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Apostolou Z, Chatzinikolaou G, Stratigi K, Garinis GA. Nucleotide Excision Repair and Transcription-Associated Genome Instability. Bioessays 2019; 41:e1800201. [PMID: 30919497 DOI: 10.1002/bies.201800201] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/10/2018] [Indexed: 12/12/2022]
Abstract
Transcription is a potential threat to genome integrity, and transcription-associated DNA damage must be repaired for proper messenger RNA (mRNA) synthesis and for cells to transmit their genome intact into progeny. For a wide range of structurally diverse DNA lesions, cells employ the highly conserved nucleotide excision repair (NER) pathway to restore their genome back to its native form. Recent evidence suggests that NER factors function, in addition to the canonical DNA repair mechanism, in processes that facilitate mRNA synthesis or shape the 3D chromatin architecture. Here, these findings are critically discussed and a working model that explains the puzzling clinical heterogeneity of NER syndromes highlighting the relevance of physiological, transcription-associated DNA damage to mammalian development and disease is proposed.
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Affiliation(s)
- Zivkos Apostolou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece.,Department of Biology, University of Crete, Vassilika Vouton, Heraklion GR71409, Crete, Greece
| | - Georgia Chatzinikolaou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece.,Department of Biology, University of Crete, Vassilika Vouton, Heraklion GR71409, Crete, Greece
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Boetefuer EL, Lake RJ, Fan HY. Mechanistic insights into the regulation of transcription and transcription-coupled DNA repair by Cockayne syndrome protein B. Nucleic Acids Res 2019; 46:7471-7479. [PMID: 30032309 PMCID: PMC6125617 DOI: 10.1093/nar/gky660] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/10/2018] [Indexed: 12/24/2022] Open
Abstract
Cockayne syndrome protein B (CSB) is a member of the SNF2/SWI2 ATPase family and is essential for transcription-coupled nucleotide excision DNA repair (TC-NER). CSB also plays critical roles in transcription regulation. CSB can hydrolyze ATP in a DNA-dependent manner, alter protein-DNA contacts and anneal DNA strands. How the different biochemical activities of CSB are utilized in these cellular processes have only begun to become clear in recent years. Mutations in the gene encoding CSB account for majority of the Cockayne syndrome cases, which result in extreme sun sensitivity, premature aging features and/or abnormalities in neurology and development. Here, we summarize and integrate recent biochemical, structural, single-molecule and somatic cell genetic studies that have advanced our understanding of CSB. First, we review studies on the mechanisms that regulate the different biochemical activities of CSB. Next, we summarize how CSB is targeted to regulate transcription under different growth conditions. We then discuss recent advances in our understanding of how CSB regulates transcription mechanistically. Lastly, we summarize the various roles that CSB plays in the different steps of TC-NER, integrating the results of different studies and proposing a model as to how CSB facilitates TC-NER.
