31 results on '"Julia Coates"'
Search Results
2. ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks
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Gabriel Balmus, Domenic Pilger, Julia Coates, Mukerrem Demir, Matylda Sczaniecka-Clift, Ana C. Barros, Michael Woods, Beiyuan Fu, Fengtang Yang, Elisabeth Chen, Matthias Ostermaier, Tatjana Stankovic, Hannes Ponstingl, Mareike Herzog, Kosuke Yusa, Francisco Munoz Martinez, Stephen T. Durant, Yaron Galanty, Petra Beli, David J. Adams, Allan Bradley, Emmanouil Metzakopian, Josep V. Forment, and Stephen P. Jackson
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Science - Abstract
Mutations in the ATM tumor suppressor gene confer hypersensitivity to DNA-damaging chemotherapeutic agents. Here, the authors provide evidence that these hypersensitivities reflect a crucial role for ATM at damaged replication forks being to prevent toxic DNA end-joining leading to chromosome fusions and cell death.
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- 2019
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3. Coordinated nuclease activities counteract Ku at single-ended DNA double-strand breaks
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Pauline Chanut, Sébastien Britton, Julia Coates, Stephen P. Jackson, and Patrick Calsou
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Science - Abstract
Homologous recombination requires end resection of the DNA at the site of the break, however the Ku dimer can sequester single-ended double-strand breaks. Here the authors show that ATM-dependent phosphorylation of CtIP, along with the actions of Mre11, impair the stable loading of Ku onto DNA.
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- 2016
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4. Correction: Corrigendum: Coordinated nuclease activities counteract Ku at single-ended DNA double-strand breaks
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Pauline Chanut, Sébastien Britton, Julia Coates, Stephen P. Jackson, and Patrick Calsou
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Science - Abstract
Nature Communications 7: Article number: 12889 (2016); Published: 19 Sep 2016; Updated: 13 Jun 2017 In this Article, the MRE11 exonuclease mutant H63D is consistently referred to incorrectly as H63N. These errors appear in the Results, Methods, Fig. 3, Fig. 4, Fig. 5, Supplementary Fig. 3, Supplementary Table 2 and Supplementary Methods.
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- 2017
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5. MDC1 PST-repeat region promotes histone H2AX-independent chromatin association and DNA damage tolerance
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Mukerrem Demir, Rimma Belotserkovskaya, Marcus D. Wilson, Matylda Sczaniecka-Clift, Israel Salguero, Julia Coates, Satpal Jhujh, Stephen P. Jackson, Salguero, Israel [0000-0001-8756-659X], Belotserkovskaya, Rimma [0000-0001-5363-251X], Jhujh, Satpal [0000-0001-5766-659X], Wilson, Marcus D. [0000-0001-9551-5514], Jackson, Stephen P. [0000-0001-9317-7937], Apollo - University of Cambridge Repository, Wilson, Marcus D [0000-0001-9551-5514], and Jackson, Stephen P [0000-0001-9317-7937]
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0301 basic medicine ,DNA Repair ,Molecular biology ,42/109 ,Amino Acid Motifs ,General Physics and Astronomy ,Cell Cycle Proteins ,environment and public health ,Histones ,chemistry.chemical_compound ,42/44 ,42/41 ,DNA Breaks, Double-Stranded ,14/19 ,lcsh:Science ,Multidisciplinary ,Histone H2AX ,Chromatin ,3. Good health ,Cell biology ,13/31 ,Histone ,biological phenomena, cell phenomena, and immunity ,Tumor Suppressor p53-Binding Protein 1 ,631/337 ,DNA repair ,DNA damage ,Science ,13/106 ,13/109 ,Biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,Cell Line ,03 medical and health sciences ,14/34 ,Humans ,Nucleosome ,Adaptor Proteins, Signal Transducing ,030102 biochemistry & molecular biology ,General Chemistry ,MDC1 ,enzymes and coenzymes (carbohydrates) ,42/35 ,030104 developmental biology ,chemistry ,14/63 ,biology.protein ,lcsh:Q ,631/80 ,DNA ,DNA Damage - Abstract
Histone H2AX and MDC1 are key DNA repair and DNA-damage signalling proteins. When DNA double-strand breaks (DSBs) occur, H2AX is phosphorylated and then recruits MDC1, which in turn serves as a docking platform to promote the localization of other factors, including 53BP1, to DSB sites. Here, by using CRISPR-Cas9 engineered human cell lines, we identify a hitherto unknown, H2AX-independent, function of MDC1 mediated by its PST-repeat region. We show that the PST-repeat region directly interacts with chromatin via the nucleosome acidic patch and mediates DNA damage-independent association of MDC1 with chromatin. We find that this region is largely functionally dispensable when the canonical γH2AX-MDC1 pathway is operative but becomes critical for 53BP1 recruitment to DNA-damage sites and cell survival following DSB induction when H2AX is not available. Consequently, our results suggest a role for MDC1 in activating the DDR in areas of the genome lacking or depleted of H2AX., MDC1 and H2AX interact and accumulate at sites of DNA damage, functioning to recruit additional factors involved in the repair process. Here the authors uncover a function for MDC1 that is independent of the presence of H2AX and is mediated through its PST-repeat region.
