These studies have been extremely useful in deciphering the core mechanism of the NER reaction, but efforts to understand how NER operates in chromatin have been hampered in part because assembling DNA into nucleosomes, the first level of chromatin compaction, is inhibitory to NER in vitro. However, recent research using biochemical, genetic and cell-based studies is now providing us with the first insights into the molecular mechanism of NER as it occurs in the cellular context. A number of recent studies have provided glimpses of a chromatin--NER connection. Here I review this literature and evaluate how it might aid our understanding, and shape our future research into NER.
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Affiliation(s)
- Simon H Reed
- Department of Pathology, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
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23
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Yu Y, Teng Y, Liu H, Reed SH, Waters R. UV irradiation stimulates histone acetylation and chromatin remodeling at a repressed yeast locus. Proc Natl Acad Sci U S A 2005; 102:8650-5. [PMID: 15939881 PMCID: PMC1150825 DOI: 10.1073/pnas.0501458102] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromatin immunoprecipitation with anti-acetyl histone H3 (K9 and K14) and anti-acetyl histone H4 (K5, K8, K12, and K16) antibodies shows that Lys-9 and/or Lys-14 of histone H3, but not the relevant sites of histone H4 in nucleosomes at the repressed MFA2 promoter, are hyperacetylated after UV irradiation. This level of histone hyperacetylation diminishes gradually as repair proceeds. Accompanying this, chromatin in the promoter becomes more accessible to restriction enzymes after UV irradiation and returns to the pre-UV state gradually. UV-related histone hyperacetylation and chromatin remodeling in the MFA2 promoter depend on Gcn5p and partially on Swi2p, respectively. Deletion of GCN5, but not of SWI2, impairs repair of DNA damage in the MFA2 promoter. The post-UV histone modifications and chromatin remodeling at the repressed MFA2 promoter do not activate MFA2 transcriptionally, nor do they require damage recognition by Rad4p or Rad14p. Furthermore, we show that UV irradiation triggers genome-wide histone hyperacetylation at both histone H3 and H4. These experiments indicate that chromatin at a yeast repressed locus undergoes active change after UV radiation treatment and that failure to achieve histone H3 hyperacetylation impairs the repair of DNA damage.
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Affiliation(s)
- Yachuan Yu
- Department of Pathology, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
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24
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Beard BC, Stevenson JJ, Wilson SH, Smerdon MJ. Base excision repair in nucleosomes lacking histone tails. DNA Repair (Amst) 2005; 4:203-9. [PMID: 15590328 DOI: 10.1016/j.dnarep.2004.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2004] [Accepted: 09/18/2004] [Indexed: 10/26/2022]
Abstract
Recently, we developed an in vitro system using human uracil DNA glycosylase (UDG), AP endonuclease (APE), DNA polymerase beta (pol beta) and rotationally positioned DNA containing a single uracil associated with a 'designed' nucleosome, to test short-patch base excision repair (BER) in chromatin. We found that UDG and APE carry out their catalytic activities with reduced efficiency on nucleosome substrates, showing a distinction between uracil facing 'out' or 'in' from the histone surface, while DNA polymerase beta (pol beta) is completely inhibited by nucleosome formation. In this report, we tested the inhibition of BER enzymes by the N-terminal 'tails' of core histones that take part in both inter- and intra-nucleosome interactions, and contain sites of post-translational modifications. Histone tails were removed by limited trypsin digestion of 'donor' nucleosome core particles and histone octamers were exchanged onto a nucleosome-positioning DNA sequence containing a single G:U mismatch. The data indicate that UDG and APE activities are not significantly enhanced with tailless nucleosomes, and the distinction between rotational settings of uracil on the histone surface is unaffected. More importantly, the inhibition of pol beta activity is not relieved by removal of the histone tails, even though these tails interact with DNA in the G:U mismatch region. Finally, inclusion of X-ray cross complement group protein 1 (XRCC1) or Werner syndrome protein (WRN) had no effect on the BER reactions. Thus, additional activities may be required in cells for efficient BER of at least some structural domains in chromatin.
