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Abbasi S, Schild-Poulter C. Mapping the Ku Interactome Using Proximity-Dependent Biotin Identification in Human Cells. J Proteome Res 2019; 18:1064-1077. [PMID: 30585729 DOI: 10.1021/acs.jproteome.8b00771] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Ku heterodimer, composed of Ku70 and Ku80, is best characterized for its role in repairing double-stranded DNA breaks but is also known to participate in other regulatory processes. Despite our understanding of Ku protein interplay during DNA repair, the extent of Ku's protein interactions in other processes has never been fully determined. Using proximity-dependent biotin identification (BioID) and affinity purification coupled to mass spectrometry (AP-MS) with wild-type Ku70, we identified candidate proteins that interact with the Ku heterodimer in HEK293 cells, in the absence of exogenously induced DNA damage. BioID analysis identified approximately 250 nuclear proteins, appearing in at least two replicates, including known Ku-interacting factors such as MRE11A, WRN, and NCOA6. Meanwhile, AP-MS analysis identified approximately 50 candidate proteins. Of the novel protein interactors identified, many were involved in functions already suspected to involve Ku such as transcriptional regulation, DNA replication, and DNA repair, while several others suggest that Ku may be involved in additional functions such as RNA metabolism, chromatin-remodeling, and microtubule dynamics. Using a combination of BioID and AP-MS, this is the first report that comprehensively characterizes the Ku protein interaction landscape, revealing new cellular processes and protein complexes involving the Ku complex.
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Affiliation(s)
- Sanna Abbasi
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry , University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Caroline Schild-Poulter
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry , University of Western Ontario , London , Ontario N6A 5B7 , Canada
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2
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Vitelli V, Galbiati A, Iannelli F, Pessina F, Sharma S, d'Adda di Fagagna F. Recent Advancements in DNA Damage-Transcription Crosstalk and High-Resolution Mapping of DNA Breaks. Annu Rev Genomics Hum Genet 2017; 18:87-113. [PMID: 28859573 DOI: 10.1146/annurev-genom-091416-035314] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Until recently, DNA damage arising from physiological DNA metabolism was considered a detrimental by-product for cells. However, an increasing amount of evidence has shown that DNA damage could have a positive role in transcription activation. In particular, DNA damage has been detected in transcriptional elements following different stimuli. These physiological DNA breaks are thought to be instrumental for the correct expression of genomic loci through different mechanisms. In this regard, although a plethora of methods are available to precisely map transcribed regions and transcription start sites, commonly used techniques for mapping DNA breaks lack sufficient resolution and sensitivity to draw a robust correlation between DNA damage generation and transcription. Recently, however, several methods have been developed to map DNA damage at single-nucleotide resolution, thus providing a new set of tools to correlate DNA damage and transcription. Here, we review how DNA damage can positively regulate transcription initiation, the current techniques for mapping DNA breaks at high resolution, and how these techniques can benefit future studies of DNA damage and transcription.
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Affiliation(s)
- Valerio Vitelli
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | | | - Fabio Iannelli
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | - Fabio Pessina
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | - Sheetal Sharma
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | - Fabrizio d'Adda di Fagagna
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy; .,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia 27100, Italy
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Grundy GJ, Moulding HA, Caldecott KW, Rulten SL. One ring to bring them all--the role of Ku in mammalian non-homologous end joining. DNA Repair (Amst) 2014; 17:30-8. [PMID: 24680220 DOI: 10.1016/j.dnarep.2014.02.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 02/25/2014] [Indexed: 12/26/2022]
Abstract
The repair of DNA double strand breaks is essential for cell survival and several conserved pathways have evolved to ensure their rapid and efficient repair. The non-homologous end joining pathway is initiated when Ku binds to the DNA break site. Ku is an abundant nuclear heterodimer of Ku70 and Ku80 with a toroidal structure that allows the protein to slide over the broken DNA end and bind with high affinity. Once locked into placed, Ku acts as a tool-belt to recruit multiple interacting proteins, forming one or more non-homologous end joining complexes that act in a regulated manner to ensure efficient repair of DNA ends. Here we review the structure and functions of Ku and the proteins with which it interacts during non-homologous end joining.
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Affiliation(s)
- Gabrielle J Grundy
- Genome Damage and Stability Centre, Science Park Road, Falmer, Brighton BN1 9RQ, UK.
| | - Hayley A Moulding
- School of Biochemistry, Medical Sciences, University Walk, Bristol BS8 1TD, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre, Science Park Road, Falmer, Brighton BN1 9RQ, UK.
| | - Stuart L Rulten
- Genome Damage and Stability Centre, Science Park Road, Falmer, Brighton BN1 9RQ, UK.
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Krietsch J, Caron MC, Gagné JP, Ethier C, Vignard J, Vincent M, Rouleau M, Hendzel MJ, Poirier GG, Masson JY. PARP activation regulates the RNA-binding protein NONO in the DNA damage response to DNA double-strand breaks. Nucleic Acids Res 2012; 40:10287-301. [PMID: 22941645 PMCID: PMC3488241 DOI: 10.1093/nar/gks798] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
After the generation of DNA double-strand breaks (DSBs), poly(ADP-ribose) polymerase-1 (PARP-1) is one of the first proteins to be recruited and activated through its binding to the free DNA ends. Upon activation, PARP-1 uses NAD+ to generate large amounts of poly(ADP-ribose) (PAR), which facilitates the recruitment of DNA repair factors. Here, we identify the RNA-binding protein NONO, a partner protein of SFPQ, as a novel PAR-binding protein. The protein motif being primarily responsible for PAR-binding is the RNA recognition motif 1 (RRM1), which is also crucial for RNA-binding, highlighting a competition between RNA and PAR as they share the same binding site. Strikingly, the in vivo recruitment of NONO to DNA damage sites completely depends on PAR, generated by activated PARP-1. Furthermore, we show that upon PAR-dependent recruitment, NONO stimulates nonhomologous end joining (NHEJ) and represses homologous recombination (HR) in vivo. Our results therefore place NONO after PARP activation in the context of DNA DSB repair pathway decision. Understanding the mechanism of action of proteins that act in the same pathway as PARP-1 is crucial to shed more light onto the effect of interference on PAR-mediated pathways with PARP inhibitors, which have already reached phase III clinical trials but are until date poorly understood.