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Affiliation(s)
- Erica L Boetefuer
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert J Lake
- Department of Internal Medicine, Division of Molecular Medicine, Program in Cancer Genetics, Epigenetics and Genomics, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - Hua-Ying Fan
- Department of Internal Medicine, Division of Molecular Medicine, Program in Cancer Genetics, Epigenetics and Genomics, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
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3
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Diderich KEM, Nicolaije C, Priemel M, Waarsing JH, Day JS, Brandt RMC, Schilling AF, Botter SM, Weinans H, van der Horst GTJ, Hoeijmakers JHJ, van Leeuwen JPTM. Bone fragility and decline in stem cells in prematurely aging DNA repair deficient trichothiodystrophy mice. AGE (DORDRECHT, NETHERLANDS) 2012; 34:845-861. [PMID: 21814739 PMCID: PMC3682057 DOI: 10.1007/s11357-011-9291-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 06/14/2011] [Indexed: 05/31/2023]
Abstract
Trichothiodystrophy (TTD) is a rare, autosomal recessive nucleotide excision repair (NER) disorder caused by mutations in components of the dual functional NER/basal transcription factor TFIIH. TTD mice, carrying a patient-based point mutation in the Xpd gene, strikingly resemble many features of the human syndrome and exhibit signs of premature aging. To examine to which extent TTD mice resemble the normal process of aging, we thoroughly investigated the bone phenotype. Here, we show that female TTD mice exhibit accelerated bone aging from 39 weeks onwards as well as lack of periosteal apposition leading to reduced bone strength. Before 39 weeks have passed, bones of wild-type and TTD mice are identical excluding a developmental defect. Albeit that bone formation is decreased, osteoblasts in TTD mice retain bone-forming capacity as in vivo PTH treatment leads to increased cortical thickness. In vitro bone marrow cell cultures showed that TTD osteoprogenitors retain the capacity to differentiate into osteoblasts. However, after 13 weeks of age TTD females show decreased bone nodule formation. No increase in bone resorption or the number of osteoclasts was detected. In conclusion, TTD mice show premature bone aging, which is preceded by a decrease in mesenchymal stem cells/osteoprogenitors and a change in systemic factors, identifying DNA damage and repair as key determinants for bone fragility by influencing osteogenesis and bone metabolism.
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Affiliation(s)
- Karin E. M. Diderich
- MGC Department of Cell Biology and Genetics, Center for Biomedical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Claudia Nicolaije
- Department of Internal Medicine, Erasmus MC, Room Ee585, P.O Box 2040, CA Rotterdam, The Netherlands
| | - Matthias Priemel
- Center of Biomechanics and Skeletal Biology, Department of Trauma Surgery, University Medical Center Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Jan H. Waarsing
- Department of Orthopaedics, Erasmus MC, 3000 DR Rotterdam, The Netherlands
| | - Judd S. Day
- Department of Orthopaedics, Erasmus MC, 3000 DR Rotterdam, The Netherlands
| | - Renata M. C. Brandt
- MGC Department of Cell Biology and Genetics, Center for Biomedical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Arndt F. Schilling
- Center of Biomechanics and Skeletal Biology, Department of Trauma Surgery, University Medical Center Hamburg Eppendorf, 20246 Hamburg, Germany
- Biomechanics Section, Hamburg University of Technology, 21073 Hamburg, Germany
| | - Sander M. Botter
- MGC Department of Cell Biology and Genetics, Center for Biomedical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, Room Ee585, P.O Box 2040, CA Rotterdam, The Netherlands
| | - Harrie Weinans
- Department of Orthopaedics, Erasmus MC, 3000 DR Rotterdam, The Netherlands
| | | | - Jan H. J. Hoeijmakers
- MGC Department of Cell Biology and Genetics, Center for Biomedical Genetics, Erasmus MC, Rotterdam, The Netherlands
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4
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Kamileri I, Karakasilioti I, Garinis GA. Nucleotide excision repair: new tricks with old bricks. Trends Genet 2012; 28:566-73. [PMID: 22824526 DOI: 10.1016/j.tig.2012.06.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/05/2012] [Accepted: 06/19/2012] [Indexed: 12/22/2022]
Abstract
Nucleotide excision repair (NER) is a major DNA repair pathway that ensures that the genome remains functionally intact and is faithfully transmitted to progeny. However, defects in NER lead, in addition to cancer and aging, to developmental abnormalities whose clinical heterogeneity and varying severity cannot be fully explained by the DNA repair deficiencies. Recent work has revealed that proteins in NER play distinct roles, including some that go well beyond DNA repair. NER factors are components of protein complexes known to be involved in nucleosome remodeling, histone ubiquitination, and transcriptional activation of genes involved in nuclear receptor signaling, stem cell reprogramming, and postnatal mammalian growth. Together, these findings add new pieces to the puzzle for understanding NER and the relevance of NER defects in development and disease.