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Affiliation(s)
- Brian C Beard
- Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA
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25
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Dip R, Camenisch U, Naegeli H. Mechanisms of DNA damage recognition and strand discrimination in human nucleotide excision repair. DNA Repair (Amst) 2005; 3:1409-23. [PMID: 15380097 DOI: 10.1016/j.dnarep.2004.05.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Indexed: 11/20/2022]
Abstract
Using only a limited repertoire of recognition subunits, the nucleotide excision repair (NER) system is able to detect a nearly infinite variety of bulky DNA lesions. This extraordinary substrate versatility has generally been ascribed to an indirect readout mechanism, whereby particular distortions of the double helix, induced by a damaged nucleotide, provide the molecular determinants not only for lesion recognition but also for subsequent verification or demarcation processes. Here, we discuss the evidence in support of a bipartite mechanism of substrate discrimination that is initiated by the detection of thermodynamically unstable base pairs followed by direct localization of the lesion through an enzymatic proofreading activity. This bipartite discrimination mechanism is part of a dynamic reaction cycle that confers high levels of selectivity to avoid futile repair events on undamaged DNA and also protect the intact complementary strand from inappropriate cleavage.
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Affiliation(s)
- Ramiro Dip
- Institute of Pharmacology and Toxicology, University of Zürich-Vetsuisse, Winterthurerstrasse 260, CH-8057 Zürich, Switzerland
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26
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Huang X, King MA, Halicka HD, Traganos F, Okafuji M, Darzynkiewicz Z. Histone H2AX phosphorylation induced by selective photolysis of BrdU-labeled DNA with UV light: relation to cell cycle phase. Cytometry A 2005; 62:1-7. [PMID: 15455410 DOI: 10.1002/cyto.a.20086] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND The induction of DNA double-strand breaks (DSBs) in chromatin triggers histone H2AX phosphorylation (on Ser-139) by ATM-, ATR-, or DNA-dependent protein kinases (DNA-PK). Phosphorylated H2AX, denoted as gammaH2AX, can be detected immunocytochemically using an antibody that is specific to the Ser-139-phosphorylated epitope. We previously reported that the induction DSBs by DNA topoisomerase I or II inhibitors can be monitored in individual cells by measuring gammaH2AX immunofluorescence (IF) by cytometry. The present study explored whether the detection of gammaH2AX IF can serve as a marker of the presence of the DNA precursor bromodeoxyuridine (BrdU) that is incorporated into DNA. METHODS HeLa cells growing on microscope slides were incubated with BrdU for 1 h, rinsed free of the precursor, and incubated for different periods for up to 12 h. The cells were then briefly incubated with Hoechst 33342 (to sensitize BrdU-labeled DNA to ultraviolet [UV] light), irradiated with 300 nm UV light to photolyze BrdU-labeled DNA, transferred back into culture for an additional hour, and fixed. Cells were concurrently immunostained for gammaH2AX (Alexa Fluor 633) and cyclin A (fluorescein isothiocyanate); their DNA was counterstained with 4,6-diamidino-2-phenylindole. The intensities of cellular far red (gammaH2AX), green (cyclin A), and blue (DNA) fluorescences were measured by laser scanning cytometry. RESULTS After a 1-h pulse of BrdU followed by exposure to UV, nearly all cells with S-phase DNA content had many-fold higher gammaH2AX IF than G(1) or G(2)/M cells. The nonirradiated cells had minimal ("programmed") expression of gammaH2AX, whereas the irradiated cells incubated without BrdU had uniformly elevated levels of gammaH2AX IF independent of the cell cycle phase. Pulse-chase experiments showed that the cohort of BrdU-labeled (gammaH2AX-positive) cells progressed through G(2)/M and into G(1) phase after 8 and 12 h of growth in BrdU-free medium, respectively. Bivariate analysis of gammaH2AX versus cyclin A expression for the gated S-phase cells showed a correlation between these variables, suggesting that the rate of BrdU incorporation (DNA replication) correlates with expression of cyclin A. CONCLUSIONS Photolysis of BrdU-labeled DNA induces DSBs and leads to H2AX phosphorylation. Detection of gammaH2AX IF indicates the presence of the incorporated BrdU, is compatible with concurrent detection of other intracellular antigens, and can be used to demonstrate cell cycle kinetics.