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Affiliation(s)
- Jana Krietsch
- Cancer Research Unit, Laval University Medical Research Center, CHUQ-CRCHUL, Genome Stability Laboratory, Laval University Cancer Research Center, Hôtel-Dieu de Québec, QC, Canada G1R 2J6
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5
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Yano KI, Morotomi-Yano K, Lee KJ, Chen DJ. Functional significance of the interaction with Ku in DNA double-strand break recognition of XLF. FEBS Lett 2011; 585:841-6. [PMID: 21349273 DOI: 10.1016/j.febslet.2011.02.020] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 01/28/2011] [Accepted: 02/14/2011] [Indexed: 11/25/2022]
Abstract
Ku heterodimer is essential for the repair of DNA double-strand breaks (DSBs) by non-homologous end-joining (NHEJ). Ku recruits XLF, also known as Cernunnos, to DSBs. Here we report domain analyses of Ku-XLF interaction. The heterodimeric domain of Ku was found to be sufficient for the recruitment of XLF to DSBs and for the interaction of Ku with XLF. A small C-terminal deletion of XLF completely abolished recruitment of XLF to DSBs and Ku-XLF interaction. This deletion also led to marked reduction of XLF-XRCC4 interaction although the XRCC4-binding site on the XLF N-terminal domain remained intact. These results demonstrate the significance of Ku-XLF interaction in the molecular assembly of NHEJ factors.
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Affiliation(s)
- Ken-ichi Yano
- Bioelectrics Research Center, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan.
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Sequences in PSF/SFPQ mediate radioresistance and recruitment of PSF/SFPQ-containing complexes to DNA damage sites in human cells. DNA Repair (Amst) 2010; 10:252-9. [PMID: 21144806 DOI: 10.1016/j.dnarep.2010.11.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 11/15/2010] [Accepted: 11/15/2010] [Indexed: 11/23/2022]
Abstract
PSF (gene name SFPQ) is a member of a small family of proteins with dual functions in RNA biogenesis and DNA repair. PSF and PSF-containing complexes stimulate double-strand break repair in cell free systems, most likely via direct interaction with the repair substrate. Prior in vitro studies are, however, insufficient to demonstrate whether PSF contributes to DNA repair in living cells. Here, we investigate the effect of miRNA-mediated PSF knockdown in human (HeLa) cells. We find that PSF is essential for reproductive viability. To circumvent this and investigate the DNA damage sensitivity phenotype, we established a genetic rescue assay based on co-transfection of PSF miRNA and mutant PSF expression constructs. Mutational analysis suggests that sequences required for viability and radioresistance are partially separable, and that the latter requires a unique N-terminal PSF domain. As an independent means to investigate PSF sequences involved in DNA repair, we established an assay based on real-time relocalization of PSF-containing complexes to sites of dense, laser-induced DNA damage in living cells. We show that relocalization is driven by sequences in PSF, rather than its dimerization partner, p54(nrb)/NONO, and that sequences required for relocalization reside in the same N-terminal domain that contributes to radioresistance. Further evidence for the importance of PSF sequences in mediating relocalization is provided by observations that PSF promotes relocalization of a third protein, PSPC1, under conditions where p54(nrb) is limiting. Together, these observations support the model derived from prior biochemical studies that PSF influences repair via direct, local, interaction with the DNA substrate.
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Chen CC, Yang YC, Wang WH, Chen CS, Chang LK. Enhancement of Zta-activated lytic transcription of Epstein-Barr virus by Ku80. J Gen Virol 2010; 92:661-8. [DOI: 10.1099/vir.0.026302-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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How transcription factors can adjust the gene expression floodgates. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2009; 102:16-37. [PMID: 20025898 DOI: 10.1016/j.pbiomolbio.2009.12.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 11/17/2009] [Accepted: 12/07/2009] [Indexed: 12/18/2022]
Abstract
The rate of transcription initiation is the main level of quantitative control of gene expression, primarily responsible for the accumulation of mRNAs in the cell. Many, if not all, molecular actors involved in transcription initiation are known but the mechanisms underlying the frequency of initiations, remain elusive. To make the connection between transcription factors and the frequency of transcription initiation, intricated aspects of this complex activity are classified i) depending on whether or not the DNA-bound transcription factors directly activate the commitment to transcription and ii) on the destructive or non-destructive effect of transcription initiation on the stability of promoter complexes. Two possible sources of synergy allowing the combinatorial specificity of transcription factors action are compared, for binding to DNA and for recruiting transcription machineries. Tentative formulations are proposed to discriminate the different micro-reversible modes of DNA binding cooperativity modulating the specificity and dosage of transcription initiation.
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Nolens G, Pignon JC, Koopmansch B, Elmoualij B, Zorzi W, De Pauw E, Winkler R. Ku proteins interact with activator protein-2 transcription factors and contribute to ERBB2 overexpression in breast cancer cell lines. Breast Cancer Res 2009; 11:R83. [PMID: 19906305 PMCID: PMC2815545 DOI: 10.1186/bcr2450] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2009] [Revised: 10/07/2009] [Accepted: 11/11/2009] [Indexed: 02/01/2023] Open
Abstract
Introduction Activator protein-2 (AP-2) α and AP-2γ transcription factors contribute to ERBB2 gene overexpression in breast cancer. In order to understand the mechanism by which the ERBB2 gene is overexpressed we searched for novel AP-2 interacting factors that contribute to its activity. Methods Ku proteins were identified as AP-2α interacting proteins by glutathione serine transferase (GST)-pull down followed by mass spectrometry. Transfection of the cells with siRNA, expression vectors and reporter vectors as well as chromatin immunoprecipitation (ChIP) assay were used to ascertain the implication of Ku proteins on ERBB2 expression. Results Nuclear proteins from BT-474 cells overexpressing AP-2α and AP-2γ were incubated with GST-AP2 or GST coated beads. Among the proteins retained specifically on GST-AP2 coated beads Ku70 and Ku80 proteins were identified by mass spectrometry. The contribution of Ku proteins to ERBB2 gene expression in BT-474 and SKBR3 cell lines was investigated by downregulating Ku proteins through the use of specific siRNAs. Depletion of Ku proteins led to downregulation of ERBB2 mRNA and protein levels. Furthermore, reduction of Ku80 in HCT116 cell line decreased the AP-2α activity on a reporter vector containing an AP-2 binding site linked to the ERBB2 core promoter, and transfection of Ku80 increased the activity of AP-2α on this promoter. Ku siRNAs also inhibited the activity of this reporter vector in BT-474 and SKBR3 cell lines and the activity of the ERBB2 promoter was further reduced by combining Ku siRNAs with AP-2α and AP-2γ siRNAs. ChIP experiments with chromatin extracted from wild type or AP-2α and AP-2γ or Ku70 siRNA transfected BT-474 cells demonstrated Ku70 recruitment to the ERBB2 proximal promoter in association with AP-2α and AP-2γ. Moreover, Ku70 siRNA like AP-2 siRNAs, greatly reduced PolII recruitment to the ERBB2 proximal promoter. Conclusions Ku proteins in interaction with AP-2 (α and γ) contribute to increased ERBB2 mRNA and protein levels in breast cancer cells.