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- 2019
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6. Shieldin complex promotes DNA end-joining and counters homologous recombination in BRCA1-null cells
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Stephen P. Jackson, Mareike Herzog, Alejandra Bruna, Luca Pellegrini, Violeta Serra, Mark J. O'Connor, Zhongwu Lai, Chloé Lescale, Jacqueline J.L. Jacobs, Fengtang Yang, Jonathan Lam, Matylda Sczaniecka-Clift, Abigail Shea, Carlos Caldas, Matthias Ostermaier, Gabriel Balmus, Julia Coates, Wenming Wei, Inge de Krijger, Yaron Galanty, Mukerrem Demir, Ludovic Deriano, Petra Beli, Domenic Pilger, Harveer Dev, Rimma Belotserkovskaya, Alistair Martin, Beiyuan Fu, Ting-Wei Will Chiang, Qian Wu, Dev, Harveer [0000-0003-2874-6894], Yang, Fengtang [0000-0002-3573-2354], Balmus, Gabriel [0000-0003-2872-4468], Serra, Violeta [0000-0001-6620-1065], Beli, Petra [0000-0001-9507-9820], Pellegrini, Luca [0000-0002-9300-497X], Deriano, Ludovic [0000-0002-9673-9525], Jacobs, Jacqueline JL [0000-0002-7704-4795], Jackson, Stephen P [0000-0001-9317-7937], Apollo - University of Cambridge Repository, Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge [UK] (CAM), Department of Biochemistry [Cambridge], Cambridge University Hospitals - NHS (CUH), Intégrité du génome, immunité et cancer - Genome integrity, Immunity and Cancer, Institut Pasteur [Paris] (IP), Netherlands Cancer Institute (NKI), Antoni van Leeuwenhoek Hospital, Cancer Research UK Cambridge Institute [Cambridge, Royaume-Uni] (CRUK), Institute of Molecular Biology (IMB), Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Wellcome Trust Sanger Institute [Hinxton, UK], AstraZeneca US [Waltham, USA], AstraZeneca [Cambridge, UK], The Wellcome Trust Sanger Institute [Cambridge], Vall d'Hebron Institute of Oncology [Barcelone] (VHIO), Vall d'Hebron University Hospital [Barcelona], The SPJ lab is largely funded by a Cancer Research UK (CRUK) Program Grant, C6/A18796, and a Wellcome Trust (WT) Investigator Award, 206388/Z/17/Z. Core infrastructure funding was provided by CRUK grant C6946/A24843 and WT grant WT203144. S.P.J. receives a salary from the University of Cambridge. H.D. is funded by WT Clinical Fellowship 206721/Z/17/Z. TWC was supported by a Cambridge International Scholarship. D.P. is funded by Cancer Research UK studentship C6/A21454. The P.B. lab is supported by the Emmy Noether Program (BE 5342/1-1) from the German Research Foundation and a Marie Curie Career Integration Grant from the European Commission (630763). The L.P. lab is funded by the WT (investigator award 104641/Z/14/Z) and the Medical Research Council (project grant MR/N000161/1). The C.C. lab was supported with funding from CRUK. The J.J. lab was supported by the European Research Council grant ERC-StG 311565, The Dutch Cancer Society (KWF) grant KWF 10999, and the Netherlands Organization for Scientific Research (NWO) as part of the National Roadmap Large-scale Research Facilities of the Netherlands, Proteins@Work (project no. 184.032.201 to the Proteomics Facility of the Netherlands Cancer Institute). The L.D. lab is funded by the Institut Pasteur, the Institut National du Cancer (no. PLBIO16-181) and the European Research Council (starting grant agreement no. 310917). W.W. is part of the Pasteur–Paris University (PPU) International PhD program and this project received funding from the CNBG company, China. Q.W. is funded by the Wellcome Trust (200814/Z/16/Z ). The V.S. lab work was funded by the Instituto de Salud Carlos III (ISCIII), an initiative of the Spanish Ministry of Economy and Innovation partially supported by European Regional Development FEDER Funds (PI17-01080 to VS), the European Research Area-NET, Transcan-2 (AC15/00063), a non-commercial research agreement with AstraZeneca UK, and structural funds from the Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR, 2017 SGR 540) and the Orozco Family. V.S. received a salary and travel support to C.C.’s lab from ISCIII (CP14/00228, MV15/00041) and the FERO Foundation., The authors thank all S.P.J. laboratory members for support and advice, and Cambridge colleagues N. Lawrence for OMX super-resolution microscopy support and R. Butler for help with computational image analyses and programming. The authors also thank S. Selivanova and S. Hough for help with plasmid amplification, sample preparation and tissue culture maintenance, K. Dry for extensive editorial assistance, F. Muñoz-Martinez for assistance with CRISPR–Cas9 knockout generation, L. Radu for assistance with protein purification, C. Lord (Institute of Cancer Research, London) for SUM149PT cells, D. Durocher (University of Toronto, Canada) for U2OS LacSceIII cells, F. Alt (Harvard University, USA) for CH12F3 cells and 53bp1 knockout CH12F3 cell clones, T. Honjo (Kyoto University, Japan) for permission to use the CH12F3 cell line, and J. Serrat in the Jacobs lab for technical assistance, Institut Pasteur [Paris], and Johannes Gutenberg - Universität Mainz (JGU)
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MESH: DNA Breaks, Double-Stranded ,RAD51 ,Cell Cycle Proteins ,Poly (ADP-Ribose) Polymerase Inhibitor ,MESH: Recombinational DNA Repair ,Mice ,MESH: Animals ,DNA Breaks, Double-Stranded ,skin and connective tissue diseases ,Cancer ,Telomere-binding protein ,Ovarian Neoplasms ,MESH: Breast Neoplasms / metabolism ,MESH: Telomere-Binding Proteins / metabolism ,3. Good health ,Cell biology ,MESH: HEK293 Cells ,MESH: Proteins / genetics ,MESH: Telomere-Binding Proteins / genetics ,MESH: Tumor Suppressor p53-Binding Protein 1 / metabolism ,MESH: Xenograft Model Antitumor Assays ,Telomere-Binding Proteins ,MESH: Ovarian Neoplasms / drug therapy ,Bone Neoplasms ,MESH: Ovarian Neoplasms / metabolism ,Article ,03 medical and health sciences ,MESH: Cell Cycle Proteins ,MESH: Bone Neoplasms / metabolism ,Humans ,MESH: Osteosarcoma / metabolism ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,MESH: Humans ,MESH: Tumor Suppressor p53-Binding Protein 1 / genetics ,Dose-Response Relationship, Drug ,HEK 293 cells ,Proteins ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,DNA ,MESH: BRCA1 Protein / deficiency ,030104 developmental biology ,Multiprotein Complexes ,MESH: Mad2 Proteins / metabolism ,MESH: Breast Neoplasms / genetics ,MESH: Bone Neoplasms / drug therapy ,Cisplatin ,Homologous recombination ,MESH: Osteosarcoma / genetics ,MESH: Female ,0301 basic medicine ,DNA End-Joining Repair ,MESH: Proteins / metabolism ,MESH: Dose-Response Relationship, Drug ,chemistry.chemical_compound ,MESH: Osteosarcoma / pathology ,MESH: Breast Neoplasms / pathology ,Homologous Recombination ,Polymerase ,MESH: Breast Neoplasms / drug therapy ,Osteosarcoma ,biology ,Chemistry ,BRCA1 Protein ,DNA damage and repair ,MESH: Poly(ADP-ribose) Polymerase Inhibitors / pharmacology ,MESH: Bone Neoplasms / genetics ,DNA-Binding Proteins ,MESH: Bone Neoplasms / pathology ,Mad2 Proteins ,Female ,MESH: Ovarian Neoplasms / genetics ,Tumor Suppressor p53-Binding Protein 1 ,MESH: Cisplatin / pharmacology ,MESH: Cell Line, Tumor ,Lymphocytes, Null ,[SDV.CAN]Life Sciences [q-bio]/Cancer ,Breast Neoplasms ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,MESH: BRCA1 Protein / genetics ,Poly(ADP-ribose) Polymerase Inhibitors ,Cell Line, Tumor ,MESH: Drug Resistance, Neoplasm* / genetics ,MESH: Mad2 Proteins / genetics ,MESH: Ovarian Neoplasms / pathology ,Animals ,MESH: Mice ,MESH: Osteosarcoma / drug therapy ,Oligonucleotide ,Protective Devices ,Recombinational DNA Repair ,Cell Biology ,MESH: Multiprotein Complexes ,Xenograft Model Antitumor Assays ,HEK293 Cells ,Drug Resistance, Neoplasm ,biology.protein ,MESH: DNA End-Joining Repair ,MESH: DNA-Binding Proteins - Abstract
International audience; BRCA1 deficiencies cause breast, ovarian, prostate and other cancers, and render tumours hypersensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. To understand the resistance mechanisms, we conducted whole-genome CRISPR-Cas9 synthetic-viability/resistance screens in BRCA1-deficient breast cancer cells treated with PARP inhibitors. We identified two previously uncharacterized proteins, C20orf196 and FAM35A, whose inactivation confers strong PARP-inhibitor resistance. Mechanistically, we show that C20orf196 and FAM35A form a complex, 'Shieldin' (SHLD1/2), with FAM35A interacting with single-stranded DNA through its C-terminal oligonucleotide/oligosaccharide-binding fold region. We establish that Shieldin acts as the downstream effector of 53BP1/RIF1/MAD2L2 to promote DNA double-strand break (DSB) end-joining by restricting DSB resection and to counteract homologous recombination by antagonizing BRCA2/RAD51 loading in BRCA1-deficient cells. Notably, Shieldin inactivation further sensitizes BRCA1-deficient cells to cisplatin, suggesting how defining the SHLD1/2 status of BRCA1-deficient tumours might aid patient stratification and yield new treatment opportunities. Highlighting this potential, we document reduced SHLD1/2 expression in human breast cancers displaying intrinsic or acquired PARP-inhibitor resistance.
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- 2018
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7. ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks
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Stephen P. Jackson, Matylda Sczaniecka-Clift, Domenic Pilger, Mukerrem Demir, Michael Woods, Petra Beli, Josep V. Forment, Kosuke Yusa, Stephen T. Durant, Julia Coates, Hannes Ponstingl, Elisabeth Chen, Anna Barros, Matthias Ostermaier, Beiyuan Fu, Gabriel Balmus, Allan Bradley, Fengtang Yang, Francisco Munoz Martinez, Tatjana Stankovic, Mareike Herzog, Emmanouil Metzakopian, David J. Adams, Yaron Galanty, Balmus, Gabriel [0000-0003-2872-4468], Pilger, Domenic [0000-0001-7339-0685], Yang, Fengtang [0000-0002-3573-2354], Chen, Elisabeth [0000-0003-2129-7985], Ponstingl, Hannes [0000-0001-7573-1703], Durant, Stephen T [0000-0003-4209-7499], Galanty, Yaron [0000-0001-7167-9004], Beli, Petra [0000-0001-9507-9820], Forment, Josep V [0000-0002-7797-2583], Jackson, Stephen P [0000-0001-9317-7937], and Apollo - University of Cambridge Repository
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DNA End-Joining Repair ,endocrine system diseases ,Ataxia Telangiectasia Mutated Proteins ,Piperazines ,law.invention ,chemistry.chemical_compound ,DNA Ligase ATP ,Mice ,0302 clinical medicine ,law ,Mice, Inbred NOD ,DNA Breaks, Double-Stranded ,lcsh:Science ,chemistry.chemical_classification ,Mice, Knockout ,0303 health sciences ,biology ,BRCA1 Protein ,Mouse Embryonic Stem Cells ,3. Good health ,Non-homologous end joining ,030220 oncology & carcinogenesis ,Female ,medicine.drug ,DNA Replication ,DNA damage ,Cell Survival ,Science ,Antineoplastic Agents ,Article ,Olaparib ,03 medical and health sciences ,Cell Line, Tumor ,medicine ,Animals ,Humans ,030304 developmental biology ,DNA ligase ,Topoisomerase ,Neoplasms, Experimental ,chemistry ,Drug Resistance, Neoplasm ,Mutation ,biology.protein ,Cancer research ,Suppressor ,Phthalazines ,lcsh:Q ,Topotecan ,CRISPR-Cas Systems ,Homologous recombination - Abstract
Mutations in the ATM tumor suppressor gene confer hypersensitivity to DNA-damaging chemotherapeutic agents. To explore genetic resistance mechanisms, we performed genome-wide CRISPR-Cas9 screens in cells treated with the DNA topoisomerase I inhibitor topotecan. Thus, we here establish that inactivating terminal components of the non-homologous end-joining (NHEJ) machinery or of the BRCA1-A complex specifically confer topotecan resistance to ATM-deficient cells. We show that hypersensitivity of ATM-mutant cells to topotecan or the poly-(ADP-ribose) polymerase (PARP) inhibitor olaparib reflects delayed engagement of homologous recombination at DNA-replication-fork associated single-ended double-strand breaks (DSBs), allowing some to be subject to toxic NHEJ. Preventing DSB ligation by NHEJ, or enhancing homologous recombination by BRCA1-A complex disruption, suppresses this toxicity, highlighting a crucial role for ATM in preventing toxic LIG4-mediated chromosome fusions. Notably, suppressor mutations in ATM-mutant backgrounds are different to those in BRCA1-mutant scenarios, suggesting new opportunities for patient stratification and additional therapeutic vulnerabilities for clinical exploitation., Mutations in the ATM tumor suppressor gene confer hypersensitivity to DNA-damaging chemotherapeutic agents. Here, the authors provide evidence that these hypersensitivities reflect a crucial role for ATM at damaged replication forks being to prevent toxic DNA end-joining leading to chromosome fusions and cell death.