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Affiliation(s)
- Irene Kamileri
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
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5
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Episkopou H, Kyrtopoulos SA, Sfikakis PP, Dimopoulos MA, Souliotis VL. The repair of melphalan-induced DNA adducts in the transcribed strand of active genes is subject to a strong polarity effect. Mutat Res 2011; 714:78-87. [PMID: 21762707 DOI: 10.1016/j.mrfmmm.2011.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 06/10/2011] [Accepted: 06/28/2011] [Indexed: 11/18/2022]
Abstract
To investigate the mechanisms of the therapeutic action and drug resistance to the nitrogen mustard melphalan, melphalan-induced DNA damage repair and chromatin structure were examined along the p53, N-ras and d-globin gene loci in cells carrying different repair activities. In nucleotide excision repair-deficient XP-A cells, similar levels of adducts were found in all fragments examined, indicating uniform distribution of DNA damage. In both, repair-proficient CS-B and XP-C cells, faster repair was observed in regions inside the transcribed N-ras and p53 genes, compared to regions on both sides outside of the genes, while no such difference was observed for the inactive d-globin gene. Moreover, very fast adduct repair on the transcribed strand of the active genes was seen immediately downstream of the transcription start site, together with a steeply decreasing gradient of repair efficiency along the gene towards the 3'-end. In all cells analyzed, the above variation in DNA repair efficiency was paralleled exactly by the variation in the degree of local chromatin condensation, more relaxed chromatin being associated with faster repair. Similar results were obtained using peripheral blood mononuclear cells from healthy volunteers, suggesting that the existence of a repair gradient along transcribed genes may be a universal phenomenon. In conclusion, these findings demonstrate that the repair of melphalan adducts in the transcribed strand of active genes is subject to a strong polarity effect arising from variations in the chromatin structure.
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Affiliation(s)
- Hara Episkopou
- Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, Athens, Greece
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6
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Karanam NK, Grabarczyk P, Hammer E, Scharf C, Venz S, Gesell-Salazar M, Barthlen W, Przybylski GK, Schmidt CA, Völker U. Proteome analysis reveals new mechanisms of Bcl11b-loss driven apoptosis. J Proteome Res 2010; 9:3799-811. [PMID: 20513151 DOI: 10.1021/pr901096u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Bcl11b protein was shown to be important for a variety of functions such as T cell differentiation, normal development of central nervous system, and DNA damage response. Malignant T cells undergo apoptotic cell death upon BCL11B down-regulation, however, the detailed mechanism of cell death is not fully understood yet. Here we employed two-dimensional difference in-gel electrophoresis (2D-DIGE), mass spectrometry and cell biological experiments to investigate the role of Bcl11b in malignant T cell lines such as Jurkat and huT78. We provide evidence for the involvement of the mitochondrial apoptotic pathway and observed cleavage and fragments of known caspase targets such as myosin, spectrin, and vimentin. Our findings suggest an involvement of ERM proteins, which were up-regulated and phosphorylated upon Bcl11b down-regulation. Moreover, the levels of several proteins implicated in cell cycle entry, including DUT-N, CDK6, MCM4, MCM6, and MAT1 were elevated. Thus, the proteome data presented here confirm previous findings concerning the consequences of BCL11B knock-down and provide new insight into the mechanisms of cell death and cell cycle disturbances induced by Bcl11b depletion.
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Affiliation(s)
- Narasimha Kumar Karanam
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt-Universität Greifswald, Germany
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7
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Sampath D, Plunkett W. The role of DNA repair in chronic lymphocytic leukemia pathogenesis and chemotherapy resistance. Curr Oncol Rep 2007; 9:361-7. [PMID: 17706164 DOI: 10.1007/s11912-007-0048-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Front-line therapy for chronic lymphocytic leukemia (CLL) with alkylating agents is associated with low rates of complete remission and no improvement in overall survival. The ability of CLL cells to efficiently repair alkylator-induced damage to DNA might explain this lack of response. Novel strategies that inhibit DNA repair, such as combinations of alkylating agents, purine nucleoside analogues, and immunotherapy, have produced durable clinical and molecular remission in both untreated and relapsed CLL. This review evaluates the contribution of DNA repair processes in the development of resistance to chemotherapy and the impact of therapies that exploit the DNA repair capacity of CLL cells to therapeutic advantage.