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Affiliation(s)
- Grégory Nolens
- Laboratory of Molecular Oncology, GIGA Cancer, University of Liège, B34, avenue de l'hopital, Liege, 4000, Belgium.
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10
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Shi L, Qiu D, Zhao G, Corthesy B, Lees-Miller S, Reeves WH, Kao PN. Dynamic binding of Ku80, Ku70 and NF90 to the IL-2 promoter in vivo in activated T-cells. Nucleic Acids Res 2007; 35:2302-10. [PMID: 17389650 PMCID: PMC1874627 DOI: 10.1093/nar/gkm117] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 02/07/2007] [Accepted: 02/08/2007] [Indexed: 01/07/2023] Open
Abstract
IL-2 gene expression in activated T-cells is initiated by chromatin remodeling at the IL-2 proximal promoter and conversion of a transcriptional repressor into a potent transcriptional activator. A purine-box regulator complex was purified from activated Jurkat T-cell nuclei based on sequence-specific DNA binding to the antigen receptor response element (ARRE)/nuclear factor of activated T-cells (NF-AT) target DNA sequence in the proximal IL-2 promoter. ARRE DNA-binding subunits were identified as NF90, NF45 and systemic lupus erythematosis autoantigens, Ku80 and Ku70. Monoclonal antibodies to Ku80, Ku70 and NF90 specifically inhibit constitutive and inducible ARRE DNA-binding activity in Jurkat T-cells. Ku80, Ku70 and NF90 bind specifically to the IL-2 gene promoter in vivo, as demonstrated by chromatin immunoprecipitation. Activation of Jurkat T-cells and mouse primary spleen cells induces binding of Ku80 and NF90 to the IL-2 promoter in vivo, and decreases binding of Ku70 to the IL-2 promoter in vivo, and these dynamic changes are inhibited by immunosuppressants cyclosporin A and triptolide. Dynamic changes in binding of Ku80, Ku70 and NF90 to the IL-2 proximal promoter in vivo correlate with chromatin remodeling and transcriptional initiation in activated T-cells.
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Affiliation(s)
- Lingfang Shi
- Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford, CA 94305-5236, USA, Immunology and Allergy, Internal Medicine Department, University of Lausanne, CH-1011, Lausanne, Switzerland, Department of Biochemistry & Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alta., Canada T2N 4N1 and Division of Rheumatology and Clinical Immunology, University of Florida, Gainesville, FL 32610-0211, USA
| | - Daoming Qiu
- Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford, CA 94305-5236, USA, Immunology and Allergy, Internal Medicine Department, University of Lausanne, CH-1011, Lausanne, Switzerland, Department of Biochemistry & Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alta., Canada T2N 4N1 and Division of Rheumatology and Clinical Immunology, University of Florida, Gainesville, FL 32610-0211, USA
| | - Guohua Zhao
- Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford, CA 94305-5236, USA, Immunology and Allergy, Internal Medicine Department, University of Lausanne, CH-1011, Lausanne, Switzerland, Department of Biochemistry & Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alta., Canada T2N 4N1 and Division of Rheumatology and Clinical Immunology, University of Florida, Gainesville, FL 32610-0211, USA
| | - Blaise Corthesy
- Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford, CA 94305-5236, USA, Immunology and Allergy, Internal Medicine Department, University of Lausanne, CH-1011, Lausanne, Switzerland, Department of Biochemistry & Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alta., Canada T2N 4N1 and Division of Rheumatology and Clinical Immunology, University of Florida, Gainesville, FL 32610-0211, USA
| | - Susan Lees-Miller
- Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford, CA 94305-5236, USA, Immunology and Allergy, Internal Medicine Department, University of Lausanne, CH-1011, Lausanne, Switzerland, Department of Biochemistry & Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alta., Canada T2N 4N1 and Division of Rheumatology and Clinical Immunology, University of Florida, Gainesville, FL 32610-0211, USA
| | - Westley H. Reeves
- Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford, CA 94305-5236, USA, Immunology and Allergy, Internal Medicine Department, University of Lausanne, CH-1011, Lausanne, Switzerland, Department of Biochemistry & Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alta., Canada T2N 4N1 and Division of Rheumatology and Clinical Immunology, University of Florida, Gainesville, FL 32610-0211, USA
| | - Peter N. Kao
- Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford, CA 94305-5236, USA, Immunology and Allergy, Internal Medicine Department, University of Lausanne, CH-1011, Lausanne, Switzerland, Department of Biochemistry & Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alta., Canada T2N 4N1 and Division of Rheumatology and Clinical Immunology, University of Florida, Gainesville, FL 32610-0211, USA
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Modifying the function of DNA repair nanomachines for therapeutic benefit. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2007; 2:74-81. [PMID: 17292118 DOI: 10.1016/j.nano.2006.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Accepted: 04/07/2006] [Indexed: 10/24/2022]
Abstract
This article, which is based on a presentation at the First Annual Meeting of the American Academy of Nanomedicine, is divided into three parts. First, we describe naturally occurring DNA repair nanomachines, using as an example the nanomachine that executes the nonhomologous end-joining (NHEJ) reaction for DNA double-strand break (DSB) repair. Second, we discuss therapeutic benefits that may be derived from the ability to modify the behavior of naturally occurring nanomachines, using as an example the concept of delaying DSB repair in rapidly dividing cancer cells to increase their natural sensitivity to radiation therapy. Third, we discuss similarities in the overall size, shape, and design of different nanomachines that manipulate DNA and RNA, and the possibility of developing nanomachines with new specificities not found in nature.