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Affiliation(s)
- Xuan Huang
- Brander Cancer Research Institute at New York Medical College, 19 Bradhurst Avenue, Hawthorne, NY 10532, USA
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27
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Fritsch O, Benvenuto G, Bowler C, Molinier J, Hohn B. The INO80 protein controls homologous recombination in Arabidopsis thaliana. Mol Cell 2004; 16:479-85. [PMID: 15525519 DOI: 10.1016/j.molcel.2004.09.034] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Revised: 05/28/2004] [Accepted: 08/30/2004] [Indexed: 10/26/2022]
Abstract
Homologous recombination (HR) serves a dual role in providing genetic flexibility and in maintaining genome integrity. Little is known about the regulation of HR and other repair pathways in the context of chromatin. We report on a mutant affected in the expression of the Arabidopsis INO80 ortholog of the SWI/SNF ATPase family, which shows a reduction of the HR frequency to 15% of that in wild-type plants. In contrast, sensitivity to genotoxic agents and efficiency of T-DNA integration remain unaffected, suggesting that INO80 is a positive regulator of HR, while not affecting other repair pathways. So far, INO80 function has only been reported in a lower eukaryote. Profiling studies on three ino80 allelic mutants show that INO80 regulates nearly 100 Arabidopsis genes. However, the transcriptional regulation of repair-related genes is unaffected in the mutant. This suggests a dual role for INO80 in transcription and DNA repair by HR.
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Affiliation(s)
- Olivier Fritsch
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
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28
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Ramsey KL, Smith JJ, Dasgupta A, Maqani N, Grant P, Auble DT. The NEF4 complex regulates Rad4 levels and utilizes Snf2/Swi2-related ATPase activity for nucleotide excision repair. Mol Cell Biol 2004; 24:6362-78. [PMID: 15226437 PMCID: PMC434245 DOI: 10.1128/mcb.24.14.6362-6378.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nucleotide excision repair factor 4 (NEF4) is required for repair of nontranscribed DNA in Saccharomyces cerevisiae. Rad7 and the Snf2/Swi2-related ATPase Rad16 are NEF4 subunits. We report previously unrecognized similarity between Rad7 and F-box proteins. Rad16 contains a RING domain embedded within its ATPase domain, and the presence of these motifs in NEF4 suggested that NEF4 functions as both an ATPase and an E3 ubiquitin ligase. Mutational analysis provides strong support for this model. The Rad16 ATPase is important for NEF4 function in vivo, and genetic analysis uncovered new interactions between NEF4 and Rad23, a repair factor that links repair to proteasome function. Elc1 is the yeast homologue of a mammalian E3 subunit, and it is a novel component of NEF4. Moreover, the E2s Ubc9 and Ubc13 were linked to the NEF4 repair pathway by genetic criteria. Mutations in NEF4 or Ubc13 result in elevated levels of the DNA damage recognition protein Rad4 and an increase in ubiquitylated species of Rad23. As Rad23 also controls Rad4 levels, these results suggest a complex system for globally regulating repair activity in vivo by controlling turnover of Rad4.