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- 2018
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8. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair
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Viji M. Draviam, Carol V. Robinson, Takashi Ochi, Shahid Mehmood, Jon Travers, Stephen P. Jackson, Qian Wu, Tom L. Blundell, Andrew N. Blackford, Julia Coates, Satpal Jhujh, and Naoka Tamura
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chemistry.chemical_classification ,DNA ligase ,Multidisciplinary ,Ku80 ,DNA repair ,DNA repair protein XRCC4 ,Biology ,Molecular biology ,Double Strand Break Repair ,3. Good health ,Chromatin ,Cell biology ,DNA End-Joining Repair ,chemistry ,Nucleotide excision repair - Abstract
A factor for repairing broken DNA Unprogrammed DNA double-strand breaks are extremely dangerous for genomic stability. Nonhomologous end-joining (NHEJ) repair systems are present in all domains of life and help deal with these potentially lethal lesions. Ochi et al. have discovered a new factor involved in NHEJ by searching for proteins with structural similarities to known NHEJ proteins. Specifically, PAXX, a paralog of XRCC1 and XLF, interacts with a key repair pathway protein, Ku, and helps promote ligation of the broken DNA. Science , this issue p. 185
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- 2015
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9. CtIP tetramer assembly is required for DNA-end resection and repair
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Neil J. Rzechorzek, Owen R. Davies, Stephen P. Jackson, Yaron Galanty, Luca Pellegrini, Rimma Belotserkovskaya, Josep V. Forment, Christopher R Morton, Julia Coates, Meidai Sun, Mukerrem Demir, Forment, Josep [0000-0002-7797-2583], Galanty, Yaron [0000-0001-7167-9004], Jackson, Stephen [0000-0001-9317-7937], Pellegrini, Luca [0000-0002-9300-497X], and Apollo - University of Cambridge Repository
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European community ,DNA Repair ,Double-Strand DNA Breaks ,education ,Library science ,homologous recombination ,Biology ,Crystallography, X-Ray ,Article ,Resection ,03 medical and health sciences ,0302 clinical medicine ,Structural Biology ,Humans ,DNA Breaks, Double-Stranded ,CtIP/RBBP8 ,Molecular Biology ,health care economics and organizations ,030304 developmental biology ,0303 health sciences ,Endodeoxyribonucleases ,gene conversion ,European research ,Extra View ,Nuclear Proteins ,Protein multimerization ,3. Good health ,DNA-end resection ,Carrier protein ,030220 oncology & carcinogenesis ,double-strand DNA break repair ,Protein Multimerization ,Carrier Proteins - Abstract
Homologous recombination (HR) is central to the repair of double-strand DNA breaks that occur in S/G2 phases of the cell cycle. HR relies on the CtIP protein (Ctp1 in fission yeast, Sae2 in budding yeast) for resection of DNA ends, a key step in generating the 3′-DNA overhangs that are required for the HR strand-exchange reaction. Although much has been learned about the biological importance of CtIP in DNA repair, our mechanistic insight into its molecular functions remains incomplete. It has been recently discovered that CtIP and Ctp1 share a conserved tetrameric architecture that is mediated by their N-terminal domains and is critical for their function in HR. The specific arrangement of protein chains in the CtIP/Ctp1 tetramer indicates that an ability to bridge DNA ends might be an important feature of CtIP/Ctp1 function, establishing an intriguing similarity with the known ability of the MRE11-RAD50-NBS1 complex to link DNA ends. Although the exact mechanism of action remains to be elucidated, the remarkable evolutionary conservation of CtIP/Ctp1 tetramerisation clearly points to its crucial role in HR.
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- 2015
10. Detection of functional protein domains by unbiased genome-wide forward genetic screening
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Julia Coates, Stephen P. Jackson, Nicola J Geisler, Fabio Puddu, Mareike Herzog, Josep V. Forment, Herzog, Mareike [0000-0001-9747-2327], Puddu, Fabio [0000-0002-2033-5209], Forment, Josep [0000-0002-7797-2583], Jackson, Stephen [0000-0001-9317-7937], and Apollo - University of Cambridge Repository
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Models, Molecular ,Protein Conformation ,Protein domain ,Poly (ADP-Ribose) Polymerase-1 ,lcsh:Medicine ,Biology ,3101 Biochemistry and Cell Biology ,Genome ,3105 Genetics ,Article ,law.invention ,Olaparib ,3102 Bioinformatics and Computational Biology ,Mice ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Protein Domains ,law ,Cell Line, Tumor ,Genetics ,Animals ,Humans ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,Genetic Testing ,lcsh:Science ,Gene ,Embryonic Stem Cells ,Gene knockout ,030304 developmental biology ,0303 health sciences ,Human Genome ,lcsh:R ,Embryonic stem cell ,Yeast ,DNA Topoisomerases, Type I ,chemistry ,FOS: Biological sciences ,Mutation ,Suppressor ,lcsh:Q ,Camptothecin ,Generic health relevance ,030217 neurology & neurosurgery ,31 Biological Sciences ,Biotechnology ,Genome-Wide Association Study - Abstract
Genetic and chemo-genetic interactions have played key roles in elucidating the molecular mechanisms by which certain chemicals perturb cellular functions. Many studies have employed gene knockout collections or gene disruption/depletion strategies to identify routes for evolving resistance to chemical agents. By contrast, searching for point-mutational genetic suppressors that can identify separation- or gain-of-function mutations, has been limited even in simpler, genetically amenable organisms such as yeast, and has not until recently been possible in mammalian cell culture systems. Here, by demonstrating its utility in identifying suppressors of cellular sensitivity to the drugs camptothecin or olaparib, we describe an approach allowing systematic, large-scale detection of spontaneous or chemically-induced suppressor mutations in yeast and in haploid mouse embryonic stem cells in a short timeframe, and with potential applications in essentially any other haploid system. In addition to its utility for molecular biology research, this protocol can be used to identify drug targets and to predict mechanisms leading to drug resistance. Mapping suppressor mutations on the primary sequence or three-dimensional structures of protein suppressor hits provides insights into functionally relevant protein domains, advancing our molecular understanding of protein functions, and potentially helping to improve drug design and applicability.