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Rouleau M, McDonald D, Gagné P, Ouellet ME, Droit A, Hunter JM, Dutertre S, Prigent C, Hendzel MJ, Poirier GG. PARP-3 associates with polycomb group bodies and with components of the DNA damage repair machinery. J Cell Biochem 2007; 100:385-401. [PMID: 16924674 DOI: 10.1002/jcb.21051] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Poly(ADP-ribose) polymerase 3 (PARP-3) is a novel member of the PARP family of enzymes that synthesize poly(ADP-ribose) on themselves and other acceptor proteins. Very little is known about this PARP, which is closely related to PARP-1 and PARP-2. By sequence analysis, we find that PARP-3 may be expressed in two isoforms which we studied in more detail to gain insight into their possible functions. We find that both PARP-3 isoforms, transiently expressed as GFP or FLAG fusions, are nuclear. Detection of endogenous PARP-3 with a specific antibody also shows a widespread nuclear distribution, appearing in numerous small foci and a small number of larger foci. Through co-localization experiments and immunoprecipitations, the larger nuclear foci were identified as Polycomb group bodies (PcG bodies) and we found that PARP-3 is part of Polycomb group protein complexes. Furthermore, using a proteomics approach, we determined that both PARP-3 isoforms are part of complexes comprising DNA-PKcs, PARP-1, DNA ligase III, DNA ligase IV, Ku70, and Ku80. Our findings suggest that PARP-3 is a nuclear protein involved in transcriptional silencing and in the cellular response to DNA damage.
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Affiliation(s)
- M Rouleau
- Health and Environment Unit, Laval University Medical Research Centre, CHUQ, Faculty of Medicine, Laval University, 2705 Blvd Laurier, Sainte-Foy, Québec, G1V 4G2, Canada
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Gullo C, Au M, Feng G, Teoh G. The biology of Ku and its potential oncogenic role in cancer. Biochim Biophys Acta Rev Cancer 2006; 1765:223-34. [PMID: 16480833 DOI: 10.1016/j.bbcan.2006.01.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Revised: 12/27/2005] [Accepted: 01/03/2006] [Indexed: 11/30/2022]
Abstract
Ku is a heterodimeric protein made up of two subunits, Ku70 and Ku80. It was originally identified as an autoantigen recognized by the sera of patients with autoimmune diseases. It is a highly versatile regulatory protein that has been implicated in multiple nuclear processes, e.g., DNA repair, telomere maintenance and apoptosis. Accordingly, Ku is thought to play a crucial role in maintenance of chromosomal integrity and cell survival. Recent reports suggest that there is a positive relationship between Ku and the development of cancer, making Ku an important candidate target for anticancer drug development. Specifically, prior studies suggest that a delicate balance exists in Ku expression, as overexpression of Ku proteins promotes oncogenic phenotypes, including hyperproliferation and resistance to apoptosis; whereas deficient or low expression of Ku leads to genomic instability and tumorigenesis. Such observations through various experimental models indicate that Ku may act as either a tumor suppressor or an oncoprotein. Hence, understanding the link between the various functions of Ku and the development of cancer in different cell systems may help in the development of novel anticancer therapeutic agents that target Ku. These studies may also increase our understanding of how Ku autoantibodies are generated in autoimmune diseases.
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Affiliation(s)
- Charles Gullo
- Multiple Myeloma Research Laboratory, MMRL, Singapore Health Services, SingHealth, 7 Hospital Drive, Block A #02-05, Singapore 169611, Republic of Singapore
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14
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Bladen CL, Lam WK, Dynan WS, Kozlowski DJ. DNA damage response and Ku80 function in the vertebrate embryo. Nucleic Acids Res 2005; 33:3002-10. [PMID: 15914672 PMCID: PMC1140083 DOI: 10.1093/nar/gki613] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cellular responses to DNA damage reflect the dynamic integration of cell cycle control, cell–cell interactions and tissue-specific patterns of gene regulation that occurs in vivo but is not recapitulated in cell culture models. Here we describe use of the zebrafish embryo as a model system to identify determinants of the in vivo response to ionizing radiation-induced DNA damage. To demonstrate the utility of the model we cloned and characterized the embryonic function of the XRCC5 gene, which encodes Ku80, an essential component of the nonhomologous end joining pathway of DNA repair. After the onset of zygotic transcription, Ku80 mRNA accumulates in a tissue-specific pattern, which includes proliferative zones of the retina and central nervous system. In the absence of genotoxic stress, zebrafish embryos with reduced Ku80 function develop normally. However, low dose irradiation of these embryos during gastrulation leads to marked apoptosis throughout the developing central nervous system. Apoptosis is p53 dependent, indicating that it is a downstream consequence of unrepaired DNA damage. Results suggest that nonhomologous end joining components mediate DNA repair to promote survival of irradiated cells during embryogenesis.
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Affiliation(s)
- Catherine L. Bladen
- Institute of Molecular Medicine and Genetics, Medical College of GeorgiaAugusta, GA 30912, USA
| | - Wai K. Lam
- Institute of Molecular Medicine and Genetics, Medical College of GeorgiaAugusta, GA 30912, USA
| | - William S. Dynan
- Institute of Molecular Medicine and Genetics, Medical College of GeorgiaAugusta, GA 30912, USA
| | - David J. Kozlowski
- Institute of Molecular Medicine and Genetics, Medical College of GeorgiaAugusta, GA 30912, USA
- Department of Cellular Biology and Anatomy, Medical College of GeorgiaAugusta, GA 30912, USA
- To whom correspondence should be addressed. Tel: +1 706 721 8760; Fax: +1 706 721 8752;
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15
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Mayeur GL, Kung WJ, Martinez A, Izumiya C, Chen DJ, Kung HJ. Ku is a novel transcriptional recycling coactivator of the androgen receptor in prostate cancer cells. J Biol Chem 2005; 280:10827-33. [PMID: 15640154 DOI: 10.1074/jbc.m413336200] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The androgen receptor (AR) dynamically assembles and disassembles multicomponent receptor complexes in order to respond rapidly and reversibly to fluctuations in androgen levels. We are interested in identifying the basal factors that compose the AR aporeceptor and holoreceptor complexes and impact the transcriptional process. Using tandem mass spectroscopy analysis, we identified the trimeric DNA-dependent protein kinase (DNA-PK) complex as the major AR-interacting proteins. AR directly interacts with both Ku70 and Ku80 in vivo and in vitro, as shown by co-immunoprecipitation, glutathione S-transferase pull-down, and Sf9 cell/baculovirus expression. The interaction was localized to the androgen receptor ligand binding domain and is independent of DNA interactions. Ku interacts with AR in the cytoplasm and nucleus regardless of the presence or absence of androgen. Ku acts as a coactivator of AR activity in a luciferase reporter assay employing both Ku-defective cells and Ku small interfering RNA knock-down in a prostate cancer cell line. DNA-PK catalytic subunit (DNA-PKcs) also acts as a coactivator of androgen receptor activity in a luciferase reporter assay employing DNA-PKcs defective cells. AR nuclear translocation is not affected in Ku defective cells, implying Ku functionality may be mainly nuclear. Chromatin immunoprecipitation experiments demonstrated that both Ku70 and Ku80 interact with the prostate-specific antigen promoter in an androgen-dependant manner. Finally, in vitro transcription assays demonstrated Ku involvement in transcriptional recycling with androgen dependent promoters.