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Affiliation(s)
- Kerrington L Ramsey
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908-0733, USA
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29
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Koeppel F, Poindessous V, Lazar V, Raymond E, Sarasin A, Larsen AK. Irofulven cytotoxicity depends on transcription-coupled nucleotide excision repair and is correlated with XPG expression in solid tumor cells. Clin Cancer Res 2004; 10:5604-13. [PMID: 15328203 DOI: 10.1158/1078-0432.ccr-04-0442] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Irofulven is a novel alkylating agent with promising clinical activity, particularly toward ovarian and hormone-refractory prostate cancers. To facilitate additional clinical development, we have aimed to identify biological markers associated with sensitivity to the compound. METHODS Fibroblasts derived from patients with xeroderma pigmentosum or Cockayne's syndrome along with a panel of 20 human cancer cell lines (eight different tumor types) were examined to establish the importance of nucleotide excision repair proteins in the sensitivity to irofulven. RESULTS Human cells deficient in nucleotide excision repair are up to 30-fold more sensitive to the cytotoxic effects of irofulven compared with repair-proficient controls, clearly indicating that nucleotide excision repair plays a crucial role in the sensitivity to the drug. Interestingly, our results show that irofulven-induced lesions are recognized by transcription-coupled repair but not by global genome repair. Another unique feature is the pronounced sensitivity of XPD and XPB helicase-deficient cells to the drug. Comparison of the IC50 values for irofulven, cisplatin, and ecteinascidin 743 with the expression levels of ERCC1, XPD, and XPG genes in different solid tumor cell lines shows no correlation between the expression levels of any of the three nucleotide excision repair proteins and the sensitivity to ecteinascidin 743. In contrast, expression of the XPG endonuclease was correlated with the cytotoxicity for irofulven and, to a lesser degree, for cisplatin. Importantly, XPG expression was also correlated with cellular nucleotide excision repair activity. CONCLUSIONS Increasing evidence indicates that compromised nucleotide excision repair activity is frequent in several solid tumor types. The results presented here suggest that XPG expression in such tumors may be a useful marker to predict their sensitivity to irofulven.
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Affiliation(s)
- Florence Koeppel
- Group of Biology and Pharmacogenetics of Human Tumors, Centre National de la Recherche Scientifique, UMR 8113, Institut Gustave-Roussy, Villejuif, France
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30
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Molinier J, Ramos C, Fritsch O, Hohn B. CENTRIN2 modulates homologous recombination and nucleotide excision repair in Arabidopsis. THE PLANT CELL 2004; 16:1633-43. [PMID: 15155891 PMCID: PMC490051 DOI: 10.1105/tpc.021378] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2004] [Accepted: 03/17/2004] [Indexed: 05/17/2023]
Abstract
A genetic screen of a population of Arabidopsis thaliana lines exhibiting enhanced somatic homologous recombination yielded a mutant affected in expression of a gene encoding a caltractin-like protein (centrin). The hyperrecombinogenic phenotype could be reproduced using RNA interference (RNAi) technology. Both the original mutant and the RNAi plants exhibited a moderate UV-C sensitivity as well as a reduced efficiency of in vitro repair of UV-damaged DNA. Transcription profiling of the mutant showed that expression of components of the nucleotide excision repair (NER) pathway and of factors involved in other DNA repair processes were significantly changed. Our data suggest an indirect involvement of centrin in recombinational DNA repair via the modulation of the NER pathway. These findings thus point to a novel interconnection between an early step of NER and homologous recombination, which may play a critical role in plant DNA repair.
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Affiliation(s)
- Jean Molinier
- Friedrich Miescher-Institute for Biomedical Research, CH-4058 Basel, Switzerland.
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31
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Salerno V, Napoli A, White MF, Rossi M, Ciaramella M. Transcriptional response to DNA damage in the archaeon Sulfolobus solfataricus. Nucleic Acids Res 2003; 31:6127-38. [PMID: 14576299 PMCID: PMC275473 DOI: 10.1093/nar/gkg831] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Exposure of cells to DNA-damaging agents triggers a complex biological response involving cell cycle arrest and modulation of gene expression. Genomic sequencing has revealed the presence of archaeal genes homologous to components of the eucaryal nucleotide excision repair (NER) pathway, which is involved in the repair of ultraviolet (UV) light-induced DNA damage. However, the events involved in the cell response to UV irradiation and their regulation have not been studied in Archaea. We show here that UV radiation induces the formation of cyclobutane pyrimidine dimers (CPDs) in the hyperthermophilic archaeon Sulfolobus solfataricus, and that these lesions are efficiently repaired in vivo in the dark, suggesting that a NER pathway is active. DNA damage is a signal for concomitant growth arrest and transcriptional induction of the NER genes XPF, XPG and XPB. The cell response to UV irradiation includes transcriptional regulation of genes encoding two DNA binding proteins involved in chromosome dynamics. Moreover, several of these genes are also strongly induced by the intercalating agent actinomycin D. Thus, response to DNA damage in S.solfataricus has features essentially conserved in all three domains of life.