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Affiliation(s)
- Deepa Sampath
- Department of Experimental Therapeutics, Unit 71, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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8
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Scicchitano DA. Transcription past DNA adducts derived from polycyclic aromatic hydrocarbons. Mutat Res 2005; 577:146-54. [PMID: 15922365 DOI: 10.1016/j.mrfmmm.2005.03.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Revised: 03/22/2005] [Accepted: 03/22/2005] [Indexed: 12/20/2022]
Abstract
The ability of a DNA lesion to block transcription is a function of many variables: (1) the ability of the RNA polymerase active site to accommodate the damaged base; (2) the size and shape of the adduct, which includes the specific modified base; (3) the stereochemistry of the adduct; (4) the base incorporated into the growing transcript; (5) and the local DNA sequence. Each of these parameters, either alone or in combination, can influence how a particular lesion in the genome will affect transcription elongation, resulting in potential clearance of the lesion via transcription-coupled DNA repair or in the formation of truncated or full-length transcripts that might encode defective proteins.
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Affiliation(s)
- David A Scicchitano
- Department of Biology, 1009 Silver Center, 100 Washington Square East, New York University, New York, NY 10003, USA.
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9
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Wu L, Chen P, Shum CH, Chen C, Barsky LW, Weinberg KI, Jong A, Triche TJ. MAT1-modulated CAK activity regulates cell cycle G(1) exit. Mol Cell Biol 2001; 21:260-70. [PMID: 11113200 PMCID: PMC88799 DOI: 10.1128/mcb.21.1.260-270.2001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The cyclin-dependent kinase (CDK)-activating kinase (CAK) is involved in cell cycle control, transcription, and DNA repair (E. A. Nigg, Curr. Opin. Cell. Biol. 8:312-317, 1996). However, the mechanisms of how CAK is integrated into these signaling pathways remain unknown. We previously demonstrated that abrogation of MAT1 (ménage à trois 1), an assembly factor and targeting subunit of CAK, induces G(1) arrest (L. Wu, P. Chen, J. J. Hwang, L. W. Barsky, K. I. Weinberg, A. Jong, and V. A. Starnes, J. Biol. Chem. 274:5564-5572, 1999). This result led us to investigate how deregulation of CAK by MAT1 abrogation affects the cell cycle G(1) exit, a process that is regulated most closely by phosphorylation of retinoblastoma tumor suppressor protein (pRb). Using mammalian cellular models that undergo G(1) arrest evoked by antisense MAT1 abrogation, we found that deregulation of CAK inhibits pRb phosphorylation and cyclin E expression, CAK phosphorylation of pRb is MAT1 dose dependent but cyclin D1/CDK4 independent, and MAT1 interacts with pRb. These results suggest that CAK is involved in the regulation of cell cycle G(1) exit while MAT1-modulated CAK formation and CAK phosphorylation of pRb may determine the cell cycle specificity of CAK in G(1) progression.
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Affiliation(s)
- L Wu
- Department of Pathology, Childrens Hospital Los Angeles Research Institute, Los Angeles, California 90027, USA.