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MESH Headings
- Androgens/metabolism
- Animals
- Antigens, Nuclear/chemistry
- Antigens, Nuclear/metabolism
- Antigens, Nuclear/physiology
- Cell Line
- Cell Line, Tumor
- Cell Nucleus/metabolism
- Chromatin/metabolism
- Chromatin Immunoprecipitation
- Cytoplasm/metabolism
- DNA/chemistry
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/metabolism
- DNA-Binding Proteins/physiology
- Electrophoresis, Polyacrylamide Gel
- Genes, Reporter
- Glutathione Transferase/metabolism
- Humans
- Immunoprecipitation
- Insecta
- Ku Autoantigen
- Ligands
- Luciferases/metabolism
- Male
- Mass Spectrometry
- Models, Genetic
- Prostatic Neoplasms/metabolism
- Protein Binding
- Protein Structure, Tertiary
- RNA/metabolism
- RNA, Small Interfering/metabolism
- Receptors, Androgen/metabolism
- Signal Transduction
- Transcription, Genetic
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Affiliation(s)
- Greg L Mayeur
- Department of Biological Chemistry, School of Medicine, University of California, Davis, UC Davis Cancer Center, Sacramento, California 95817, USA
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16
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Bladen CL, Udayakumar D, Takeda Y, Dynan WS. Identification of the polypyrimidine tract binding protein-associated splicing factor.p54(nrb) complex as a candidate DNA double-strand break rejoining factor. J Biol Chem 2004; 280:5205-10. [PMID: 15590677 DOI: 10.1074/jbc.m412758200] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The biological effects of ionizing radiation are attributable, in large part, to induction of DNA double-strand breaks. We report here the identification of a new protein factor that reconstitutes efficient double-strand break rejoining when it is added to a reaction containing the five other polypeptides known to participate in the human nonhomologous end-joining pathway. The factor is a stable heteromeric complex of polypyrimidine tract-binding protein-associated splicing factor (PSF) and a 54-kDa nuclear RNA-binding protein (p54(nrb)). These polypeptides, to which a variety of functions have previously been attributed, share extensive homology, including tandem RNA recognition motif domains. The PSF.p54(nrb) complex cooperates with Ku protein to form a functional preligation complex with substrate DNA. Based on structural comparison with related proteins, we propose a model where the four RNA recognition motif domains in the heteromeric PSF.p54(nrb) complex cooperate to align separate DNA molecules.
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Affiliation(s)
- Catherine L Bladen
- Program in Gene Regulation and Cancer Biology, Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, GA 30912, USA
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17
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Sucharov CC, Helmke SM, Langer SJ, Perryman MB, Bristow M, Leinwand L. The Ku protein complex interacts with YY1, is up-regulated in human heart failure, and represses alpha myosin heavy-chain gene expression. Mol Cell Biol 2004; 24:8705-15. [PMID: 15367688 PMCID: PMC516749 DOI: 10.1128/mcb.24.19.8705-8715.2004] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human heart failure is accompanied by repression of genes such as alpha myosin heavy chain (alphaMyHC) and SERCA2A and the induction of fetal genes such as betaMyHC and atrial natriuretic factor. It seems likely that changes in MyHC isoforms contribute to the poor contractility seen in heart failure, because small changes in isoform composition can have a major effect on the contractility of cardiac myocytes and the heart. Our laboratory has recently shown that YY1 protein levels are increased in human heart failure and that YY1 represses the activity of the human alphaMyHC promoter. We have now identified a region of the alphaMyHC promoter that binds a factor whose expression is increased sixfold in failing human hearts. Through peptide mass spectrometry, we identified this binding activity to be a heterodimer of Ku70 and Ku80. Expression of Ku represses the human alphaMyHC promoter in neonatal rat ventricular myocytes. Moreover, overexpression of Ku70/80 decreases alphaMyHC mRNA expression and increases skeletal alpha-actin. Interestingly, YY1 interacts with Ku70 and Ku80 in HeLa cells. Together, YY1, Ku70, and Ku80 repress the alphaMyHC promoter to an extent that is greater than that with YY1 or Ku70/80 alone. Our results suggest that Ku is an important factor in the repression of the human alphaMyHC promoter during heart failure.
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Affiliation(s)
- Carmen C Sucharov
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, USA
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18
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Abstract
Cells induce the expression of DNA-repair enzymes, activate cell-cycle checkpoints and, under some circumstances, undergo apoptosis in response to DNA-damaging agents. The mechanisms by which these cellular responses are triggered are not well understood, but there is recent evidence that the transcription machinery might be used in DNA-damage surveillance and in triggering DNA-damage responses to suppress mutagenesis. Transcription might also act as a DNA-damage dosimeter where the severity of blockage determines whether or not to induce cell death. Could transcription therefore be a potential therapeutic target for anticancer strategies?
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Affiliation(s)
- Mats Ljungman
- Department of Radiation Oncology, Division of Radiation and Cancer Biology, University of Michigan Comprehensive Cancer Center, University of Michigan Medical School, University of Michigan, Ann Arbor, Michigan 48109-0936, USA.