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Affiliation(s)
- Vincenzo Salerno
- Institute of Protein Biochemistry, Consiglio Nazionale delle Ricerche, Via P. Castellino, 80131 Naples, Italy
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32
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Riedl T, Hanaoka F, Egly JM. The comings and goings of nucleotide excision repair factors on damaged DNA. EMBO J 2003; 22:5293-303. [PMID: 14517266 PMCID: PMC204472 DOI: 10.1093/emboj/cdg489] [Citation(s) in RCA: 337] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To understand the mechanism of nucleotide excision repair (NER), one of the major human DNA repair pathways, we have set up a DNA repair system in which a linear damaged DNA substrate is immobilized by its terminus. By isolating functionally active intermediate complexes, our data dissect the ordered arrival and displacement of NER factors in the progress of the dual incision step. We describe (i) the role of ATP in remodelling the NER-initiating complex of XPC/TFIIH/damaged DNA as a prerequisite for the recruitment of the next NER factors; (ii) the coordination between damage removal and DNA resynthesis and the release of XPC-HR23B, TFIIH and XPA upon arrival of XPG and XPF-ERCC1, respectively; (iii) how RPA remains associated with the excised DNA initiating the assembly of resynthesis factors such as PCNA; (iv) the recycling of XPC-HR23B, TFIIH and XPA in the NER; and the shuttling of TFIIH between NER and transcription. Thus, our findings define multiple functions of NER factors to explain the molecular basis of human NER disorders.
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Affiliation(s)
- Thilo Riedl
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, B.P. 10142, 67404 Illkirch, C.U. de Strasbourg, France
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33
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Flohr C, Bürkle A, Radicella JP, Epe B. Poly(ADP-ribosyl)ation accelerates DNA repair in a pathway dependent on Cockayne syndrome B protein. Nucleic Acids Res 2003; 31:5332-7. [PMID: 12954769 PMCID: PMC203308 DOI: 10.1093/nar/gkg715] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Activation of poly(ADP-ribose)polymerases 1 and 2 (PARP-1 and PARP-2) is one of the earliest responses of mammalian cells to DNA damage by numerous genotoxic agents. We have analysed the influence of PARP inhibition, either achieved by over-expression of the DNA binding domain of PARP-1 or by treatment with 3,4-dihydro-5-[4-(1-piperidinyl)butoxyl]-1(2H)-isoquinolinone, on the repair of single-strand breaks (SSB), pyrimidine dimers and oxidative base modifications sensitive to Fpg protein (mostly 8-hydroxyguanine) in mammalian cells at very low, non-cytotoxic levels of DNA damage. The data show that the repair rates of all three types of DNA damage are significantly lower in PARP-inhibited cells. Importantly, the retardation of the repair of base modifications is not associated with accumulation of intermediates such as SSB or abasic sites. Moreover, the influence of the PARP inhibition is not observed in cells deficient in Cockayne syndrome B protein (Csb). The results indicate that PARP activation and Csb are both involved in a novel mechanism that accelerates the global repair of various types of DNA modifications.