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- 2017
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11. Correction: Corrigendum: Coordinated nuclease activities counteract Ku at single-ended DNA double-strand breaks
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Stephen P. Jackson, Julia Coates, Sébastien Britton, Pauline Chanut, and Patrick Calsou
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Double strand ,Exonuclease ,Nuclease ,Multidisciplinary ,biology ,Chemistry ,Science ,Mutant ,General Physics and Astronomy ,General Chemistry ,Molecular biology ,General Biochemistry, Genetics and Molecular Biology ,chemistry.chemical_compound ,biology.protein ,DNA - Abstract
Nature Communications 7: Article number: 12889 (2016); Published: 19 Sep 2016; Updated: 13 Jun 2017 In this Article, the MRE11 exonuclease mutant H63D is consistently referred to incorrectly as H63N. These errors appear in the Results, Methods, Fig. 3, Fig. 4, Fig. 5, Supplementary Fig. 3, Supplementary Table 2 and Supplementary Methods.
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- 2017
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12. A new method for high-resolution imaging of Ku foci to decipher mechanisms of DNA double-strand break repair
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Julia Coates, Sébastien Britton, and Stephen P. Jackson
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DNA Repair ,Ku Autoantigen ,DNA repair ,Biology ,DNA-binding protein ,Tools ,Mice ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Animals ,Humans ,DNA Breaks, Double-Stranded ,High resolution imaging ,Research Articles ,Cells, Cultured ,030304 developmental biology ,Microscopy ,0303 health sciences ,Antigens, Nuclear ,Cell Biology ,DNA repair protein XRCC4 ,Molecular biology ,Double Strand Break Repair ,3. Good health ,Cell biology ,DNA-Binding Proteins ,chemistry ,030220 oncology & carcinogenesis ,DECIPHER ,DNA - Abstract
A combination of RNase- and detergent-based preextraction with high-resolution microscopy allows the detection of Ku and other DNA repair proteins at single double-strand breaks in cells., DNA double-strand breaks (DSBs) are the most toxic of all genomic insults, and pathways dealing with their signaling and repair are crucial to prevent cancer and for immune system development. Despite intense investigations, our knowledge of these pathways has been technically limited by our inability to detect the main repair factors at DSBs in cells. In this paper, we present an original method that involves a combination of ribonuclease- and detergent-based preextraction with high-resolution microscopy. This method allows direct visualization of previously hidden repair complexes, including the main DSB sensor Ku, at virtually any type of DSB, including those induced by anticancer agents. We demonstrate its broad range of applications by coupling it to laser microirradiation, super-resolution microscopy, and single-molecule counting to investigate the spatial organization and composition of repair factories. Furthermore, we use our method to monitor DNA repair and identify mechanisms of repair pathway choice, and we show its utility in defining cellular sensitivities and resistance mechanisms to anticancer agents.
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- 2013
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13. Genome-wide genetic screening with chemically mutagenized haploid embryonic stem cells
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Stephen P. Jackson, Mareike Herzog, Bianca V. Gapp, Josep V. Forment, Julia Coates, David J. Adams, Tomasz Konopka, Sebastian M.B. Nijman, and Thomas M. Keane
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0301 basic medicine ,ved/biology.organism_classification_rank.species ,Mutagenesis (molecular biology technique) ,Synthetic lethality ,Biology ,Genome ,Article ,Cell Line ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Animals ,Genetic Testing ,Model organism ,Molecular Biology ,Genetics ,ved/biology ,Point mutation ,Mouse Embryonic Stem Cells ,Cell Biology ,Embryonic stem cell ,3. Good health ,030104 developmental biology ,Mutagenesis ,Stem cell ,Chemical genetics ,030217 neurology & neurosurgery - Abstract
A genetic screening approach using chemically mutagenized haploid mouse embryonic stem cells combined with next-generation sequencing identified recessive suppressor point mutations that elicit resistance to 6-thioguanine. In model organisms, classical genetic screening via random mutagenesis provides key insights into the molecular bases of genetic interactions, helping to define synthetic lethality, synthetic viability and drug-resistance mechanisms. The limited genetic tractability of diploid mammalian cells, however, precludes this approach. Here, we demonstrate the feasibility of classical genetic screening in mammalian systems by using haploid cells, chemical mutagenesis and next-generation sequencing, providing a new tool to explore mammalian genetic interactions.
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- 2016
14. RNF4, a SUMO-targeted ubiquitin E3 ligase, promotes DNA double-strand break repair
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Yaron Galanty, Julia Coates, Stephen P. Jackson, and Rimma Belotserkovskaya
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Proteasome Endopeptidase Complex ,DNA Repair ,DNA repair ,Ubiquitin-Protein Ligases ,cells ,genetic processes ,SUMO protein ,DNA, Single-Stranded ,Cell Cycle Proteins ,Biology ,Histones ,03 medical and health sciences ,DDB1 ,0302 clinical medicine ,Ubiquitin ,Cell Line, Tumor ,Replication Protein A ,Genetics ,Humans ,DNA Breaks, Double-Stranded ,Replication protein A ,Adaptor Proteins, Signal Transducing ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,DNA ligase ,Nuclear Proteins ,DNA repair protein XRCC4 ,Molecular biology ,Ubiquitin ligase ,enzymes and coenzymes (carbohydrates) ,chemistry ,030220 oncology & carcinogenesis ,Trans-Activators ,health occupations ,biology.protein ,Rad51 Recombinase ,Transcription Factors ,Research Paper ,Developmental Biology - Abstract
Protein ubiquitylation and sumoylation play key roles in regulating cellular responses to DNA double-strand breaks (DSBs). Here, we show that human RNF4, a small ubiquitin-like modifier (SUMO)-targeted ubiquitin E3 ligase, is recruited to DSBs in a manner requiring its SUMO interaction motifs, the SUMO E3 ligases PIAS1 and PIAS4, and various DSB-responsive proteins. Furthermore, we reveal that RNF4 depletion impairs ubiquitin adduct formation at DSB sites and causes persistent histone H2AX phosphorylation (γH2AX) associated with defective DSB repair, hypersensitivity toward DSB-inducing agents, and delayed recovery from radiation-induced cell cycle arrest. We establish that RNF4 regulates turnover of the DSB-responsive factors MDC1 and replication protein A (RPA) at DNA damage sites and that RNF4-depleted cells fail to effectively replace RPA by the homologous recombination factors BRCA2 and RAD51 on resected DNA. Consistent with previous data showing that RNF4 targets proteins to the proteasome, we show that the proteasome component PSMD4 is recruited to DNA damage sites in a manner requiring its ubiquitin-interacting domains, RNF4 and RNF8. Finally, we establish that PSMD4 binds MDC1 and RPA1 in a DNA damage-induced, RNF4-dependent manner and that PSMD4 depletion cause MDC1 and γH2AX persistence in irradiated cells. RNF4 thus operates as a DSB response factor at the crossroads between the SUMO and ubiquitin systems.