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19
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Liu X, Tiwari RK, Geliebter J, Wu JM, Godfrey HP. Interaction of a Mycobacterium tuberculosis repetitive DNA sequence with eukaryotic proteins. Biochem Biophys Res Commun 2004; 320:966-72. [PMID: 15240143 DOI: 10.1016/j.bbrc.2004.06.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis infects one-third of the world's population and causes two million deaths annually. Its intracellular residence raises the possibility that bacterial nucleic acids might interact with key host proteins and contribute to the pathophysiology of infection. To test this hypothesis, we searched for motifs closely resembling eukaryotic transcription factor binding sites in the M. tuberculosis H37Rv genome and found activator protein-2 and zinc finger protein-5 binding motifs in a 36-nucleotide repetitive mycobacterial DNA sequence (RPT1). RPT1 bound specifically to nuclear extract proteins from U937, A549, and HeLa cells in electrophoretic mobility shift assays but not to activator protein-2. Several nuclear and cytosolic proteins showing at least partial binding specificity for RPT1 were isolated from U937 and A549 cells by pull-down assays, including Ku70 (DNA-dependent protein kinase subunit) and poly(ADP-ribose) polymerase-1. RPT1 also specifically activated DNA-dependent protein phosphorylation. These results suggest that mycobacterial nucleic acid fragments may interact specifically with eukaryotic regulatory proteins which might contribute to bacterial life-cycle maintenance.
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Affiliation(s)
- Xinyan Liu
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA
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20
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Wang H, Fang R, Cho JY, Libermann TA, Oettgen P. Positive and Negative Modulation of the Transcriptional Activity of the ETS Factor ESE-1 through Interaction with p300, CREB-binding Protein, and Ku 70/86. J Biol Chem 2004; 279:25241-50. [PMID: 15075319 DOI: 10.1074/jbc.m401356200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Epithelium-specific ETS (ESE)-1 is a prototypic member of a novel subset of the ETS transcription factor family that is predominantly expressed in cells of epithelial origin but can also be induced in other cell types including vascular endothelial and smooth muscle cells in response to inflammatory stimuli. To further define the molecular mechanisms by which the transcriptional activity of ESE-1 is regulated, we have focused our attention on identifying proteins that interact with ESE-1. We have determined that Ku70, Ku86, p300, and CREB-binding protein (CBP) are ESE-1 interacting proteins. The Ku proteins have previously been shown to bind to breaks in DNA where they function to recruit additional proteins that promote DNA repair. Interestingly, Ku70 and Ku 86 negatively regulate the transcriptional activity of ESE-1. Using a series of deletion constructs, we have determined that the Ku proteins bind to the DNA-binding domain of ESE-1. The Ku proteins inhibit the ability of ESE-1 to bind to oligonucleotide probes in gel mobility shift assays. The finding that Ku proteins can interact with other transcription factors and block their function has not been previously demonstrated. In contrast, co-transfection of p300 and CBP with ESE-1 enhances the transcriptional activity of ESE-1. Moreover, the induction of ESE-1 in response to inflammatory cytokine interleukin-1 is associated with a parallel increase of the expression of p300 in vascular endothelial cells, suggesting that in the setting of inflammation, the transcriptional activity of ESE-1 is positively modulated by interaction with the transcriptional co-activator p300. In summary, our results demonstrated that the activity of ESE-1 is positively and negatively modulated by other interacting proteins including Ku70, Ku86, p300, and CBP.
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Affiliation(s)
- Hong Wang
- Cardiology Division, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115, USA
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21
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Affiliation(s)
- Jessica A Downs
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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22
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Gaudreault I, Guay D, Lebel M. YB-1 promotes strand separation in vitro of duplex DNA containing either mispaired bases or cisplatin modifications, exhibits endonucleolytic activities and binds several DNA repair proteins. Nucleic Acids Res 2004; 32:316-27. [PMID: 14718551 PMCID: PMC373280 DOI: 10.1093/nar/gkh170] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
YB-1 is a multifunctional protein involved in the regulation of transcription, translation, mRNA splicing and probably DNA repair. It contains a conserved cold shock domain and it binds strongly to inverted CCAAT box of different promoters. In this study, we have found that purified YB-1 oligomerizes readily in solutions to form trimers, hexamers and oligomers of 12 molecules. The presence of ATP changed the conformation of YB-1 in such a way that only dimers were detected by gel filtration analyses. Purified YB-1 can separate different DNA duplexes containing blunt ends, 5' or 3' recessed ends, or forked structures. This strand separation activity is increased on cisplatin-modified DNA or with duplex molecules containing mismatches. In addition to its exonuclease activity, YB-1 exhibits endonucleolytic activities in vitro. Finally, YB-1 affinity chromatography experiments have indicated that in addition to prespliceosome factors like nucleolin and ALY, YB-1 binds the DNA repair proteins MSH2, DNA polymerase delta, Ku80 and WRN proteins in vitro. Furthermore, immunofluorescence studies have shown that YB-1 re-localizes from the cytoplasm to nuclear areas containing either Ku80 or MSH2 proteins in human 293 embryonic kidney cells. These results suggest that YB-1 is involved in base excision and mismatch repair pathways.
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Affiliation(s)
- Isabelle Gaudreault
- Centre de Recherche en Cancérologie de l'Université Laval, Hôpital Hôtel-Dieu de Québec, Centre Hospitalier Universitaire de Québec, 9 McMahon Street, Québec, G1R 2J6, Canada
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23
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Diggle CP, Bentley J, Kiltie AE. Development of a rapid, small-scale DNA repair assay for use on clinical samples. Nucleic Acids Res 2003; 31:e83. [PMID: 12888535 PMCID: PMC169971 DOI: 10.1093/nar/gng083] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Double-strand breaks (DSBs) are the most lethal form of DNA damage. They can be repaired by one of two pathways, homologous recombination and non-homologous end joining (NHEJ). A NHEJ assay has previously been reported which measures joining using cell-free extracts and a linearised plasmid as DNA substrate. This assay was designed for 3 x 10(9) cells grown in vitro and utilised radioactively labelled substrate. We have scaled down the method to use smaller cell numbers in a variety of cell lines. Altering the cellular extraction procedure decreased background DNA contamination. The cleaner preparations allowed us to use SYBR Green I staining to identify joined products, which was as sensitive as 32P-end-labelled DNA. NHEJ was found in established tumour cell lines from different originating tissues, though actual levels and fidelity of repair differed. This method also allowed end joining to be assessed in clinical specimens (human blood, brain and bladder tumours) within 24 h of receiving samples. The application of this method will allow investigation of the role of DSB DNA repair pathways in human tumours.