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10
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Vessey CJ, Norbury CJ, Hickson ID. Genetic disorders associated with cancer predisposition and genomic instability. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1999; 63:189-221. [PMID: 10506832 DOI: 10.1016/s0079-6603(08)60723-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Genomic instability in its broadest sense is a feature of virtually all neoplastic cells. In addition to the mutations and/or gene amplifications that appear to be a prerequisite for the acquisition of a neoplastic phenotype, human cancers exhibit other "markers" of genomic instability--in particular, a high degree of aneuploidy. Indeed, many studies have shown that aneuploidy is an almost invariant feature of cancer cells, and it has been argued by some that the emergence of aneuploid cells is a necessary step during tumorigenesis. The functional link between genomic instability and cancer is strengthened by the existence of several "genetic instability" disorders of humans that are associated with a moderate to severe increase in the incidence of cancers. These disorders include ataxia telangiectasia, Bloom's syndrome, Fanconi anemia, xeroderma pigmentosum, and Nijmegen breakage syndrome, all of which are very rare and are inherited in a recessive manner. Analysis of the cells from such cancer-prone individuals is clearly a potentially fruitful approach for delineating the genetic basis for instability in the genome. It is assumed that by identifying the underlying cause of genetic instability in these disorders, one can derive valuable information not only about the basis of particular genetic diseases, but also about the underlying causes of genomic instability in sporadic cancers in the general population. In this article, we review the clinical and cellular properties of genetic instability disorders associated with cancer predisposition. In particular, we focus on the rapid advances made in our understanding of these disorders that have derived from the cloning of the genes mutated in each case. Because in many instances the affected genes have analogs in lower eukaryotic species, we shall discuss how studies in yeasts in particular have proved valuable in our understanding of human diseases and predisposition to cancer.
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Affiliation(s)
- C J Vessey
- Imperial Cancer Research Fund Laboratories, University of Oxford, John Radcliffe Hospital, United Kingdom
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11
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Wu L, Chen P, Hwang JJ, Barsky LW, Weinberg KI, Jong A, Starnes VA. RNA antisense abrogation of MAT1 induces G1 phase arrest and triggers apoptosis in aortic smooth muscle cells. J Biol Chem 1999; 274:5564-72. [PMID: 10026172 DOI: 10.1074/jbc.274.9.5564] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human MAT1 gene (ménage à trois 1) is an assembly factor and a targeting subunit of cyclin-dependent kinase (CDK)-activating kinase. The novel mechanisms by which MAT1 forms an active CDK-activating kinase and determines substrate specificity of CDK7-cyclin H are involved in the cell cycle, DNA repair, and transcription. Hyperplasia of vascular smooth muscle cells (SMC) is a fundamental pathologic feature of luminal narrowing in vascular occlusive diseases, and nothing is yet known regarding the cell cycle phase specificity of the MAT1 gene in its involvement in SMC proliferation. To investigate such novel regulatory pathways, MAT1 expression was abrogated by retrovirus-mediated gene transfer of antisense MAT1 RNA in cultured rat aortic SMCs. We show that abrogation of MAT1 expression retards SMC proliferation and inhibits cell activation from a nonproliferative state. Furthermore, we have demonstrated that these effects are due to G1 phase arrest and apoptotic cell death. Our studies indicate a link between cell cycle control and apoptosis and reveal a potential mechanism for coupling the regulation of MAT1 with G1 exit and prevention of apoptosis.
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Affiliation(s)
- L Wu
- Division of Cardiothoracic Surgery, Childrens Hospital Los Angeles Research Institute, University of Southern California School of Medicine, Los Angeles, California 90027, USA.
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12
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Affiliation(s)
- L H Mullenders
- Department of Radiation Genetics and Chemical Mutagenesis-MGC, Leiden University Medical Center, Netherlands.
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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. [PMID: 9729332 DOI: 10.1016/s0027-5107(98)00105-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
New findings concerning the molecular mechanisms of nucleotide excision repair (NER) are discussed.