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- 2012
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15. Replication stress induces 53BP1-containing OPT domains in G1 cells
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Daniela S. Dimitrova, Rimma Belotserkovskaya, Stephen P. Jackson, Peter Fraser, Charles R. Bradshaw, Sophie E. Polo, Jeanine A. Harrigan, and Julia Coates
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Aphidicolin ,DNA Replication ,Transcription, Genetic ,DNA damage ,Biology ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Control of chromosome duplication ,Humans ,Research Articles ,Cells, Cultured ,030304 developmental biology ,0303 health sciences ,Chromosomal fragile site ,DNA replication ,G1 Phase ,Intracellular Signaling Peptides and Proteins ,Cell Biology ,G2-M DNA damage checkpoint ,Molecular biology ,3. Good health ,chemistry ,030220 oncology & carcinogenesis ,Origin recognition complex ,Tumor Suppressor p53-Binding Protein 1 ,Chromatin immunoprecipitation ,Octamer Transcription Factor-1 ,Transcription Factors - Abstract
53BP1-OPT domains, nuclear bodies that arise in G1 cells at sites of DNA damage induced by incomplete DNA replication, preferentially localize to chromosomal common fragile sites., Chromosomal deletions and rearrangements in tumors are often associated with common fragile sites, which are specific genomic loci prone to gaps and breaks in metaphase chromosomes. Common fragile sites appear to arise through incomplete DNA replication because they are induced after partial replication inhibition by agents such as aphidicolin. Here, we show that in G1 cells, large nuclear bodies arise that contain p53 binding protein 1 (53BP1), phosphorylated H2AX (γH2AX), and mediator of DNA damage checkpoint 1 (MDC1), as well as components of previously characterized OPT (Oct-1, PTF, transcription) domains. Notably, we find that incubating cells with low aphidicolin doses increases the incidence and number of 53BP1-OPT domains in G1 cells, and by chromatin immunoprecipitation and massively parallel sequencing analysis of γH2AX, we demonstrate that OPT domains are enriched at common fragile sites. These findings invoke a model wherein incomplete DNA synthesis during S phase leads to a DNA damage response and formation of 53BP1-OPT domains in the subsequent G1.
- Published
- 2011
16. Mammalian SUMO E3-ligases PIAS1 and PIAS4 promote responses to DNA double-strand breaks
- Author
-
Sophie E. Polo, Julia Coates, Kyle M. Miller, Yaron Galanty, Stephen P. Jackson, and Rimma Belotserkovskaya
- Subjects
0303 health sciences ,Multidisciplinary ,biology ,DNA repair ,SUMO protein ,SUMO2 ,Article ,Ubiquitin ligase ,Cell biology ,MDC1 ,enzymes and coenzymes (carbohydrates) ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Ubiquitin ,H2AFX ,chemistry ,Biochemistry ,030220 oncology & carcinogenesis ,biology.protein ,DNA ,030304 developmental biology - Abstract
The occurrence of a double-strand break in DNA activates a complex series of events that recruit to the break many proteins involved in its repair. A number of these proteins are modified by addition of a small protein, SUMO; this modification is performed SUMO ligases. In this work, Jackson and colleagues show that two such ligases, PIAS1 and PIAS4, add various SUMOs onto DNA repair proteins at double-strand breaks. The PIAS ligases are recruited via their SAP domains, and their activity is required for effective repair. SUMOylation by PIAS1 and PIAS4 is also necessary for the further modification of certain repair factors by ubiquitin, a somewhat larger protein adduct related to SUMO. The successive SUMOylation and ubiquitylation of repair proteins regulates their targeting to, and repair of, DNA breaks. Following the formation of a DNA double-strand break (DSB), cells activate the DNA-damage response and recruit a number of proteins to the lesion. Some of these proteins are modified by the attachment of small ubiquitin-related modifier (SUMO). Here, SUMO1, SUMO2 and SUMO3 are shown to accumulate at DSB sites in mammalian cells. SUMO1 and SUMO2/3 accrual requires the E3 ligase enzymes PIAS4 and PIAS1, which promote DSB repair. DNA double-strand breaks (DSBs) are highly cytotoxic lesions that are generated by ionizing radiation and various DNA-damaging chemicals. Following DSB formation, cells activate the DNA-damage response (DDR) protein kinases ATM, ATR and DNA-PK (also known as PRKDC). These then trigger histone H2AX (also known as H2AFX) phosphorylation and the accumulation of proteins such as MDC1, 53BP1 (also known as TP53BP1), BRCA1, CtIP (also known as RBBP8), RNF8 and RNF168/RIDDLIN into ionizing radiation-induced foci (IRIF) that amplify DSB signalling and promote DSB repair1,2. Attachment of small ubiquitin-related modifier (SUMO) to target proteins controls diverse cellular functions3,4,5,6. Here, we show that SUMO1, SUMO2 and SUMO3 accumulate at DSB sites in mammalian cells, with SUMO1 and SUMO2/3 accrual requiring the E3 ligase enzymes PIAS4 and PIAS1. We also establish that PIAS1 and PIAS4 are recruited to damage sites via mechanisms requiring their SAP domains, and are needed for the productive association of 53BP1, BRCA1 and RNF168 with such regions. Furthermore, we show that PIAS1 and PIAS4 promote DSB repair and confer ionizing radiation resistance. Finally, we establish that PIAS1 and PIAS4 are required for effective ubiquitin-adduct formation mediated by RNF8, RNF168 and BRCA1 at sites of DNA damage7,8,9,10,11. These findings thus identify PIAS1 and PIAS4 as components of the DDR and reveal how protein recruitment to DSB sites is controlled by coordinated SUMOylation and ubiquitylation.