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Affiliation(s)
- Christine P Diggle
- Cancer Research UK Clinical Centre, St James's University Hospital, Leeds LS9 7TF, UK
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24
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Abstract
Gene transcription is repetitive, enabling the synthesis of multiple copies of identical RNA molecules from the same template. The cyclic process of RNA synthesis from active genes, referred to as transcription reinitiation, contributes significantly to the level of RNAs in living cells. Contrary to the perception that multiple transcription cycles are a mere iteration of mechanistically identical steps, a large body of evidence indicates that, in most transcription systems, reinitiation involves highly specific and regulated pathways. These pathways influence the availability for reinitiation of template DNA and/or transcription proteins, and represent an important yet poorly characterized aspect of gene regulation.
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Affiliation(s)
- Giorgio Dieci
- Dipartimento di Biochimica e Biologia Molecolare, Università di Parma, Italy.
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25
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Ko L, Chin WW. Nuclear receptor coactivator thyroid hormone receptor-binding protein (TRBP) interacts with and stimulates its associated DNA-dependent protein kinase. J Biol Chem 2003; 278:11471-9. [PMID: 12519782 DOI: 10.1074/jbc.m209723200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nuclear receptors mediate gene activation through ligand-dependent interaction with coactivators. We previously cloned and characterized thyroid hormone receptor-binding protein, TRBP (NcoA6: AIB3/ASC-2/RAP250/PRIP/TRBP/NRC), as an LXXLL-containing coactivator that associates with coactivator complexes through its C terminus. To search for protein factors involved in TRBP action, we identified a distinct set of proteins from HeLa nuclear extract that interacts with the C terminus of TRBP. Analysis by mass spectrometric protein sequencing revealed a DNA-dependent protein kinase (DNA-PK) complex including its catalytic subunit and regulatory subunits, Ku70 and Ku86. DNA-PK is a heterotrimeric nuclear phosphatidylinositol 3-kinase that functions in DNA repair, recombination, and transcriptional regulation. DNA-PK phosphorylates TRBP at its C-terminal region, which directly interacts with Ku70 but not Ku86 in vitro. In addition, in the absence of DNA, TRBP itself activates DNA-PK, and the TRBP-stimulated DNA-PK activity has an altered phosphorylation pattern from DNA-stimulated activity. An anti-TRBP antibody inhibits TRBP-induced kinase activity, suggesting that protein content of TRBP is responsible for the stimulation of DNA-independent kinase activity. Furthermore, in DNA-PK-deficient scid cells, TRBP-mediated transactivation is significantly impaired, and nuclear localization of TRBP is altered. The activation of DNA-PK in the absence of DNA ends by the coactivator TRBP suggests a novel mechanism of coactivator-stimulated DNA-PK phosphorylation in transcriptional regulation.
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Affiliation(s)
- Lan Ko
- Department of Gene Regulation, Bone and Inflammation Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, USA.
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26
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Sallmyr A, Du L, Bredberg A. An inducible Ku86-degrading serine protease in human cells. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1593:57-68. [PMID: 12431784 DOI: 10.1016/s0167-4889(02)00331-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The Ku autoantigen has been implicated in a number of cellular functions including growth control, immunoglobulin gene rearrangement and DNA repair. A variant truncated form of Ku86, with an apparent molecular weight of 70 kDa, has been reported to be present in many human cell types. We have previously shown that the amount of variant Ku86 is strongly increased in human peripheral blood mononuclear cells (PBMC) by storage of blood prior to isolation of the PBMC. In this study we report that formation of variant Ku86 in protein extracts is mediated by an inducible trypsin-like serine protease with a higher concentration in the nuclear compartment, as compared with the cytoplasm. However, experiments with SDS-PAGE assay of whole cells yielded no evidence of truncated Ku86, suggesting that the protease is not active in intact cells, but is exerting a marked activity during the protein extraction procedure. Interestingly, the protease level became markedly reduced upon transfer of the cells to growth medium. Protease induction did not correlate with apoptosis, necrotic cell death or with signs of general proteolysis or cytotoxicity. Our findings have methodological implications for the interpretation of experimental Ku86 data, and suggest that this protease may play a role for cellular regulation of Ku function.
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Affiliation(s)
- Annahita Sallmyr
- Department of Medical Microbiology, Lund University, Malmö University Hospital, 205 02 Malmö, Sweden
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27
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Mo X, Dynan WS. Subnuclear localization of Ku protein: functional association with RNA polymerase II elongation sites. Mol Cell Biol 2002; 22:8088-99. [PMID: 12391174 PMCID: PMC134733 DOI: 10.1128/mcb.22.22.8088-8099.2002] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ku is an abundant nuclear protein with an essential function in the repair of DNA double-strand breaks. Various observations suggest that Ku also interacts with the cellular transcription machinery, although the mechanism and significance of this interaction are not well understood. In the present study, we investigated the subnuclear distribution of Ku in normally growing human cells by using confocal microscopy, chromatin immunoprecipitation, and protein immunoprecipitation. All three approaches indicated association of Ku with RNA polymerase II (RNAP II) elongation sites. This association occurred independently of the DNA-dependent protein kinase catalytic subunit and was highly selective. There was no detectable association with the initiating isoform of RNAP II or with the general transcription initiation factors. In vitro protein-protein interaction assays demonstrated that the association of Ku with elongation proteins is mediated, in part, by a discrete C-terminal domain in the Ku80 subunit. Functional disruption of this interaction with a dominant-negative mutant inhibited transcription in vitro and in vivo and suppressed cell growth. These results suggest that association of Ku with transcription sites is important for maintenance of global transcription levels. Tethering of double-strand break repair proteins to defined subnuclear structures may also be advantageous in maintenance of genome stability.