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Affiliation(s)
- Claudia Flohr
- Institute of Pharmacy, University of Mainz, 55099 Mainz, Germany
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34
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Beard BC, Wilson SH, Smerdon MJ. Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes. Proc Natl Acad Sci U S A 2003; 100:7465-70. [PMID: 12799467 PMCID: PMC164609 DOI: 10.1073/pnas.1330328100] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2003] [Indexed: 11/18/2022] Open
Abstract
The majority of DNA in eukaryotic cells exists in the highly condensed structural hierarchy of chromatin, which presents a challenge to DNA repair enzymes in that recognition, incision, and restoration of the original sequence at most sites must take place within these structural constraints. To test base excision repair (BER) activities on chromatin substrates, an in vitro system was developed that uses human uracil DNA glycosylase (UDG), apyrimidinic/apurinic endonuclease (APE), and DNA polymerase beta (pol beta) on homogeneously damaged, rotationally positioned DNA in nucleosomes. We find that UDG and APE carry out their combined catalytic activities with reduced efficiency on nucleosome substrates ( approximately 10% of that on naked DNA). Furthermore, these enzymes distinguish between two different rotational settings of the lesion on the histone surface, showing a 2- to 3-fold difference in activity between uracil facing "toward" and "away from" the histones. However, UDG and APE will digest such substrates to completion in a concentration-dependent manner. Conversely, the synthesis activity of pol beta is inhibited completely by nucleosome substrates and is independent of enzyme concentration. These results suggest that the first two steps of BER, UDG and APE, may occur "unassisted" in chromatin, whereas downstream factors in this pathway (i.e., pol beta) may require nucleosome remodeling for efficient DNA BER in at least some regions of chromatin in eukaryotic cells.
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Affiliation(s)
- Brian C Beard
- Department of Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA
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35
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Benecke A. Genomic Plasticity and Information Processing by Transcription Coregulators. ACTA ACUST UNITED AC 2003. [DOI: 10.1159/000070463] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Birger Y, West KL, Postnikov YV, Lim JH, Furusawa T, Wagner JP, Laufer CS, Kraemer KH, Bustin M. Chromosomal protein HMGN1 enhances the rate of DNA repair in chromatin. EMBO J 2003; 22:1665-75. [PMID: 12660172 PMCID: PMC152887 DOI: 10.1093/emboj/cdg142] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We report that HMGN1, a nucleosome binding protein that destabilizes the higher-order chromatin structure, modulates the repair rate of ultraviolet light (UV)-induced DNA lesions in chromatin. Hmgn1(-/-) mouse embryonic fibroblasts (MEFs) are hypersensitive to UV, and the removal rate of photoproducts from the chromatin of Hmgn1(-/-) MEFs is decreased as compared with the chromatin of Hmgn1(+/+) MEFs; yet, host cell reactivation assays and DNA array analysis indicate that the nucleotide excision repair (NER) pathway in the Hmgn1(-/-) MEFs remains intact. The UV hypersensitivity of Hmgn1(-/-) MEFs could be rescued by transfection with plasmids expressing wild-type HMGN1 protein, but not with plasmids expressing HMGN1 mutants that do not bind to nucleosomes or do not unfold chromatin. Transcriptionally active genes, the main target of the NER pathways in mice, contain HMGN1 protein, and loss of HMGN1 protein reduces the accessibility of transcribed genes to nucleases. By reducing the compaction of the higher-order chromatin structure, HMGN1 facilitates access to UV-damaged DNA sites and enhances the rate of DNA repair in chromatin.
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Affiliation(s)
- Yehudit Birger
- Protein Section, LM, Basic Research Laboratory, CCR, NCI, NIH, Bethesda, MD 20892, USA
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37
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Huggins CF, Chafin DR, Aoyagi S, Henricksen LA, Bambara RA, Hayes JJ. Flap endonuclease 1 efficiently cleaves base excision repair and DNA replication intermediates assembled into nucleosomes. Mol Cell 2002; 10:1201-11. [PMID: 12453426 DOI: 10.1016/s1097-2765(02)00736-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Flap Endonuclease 1 (FEN1) plays important roles both in DNA replication and in base excision repair (BER). However, in both processes FEN1 substrates are likely to be assembled into chromatin. In order to examine how FEN1 is able to work within chromatin, we prepared model nucleosome substrates containing FEN1-cleavable DNA flaps. We find that human FEN1 binds and cleaves such substrates with efficiencies similar to that displayed with naked DNA. Moreover, we demonstrate that both FEN1 and human DNA ligase I can operate successively on DNA within the same nucleosome. These results suggest that some BER steps may not require nucleosome remodeling in vivo and that FEN 1 activity during Okazaki fragment processing can occur on nucleosomal substrates.
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Affiliation(s)
- Christine F Huggins
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
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