- Published
- 2009
- Full Text
- View/download PDF
17. Trail of Tears
- Author
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Julia Coates and Julia Coates
- Subjects
- Trail of Tears, 1838-1839--Juvenile literature, Indians of North America--Relocation--Southern, Cherokee Indians--History--Juvenile literature, Cherokee Indians--Relocation--Juvenile literat, SOCIAL SCIENCE / Ethnic Studies / Native American, HISTORY / Native American
- Abstract
This book covers a critical event in U.S. history: the period of Indian removal and resistance from 1817 to 1839, documenting the Cherokee experience as well as Jacksonian policy and Native-U.S. relations.This book provides an outstanding resource that introduces readers to Indian removal and resistance, and supports high school curricula as well as the National Standards for U.S. History (Era 4: Expansion and Reform). Focusing specifically on the Trail of Tears and the experiences of the Cherokee Nation while also covering earlier events and the aftermath of removal, the clearly written, topical chapters follow the events as they unfolded in Alabama, Georgia, North Carolina, and Tennessee, as well as the New England region and Washington, DC.Written by a tribal council representative of the Cherokee Nation, this book offers the most current perspectives, incorporating key issues of assimilation, sovereignty, and Cherokee resistance and resilience throughout. The text also addresses important topics that predate removal in the 19th century, such as the first treaty between the Cherokees and Great Britain in 1721, the French and Indian Wars, the American Revolution, proclamation of Cherokee nationality in the 1791 Treaty of Holston, and the U.S. Constitution.
- Published
- 2014
18. Trail of Tears
- Author
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Julia Coates
- Published
- 2015
- Full Text
- View/download PDF
19. Systematic E2 screening reveals a UBE2D-RNF138-CtIP axis promoting DNA repair
- Author
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Yaron Galanty, Mukerrem Demir, Julia Coates, Matthew Cornwell, Satpal Jhujh, Petra Beli, Stephen P. Jackson, Christine K. Schmidt, Matylda Sczaniecka-Clift, Galanty, Yaron [0000-0001-7167-9004], Jackson, Stephen [0000-0001-9317-7937], and Apollo - University of Cambridge Repository
- Subjects
Genome instability ,DNA repair ,Cell Survival ,Ubiquitin-Protein Ligases ,Green Fluorescent Proteins ,Immunoblotting ,Ubiquitin-conjugating enzyme ,medicine.disease_cause ,Article ,Ubiquitin ,Cell Line, Tumor ,medicine ,Humans ,DNA Breaks, Double-Stranded ,Endodeoxyribonucleases ,Microscopy, Confocal ,biology ,Cell Cycle ,Ubiquitination ,Nuclear Proteins ,Recombinational DNA Repair ,Cell Biology ,Cell cycle ,Ubiquitin ligase ,Cell biology ,HEK293 Cells ,Ubiquitin-Conjugating Enzymes ,biology.protein ,RNA Interference ,Homologous recombination ,Carcinogenesis ,Carrier Proteins - Abstract
Ubiquitylation is crucial for proper cellular responses to DNA double-strand breaks (DSBs). If unrepaired, these highly cytotoxic lesions cause genome instability, tumourigenesis, neurodegeneration or premature ageing. Here, we conduct a comprehensive, multilayered screen to systematically profile all human ubiquitin E2-enzymes for impacts on cellular DSB responses. Applying a widely applicable approach, we use an exemplary E2 family, UBE2Ds, to identify ubiquitylation-cascade components downstream of E2s. Thus, we uncover the nuclear E3-ligase RNF138 as a key homologous recombination (HR)-promoting factor that functions with UBE2Ds in cells. Mechanistically, UBE2Ds and RNF138 accumulate at DNA-damage sites and act at early resection stages by promoting CtIP ubiquitylation and accrual. This work supplies insights into regulation of DSB repair by HR. Moreover, it provides a rich information resource on E2s that can be exploited by follow-on studies.
- Published
- 2015
20. Single-stranded DNA oligomers stimulate error-prone alternative repair of DNA double-strand breaks through hijacking Ku protein
- Author
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Ying, Yuan, Sébastien, Britton, Christine, Delteil, Julia, Coates, Stephen P, Jackson, Nadia, Barboule, Philippe, Frit, and Patrick, Calsou
- Subjects
DNA-Binding Proteins ,DNA End-Joining Repair ,Oligodeoxyribonucleotides ,fungi ,DNA, Single-Stranded ,Humans ,Antigens, Nuclear ,DNA Breaks, Double-Stranded ,DNA ,Genome Integrity, Repair and Replication ,Ku Autoantigen ,HeLa Cells - Abstract
In humans, DNA double-strand breaks (DSBs) are repaired by two mutually-exclusive mechanisms, homologous recombination or end-joining. Among end-joining mechanisms, the main process is classical non-homologous end-joining (C-NHEJ) which relies on Ku binding to DNA ends and DNA Ligase IV (Lig4)-mediated ligation. Mostly under Ku- or Lig4-defective conditions, an alternative end-joining process (A-EJ) can operate and exhibits a trend toward microhomology usage at the break junction. Homologous recombination relies on an initial MRN-dependent nucleolytic degradation of one strand at DNA ends. This process, named DNA resection generates 3′ single-stranded tails necessary for homologous pairing with the sister chromatid. While it is believed from the current literature that the balance between joining and recombination processes at DSBs ends is mainly dependent on the initiation of resection, it has also been shown that MRN activity can generate short single-stranded DNA oligonucleotides (ssO) that may also be implicated in repair regulation. Here, we evaluate the effect of ssO on end-joining at DSB sites both in vitro and in cells. We report that under both conditions, ssO inhibit C-NHEJ through binding to Ku and favor repair by the Lig4-independent microhomology-mediated A-EJ process.