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Affiliation(s)
- P Karmarkar
- MGC-Department of Radiation Genetics and Chemical Mutagenesis, Leiden University Medical Centre, P.O. Box 9503, 2300 RA Leiden, Netherlands
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14
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Vrieling H, van Zeeland AA, Mullenders LH. Transcription coupled repair and its impact on mutagenesis. Mutat Res 1998; 400:135-42. [PMID: 9685614 DOI: 10.1016/s0027-5107(98)00064-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- H Vrieling
- Department of Radiation Genetics and Chemical Mutagenesis-MGC, Leiden University Medical Centre, PO Box 9503, 2300 RA Leiden, Netherlands
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15
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Aboussekhra A, Thoma F. Nucleotide excision repair and photolyase preferentially repair the nontranscribed strand of RNA polymerase III-transcribed genes in Saccharomyces cerevisiae. Genes Dev 1998; 12:411-21. [PMID: 9450934 PMCID: PMC316483 DOI: 10.1101/gad.12.3.411] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A high-resolution primer extension technique was used to study the relationships between repair, transcription, and mutagenesis in RNA polymerase III transcribed genes in Saccharomyces cerevisiae. The in vivo repair of UV-induced DNA damage by nucleotide excision repair (NER) and by photoreactivation is shown to be preferential for the nontranscribed strand (NTS) of the SNR6 gene. This is in contrast to RNA polymerase II genes in which the NER is preferential for the transcribed strand (TS). The repair-strand bias observed in SNR6 was abolished by inactivation of transcription in a snr6Delta2 mutant, showing a contribution of RNA polymerase III transcription in this phenomenon. The same strand bias for NER (slow in TS, fast in NTS) was discovered in the SUP4 gene, but only outside of the intragenic promoter element (box A). Unexpectedly, the repair in the transcribed box A was similar on both strands. The strand specificity as well as the repair heterogeneity determined in the transcribed strand of the SUP4 gene, correlate well with the previously reported site- and strand-specific mutagenesis in this gene. These findings present a novel view regarding the relationships between DNA repair, mutagenesis, and transcription.
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Affiliation(s)
- A Aboussekhra
- Institut für Zellbiologie, Swiss Federal Institute of Technology (ETH)-Zürich, Hönggerberg, CH-8093 Zürich, Switzerland
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16
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Dianov GL, Houle JF, Iyer N, Bohr VA, Friedberg EC. Reduced RNA polymerase II transcription in extracts of cockayne syndrome and xeroderma pigmentosum/Cockayne syndrome cells. Nucleic Acids Res 1997; 25:3636-42. [PMID: 9278484 PMCID: PMC146943 DOI: 10.1093/nar/25.18.3636] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The hereditary disease Cockayne syndrome (CS) is a complex clinical syndrome characterized by arrested post-natal growth as well as neurological and other defects. The CSA and CSB genes are implicated in this disease. The clinical features of CS can also accompany the excision repair-defective hereditary disorder xeroderma pigmentosum (XP) from genetic complementation groups B, D or G. The XPB and XPD proteins are subunits of RNA polymerase II (RNAP II) transcription factor IIH (TFIIH). We show here that extracts of CS-A and CS-B cells, as well as those from XP-B/CS cells, support reduced levels of RNAP II transcription in vitro and that this feature is dependent on the state or quality of the template.
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Affiliation(s)
- G L Dianov
- Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
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17
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Kim N, Kage K, Matsuda F, Lefranc MP, Storb U. B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes. J Exp Med 1997; 186:413-9. [PMID: 9236193 PMCID: PMC2198998 DOI: 10.1084/jem.186.3.413] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/1997] [Revised: 05/19/1997] [Indexed: 02/04/2023] Open
Abstract
Recent experiments have strongly suggested that the process of somatic mutation is linked to transcription initiation. It was postulated that a mutator factor loads onto the RNA polymerase and, during elongation, causes transcriptional arrest that activates DNA repair, thus occasionally causing errors in the DNA sequence. We report the analysis of the role of one of the known DNA repair systems, nucleotide excision repair (NER), in somatic mutation. Epstein-Barrvirus-transformed B cells from patients with defects in NER (XP-B, XP-D, XP-V, and CS-A) were studied. Their heavy and light chain genes show a high frequency of point mutations in the variable (V), but not in the constant (C) regions. This suggests that these B cells can undergo somatic hypermutation despite significant defects in NER. Thus, it is doubtful that NER is an essential part of the mechanism of somatic hypermutation of Ig genes. As an aside, NER seems also not involved in Ig gene switch recombination.