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Affiliation(s)
- Xianming Mo
- Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, Georgia 30912, USA
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28
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Willis DM, Loewy AP, Charlton-Kachigian N, Shao JS, Ornitz DM, Towler DA. Regulation of osteocalcin gene expression by a novel Ku antigen transcription factor complex. J Biol Chem 2002; 277:37280-91. [PMID: 12145306 DOI: 10.1074/jbc.m206482200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We previously described an osteocalcin (OC) fibroblast growth factor (FGF) response element (FRE) DNA binding activity as a target of Msx2 transcriptional regulation. We now identify Ku70, Ku80, and Tbdn100, a variant of Tubedown-1, as constituents of the purified OCFRE-binding complex. Northern and Western blot analyses demonstrate expression of Ku and Tbdn100 in MC3T3E1 osteoblasts. FGF2 treatment regulates Ku, but not Tbdn100, protein accumulation. Gel supershift studies confirm sequence-specific DNA binding of Ku in the OCFRE complex; chromatin immunoprecipitation assays confirm association of Ku and Tbdn100 with the endogenous OC promoter. In the promoter region -154 to -113, the OCFRE is juxtaposed to OSE2, an osteoblast-specific element that binds Runx2 (Osf2, Cbfa1). Expression of the Ku.Tbdn100 complex up-regulates both the basal and Runx2-dependent transcription driven by this 42-bp OC promoter element, reconstituted in CV-1 cells. Synergistic transactivation occurs in the presence of activated FGF receptor 2 signaling. Msx2 suppresses Ku- and Runx2-dependent transcription; suppression is dependent upon the Msx2 homeodomain NH(2)-terminal arm and extension. Pull-down assays confirm physical interactions between Ku and these co-regulatory transcription factors, consistent with the functional interactions identified. Finally, cultured Ku70 -/- calvarial cells exhibit a profound, selective deficiency in OC expression as compared with wild-type calvarial cells, confirming the biochemical data showing a role for Ku in OC transcription. In toto, these data indicate that a novel Ku antigen complex assembles on the OC promoter, functioning in concert with Msx2 and Runx2 to regulate OC gene expression.
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Affiliation(s)
- David M Willis
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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29
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Karmakar P, Snowden CM, Ramsden DA, Bohr VA. Ku heterodimer binds to both ends of the Werner protein and functional interaction occurs at the Werner N-terminus. Nucleic Acids Res 2002; 30:3583-91. [PMID: 12177300 PMCID: PMC134248 DOI: 10.1093/nar/gkf482] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The human Werner syndrome protein, WRN, is a member of the RecQ helicase family and contains 3'-->5' helicase and 3'-->5' exonuclease activities. Recently, we showed that the exonuclease activity of WRN is greatly stimulated by the human Ku heterodimer protein. We have now mapped this interaction physically and functionally. The Ku70 subunit specifically interacts with the N-terminus (amino acids 1-368) of WRN, while the Ku80 subunit interacts with its C-terminus (amino acids 940- 1432). Binding between Ku70 and the N-terminus of WRN (amino acids 1-368) is sufficient for stimulation of WRN exonuclease activity. A mutant Ku heterodimer of full-length Ku80 and truncated Ku70 (amino acids 430-542) interacts with C-WRN but not with N-WRN and cannot stimulate WRN exonuclease activity. This emphasizes the functional significance of the interaction between the N-terminus of WRN and Ku70. The interaction between Ku80 and the C-terminus of WRN may modulate some other, as yet unknown, function. The strong interaction between Ku and WRN suggests that these two proteins function together in one or more pathways of DNA metabolism.
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Affiliation(s)
- Parimal Karmakar
- Laboratory of Molecular Gerontology, Box 1, National Institute on Aging, IRP, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224-6825, USA
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30
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Conway C, McCulloch R, Ginger ML, Robinson NP, Browitt A, Barry JD. Ku is important for telomere maintenance, but not for differential expression of telomeric VSG genes, in African trypanosomes. J Biol Chem 2002; 277:21269-77. [PMID: 11919193 DOI: 10.1074/jbc.m200550200] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosome antigenic variation, involving differential expression of variant surface glycoprotein (VSG) genes, has a strong association with telomeres and with DNA recombination. All expressed VSGs are telomeric, and differential activation involves recombination into the telomeric environment or silencing/activation of subtelomeric promoters. A number of pathogen contingency gene systems associated with immune evasion involve telomeric loci, which has prompted speculation that chromosome ends provide conditions conducive for the operation of rapid gene switching mechanisms. Ku is a protein associated with eukaryotic telomeres that is directly involved in DNA recombination and in gene silencing. We have tested the hypothesis that Ku in trypanosomes is centrally involved in differential VSG expression. We show, via the generation of null mutants, that trypanosome Ku is closely involved in telomere length maintenance, more so for a transcriptionally active than an inactive telomere, but exhibits no detectable influence on DNA double strand break repair. The absence of Ku and the consequent great shortening of telomeres had no detectable influence either on the rate of VSG switching or on the silencing of the telomeric promoters of the VSG subset that is expressed in the tsetse fly.
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Affiliation(s)
- Colin Conway
- Wellcome Centre for Molecular Parasitology, University of Glasgow, Anderson College, 56 Dumbarton Road, Glasgow, G11 6NU, Scotland, United Kingdom
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31
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Huang J, Dynan WS. Reconstitution of the mammalian DNA double-strand break end-joining reaction reveals a requirement for an Mre11/Rad50/NBS1-containing fraction. Nucleic Acids Res 2002; 30:667-74. [PMID: 11809878 PMCID: PMC100305 DOI: 10.1093/nar/30.3.667] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2001] [Revised: 12/06/2001] [Accepted: 12/06/2001] [Indexed: 12/14/2022] Open
Abstract
The non-homologous end-joining pathway promotes direct enzymatic rejoining of DNA double-strand breaks (DSBs) and is an important determinant of genome stability in eukaryotic cells. Although previous work has shown that this pathway requires Ku, DNA-PKcs and the DNA ligase IV/XRCC4 complex, we found that these proteins alone did not promote efficient joining of cohesive-ended DNA fragments in a cell-free assay. To identify factors that were missing from the reaction, we screened fractions from HeLa cell extracts for the ability to stimulate the joining of cohesive DNA ends in a complementation assay containing other known proteins required for DNA DSB repair. We identified a factor that restored end-joining activity to the level observed in crude nuclear extracts. Factor activity copurified with Rad50, Mre11 and NBS1, three proteins that have previously been implicated in DSB repair by genetic and cytologic evidence. Factor activity was inhibited by anti-Mre11 antibody. The reconstituted system remained fully dependent on DNL IV/XRCC4 and at least partially dependent on Ku, but the requirement for DNA-PKcs was progressively lost as other components were purified. Results support a model where DNA-PKcs acts early in the DSB repair pathway to regulate progression of the reaction, and where Mre11, Rad50 and NBS1 play a key role in aligning DNA ends in a synaptic complex immediately prior to ligation.
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Affiliation(s)
- Juren Huang
- Institute of Molecular Medicine and Genetics, Program in Gene Regulation, CB-2803, Medical College of Georgia, 1120 15th Street, Augusta, GA 30912, USA
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