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Affiliation(s)
- N Kim
- Department of Biochemistry, University of Chicago, Illinois 60637, USA
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18
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Abstract
BACKGROUND Xeroderma pigmentosum is an extremely rare, autosomal recessive disease characterized by a more than 1000-fold increase in nonmelanoma skin cancer. Individuals with this disease can be divided into eight complementation groups: A-G and V for variant. Each one represents a different genetic defect in DNA repair. OBJECTIVE To review the molecular basis of xeroderma pigmentosum. RESULTS Deficiencies in various gene products in the nucleotide excision repair pathway cause xeroderma pigmentosum in complementation groups A-G. The molecular basis of the variant group remains to be elucidated. CONCLUSIONS Research into the genetic defects underlying xeroderma pigmentosum have led to an increased understanding of nucleotide excision repair.
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Affiliation(s)
- N E Copeland
- Department of Dermatology, Indiana University, Indianapolis, USA
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19
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Bregman DB, Halaban R, van Gool AJ, Henning KA, Friedberg EC, Warren SL. UV-induced ubiquitination of RNA polymerase II: a novel modification deficient in Cockayne syndrome cells. Proc Natl Acad Sci U S A 1996; 93:11586-90. [PMID: 8876179 PMCID: PMC38101 DOI: 10.1073/pnas.93.21.11586] [Citation(s) in RCA: 253] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Damage to actively transcribed DNA is preferentially repaired by the transcription-coupled repair (TCR) system. TCR requires RNA polymerase II (Pol II), but the mechanism by which repair enzymes preferentially recognize and repair DNA lesions on Pol II-transcribed genes is incompletely understood. Herein we demonstrate that a fraction of the large subunit of Pol II (Pol II LS) is ubiquitinated after exposing cells to UV-radiation or cisplatin but not several other DNA damaging agents. This novel covalent modification of Pol II LS occurs within 15 min of exposing cells to UV-radiation and persists for about 8-12 hr. Ubiquitinated Pol II LS is also phosphorylated on the C-terminal domain. UV-induced ubiquitination of Pol II LS is deficient in fibroblasts from individuals with two forms of Cockayne syndrome (CS-A and CS-B), a rare disorder in which TCR is disrupted. UV-induced ubiquitination of Pol II LS can be restored by introducing cDNA constructs encoding the CSA or CSB genes, respectively, into CS-A or CS-B fibroblasts. These results suggest that ubiquitination of Pol II LS plays a role in the recognition and/or repair of damage to actively transcribed genes. Alternatively, these findings may reflect a role played by the CSA and CSB gene products in transcription.
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Affiliation(s)
- D B Bregman
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
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20
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Preston RJ. Interindividual variations in susceptibility and sensitivity: linking risk assessment and risk management. Toxicology 1996; 111:331-41. [PMID: 8711747 DOI: 10.1016/0300-483x(96)03386-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In the past few years, our knowledge of mammalian genomes has increased enormously. Our understanding of the molecular basis of the normal cellular processes of DNA replication and repair and cell cycle control, together with how their fidelity malfunctions as part of tumor development, has increased in parallel. This has led to a clearer appreciation that there are subpopulations that have been generically described as being genetically or otherwise susceptible to the induction of cancer or birth defects. The term susceptibility is a default option, since there clearly will be a very broad range of sensitivities among the so-called susceptible populations, dependent upon the specific underlying mechanism. This could lead to the conduct of risk assessments for each specific situation, involving both genotypes of individuals and agents of concern. This would ideally take into account the effects on response of various modifying factors, genetic and other. One advantage to be gained from this approach is the ability to determine if a particular susceptibility places subpopulations at extreme risk as compared to the overall normal distribution of risk in the population, or whether such a susceptible population presents a slight extension of the upper bound of the risk distribution or lies within the normal distribution. In addition, the specific mechanism of the susceptibility as related to exposure scenarios and the magnitude and demographics of the susceptible populations need to be taken into account. Thus, the management of risk has to be linked to the specific risk assessment. For many of the so-called susceptible populations an uncertainty factor of less than 10, even including 1, would be predicted to bring the risk within the normal distribution. It is hoped that as more mechanistic information on susceptibility becomes available and a specific risk can be defined, the practice of risk management will be considerably improved.
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Affiliation(s)
- R J Preston
- Chemical Industry Institute of Toxicology, Research Triangle Park, NC 27709,
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21
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Affiliation(s)
- M Hall
- Cancer Research Campaign Mammalian Cell DNA Repair Group, Department of Zoology, Cambridge, U.K
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22
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Nassal M, Rieger A. A bulged region of the hepatitis B virus RNA encapsidation signal contains the replication origin for discontinuous first-strand DNA synthesis. J Virol 1996; 70:2764-73. [PMID: 8627750 PMCID: PMC190133 DOI: 10.1128/jvi.70.5.2764-2773.1996] [Citation(s) in RCA: 124] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Human hepatitis B virus (HBV) is a small DNA virus that replicates inside the viral nucleocapsid by reverse transcription of an RNA intermediate. Encapsidation of this RNA pregenome is mediated by the interaction of the viral replication enzyme P with the structured 5'-proximal RNA element epsilon; replication was thought to start in the 3'-proximal direct repeat DR1*. However, recent data obtained with the duck hepatitis B virus indicated a novel, discontinuous mechanism of negative-strand DNA synthesis. Here we demonstrate, using DNA transfection of complete HBV genomes, that the 3'-half of a 6-nucleotide bulge in HBV epsilon whose primary sequence is not important for encapsidation serves as template for a short DNA primer that is subsequently transferred to DR1*. Apparently, P protein copies any template sequence that does not interfere with epsilon structure; however, altered primary sequences can induce polymerase stuttering, resulting in extended primers containing more than one equivalent of the template sequence. The importance of the bulged structure is emphasized by the dependence of primer length on bulge size. Transfer specificity is in part controlled by sequence complementarity. The strategy of using the 5' encapsidation signal as the origin of replication for discontinuous negative-strand DNA synthesis, common to mammalian and avian hepadnaviruses, suggests the evolutionary origin of hepatitis B viruses to lie between that of modern retroviruses and primitive retroelements like the Mauriceville retroplasmid.
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Affiliation(s)
- M Nassal
- Zentrum für Molekulare Biologie, Universität Heidelberg, Germany
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23
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Roy R, Adamczewski JP, Seroz T, Vermeulen W, Tassan JP, Schaeffer L, Nigg EA, Hoeijmakers JH, Egly JM. The MO15 cell cycle kinase is associated with the TFIIH transcription-DNA repair factor. Cell 1994; 79:1093-101. [PMID: 8001135 DOI: 10.1016/0092-8674(94)90039-6] [Citation(s) in RCA: 360] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A protein kinase activity that phosphorylates the C-terminal domain (CTD) of RNA polymerase II and is associated with the basal transcription-repair factor TFIIH (also called BTF2) resides with MO15, a cyclin-dependent protein kinase that was first found to be involved in cell cycle regulation. Using in vivo and in vitro repair assays, we show that MO15 is important for nucleotide excision repair, most likely through its association with TFIIH, thus providing an unexpected link among three important cellular mechanisms.
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Affiliation(s)
- R Roy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Illkirch, France
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