- Published
- 2015
21. Damage-induced BRCA1 phosphorylation by Chk2 contributes to the timing of end resection
- Author
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Hui Kuan Lin, Huai-Chin Chiang, Chu-Xia Deng, Balaji Parameswaran, Richard Baer, Rong Li, Yunzhe Lu, Tanya T. Paull, Yanfen Hu, and Julia Coates
- Subjects
Time Factors ,endocrine system diseases ,Ataxia Telangiectasia Mutated Proteins ,Biology ,Poly(ADP-ribose) Polymerase Inhibitors ,environment and public health ,Mice ,Replication Protein A ,Animals ,Humans ,DNA Breaks, Double-Stranded ,Phosphorylation ,skin and connective tissue diseases ,Molecular Biology ,Replication protein A ,Kinase ,BRCA1 Protein ,Protein Stability ,Ubiquitination ,Cell Biology ,Cell cycle ,DNA repair protein XRCC4 ,Fibroblasts ,enzymes and coenzymes (carbohydrates) ,Checkpoint Kinase 2 ,HEK293 Cells ,MRN complex ,Rad50 ,Multiprotein Complexes ,Cancer research ,biological phenomena, cell phenomena, and immunity ,Homologous recombination ,Developmental Biology ,Reports ,DNA Damage - Abstract
The BRCA1 tumor suppressor plays an important role in homologous recombination (HR)-mediated DNA double-strand-break (DSB) repair. BRCA1 is phosphorylated by Chk2 kinase upon γ-irradiation, but the role of Chk2 phosphorylation is not understood. Here, we report that abrogation of Chk2 phosphorylation on BRCA1 delays end resection and the dispersion of BRCA1 from DSBs but does not affect the assembly of Mre11/Rad50/NBS1 (MRN) and CtIP at DSBs. Moreover, we show that BRCA1 is ubiquitinated by SCF(Skp2) and that abrogation of Chk2 phosphorylation impairs its ubiquitination. Our study suggests that BRCA1 is more than a scaffold protein to assemble HR repair proteins at DSBs, but that Chk2 phosphorylation of BRCA1 also serves as a built-in clock for HR repair of DSBs. BRCA1 is known to inhibit Mre11 nuclease activity. SCF(Skp2) activity appears at late G1 and peaks at S/G2, and is known to ubiquitinate phosphodegron motifs. The removal of BRCA1 from DSBs by SCF(Skp2)-mediated degradation terminates BRCA1-mediated inhibition of Mre11 nuclease activity, allowing for end resection and restricting the initiation of HR to the S/G2 phases of the cell cycle.
- Published
- 2015
22. Damage-induced BRCA1 phosphorylation by Chk2 contributes to the timing of end resection
- Author
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Balaji Parameswaran, Huai-Chin Chiang, Yunzhe Lu, Julia Coates, Chu-Xia Deng, Richard Baer, Hui-Kuan Lin, Rong Li, Tanya T Paull, Yanfen Hu, Balaji Parameswaran, Huai-Chin Chiang, Yunzhe Lu, Julia Coates, Chu-Xia Deng, Richard Baer, Hui-Kuan Lin, Rong Li, Tanya T Paull, and Yanfen Hu
- Published
- 2015
- Full Text
- View/download PDF
23. CDK targeting of NBS1 promotes DNA-end resection, replication restart and homologous recombination
- Author
-
Jiri Bartek, Jiri Lukas, Julia Coates, Jacob Falck, Martin Mistrik, Josep V. Forment, and Stephen P. Jackson
- Subjects
DNA Replication ,DNA Repair ,DNA repair ,Cell Cycle Proteins ,Biochemistry ,03 medical and health sciences ,0302 clinical medicine ,MRE11 Homologue Protein ,Cyclin-dependent kinase ,Cell Line, Tumor ,CDC2 Protein Kinase ,Genetics ,Serine ,Humans ,DNA Breaks, Double-Stranded ,DNA Cleavage ,Phosphorylation ,Homologous Recombination ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,biology ,Scientific Reports ,DNA replication ,Nuclear Proteins ,Cell cycle ,Molecular biology ,Acid Anhydride Hydrolases ,DNA-Binding Proteins ,enzymes and coenzymes (carbohydrates) ,DNA Repair Enzymes ,MRN complex ,Amino Acid Substitution ,030220 oncology & carcinogenesis ,biology.protein ,Mutagenesis, Site-Directed ,biological phenomena, cell phenomena, and immunity ,Homologous recombination ,Protein Processing, Post-Translational - Abstract
The conserved MRE11–RAD50–NBS1 (MRN) complex is an important sensor of DNA double-strand breaks (DSBs) and facilitates DNA repair by homologous recombination (HR) and end joining. Here, we identify NBS1 as a target of cyclin-dependent kinase (CDK) phosphorylation. We show that NBS1 serine 432 phosphorylation occurs in the S, G2 and M phases of the cell cycle and requires CDK activity. This modification stimulates MRN-dependent conversion of DSBs into structures that are substrates for repair by HR. Impairment of NBS1 phosphorylation not only negatively affects DSB repair by HR, but also prevents resumption of DNA replication after replication-fork stalling. Thus, CDK-mediated NBS1 phosphorylation defines a molecular switch that controls the choice of repair mode for DSBs.
- Published
- 2012
24. Characterisation and correction of a mammalian cell mutant defective in late step of base excision repair
- Author
-
Marcia Hall, Anderson J. Ryan, Robert T. Johnson, A. L. Evans, Julia Coates, and Simon Bouffler
- Subjects
Alkylating Agents ,DNA Repair ,DNA damage ,DNA repair ,information science ,Sulfuric Acid Esters ,Biology ,Transfection ,O(6)-Methylguanine-DNA Methyltransferase ,Bacterial Proteins ,Escherichia coli ,Genetics ,Animals ,Humans ,AP site ,Cell Line, Transformed ,Recombination, Genetic ,chemistry.chemical_classification ,DNA ligase ,Deer ,Escherichia coli Proteins ,fungi ,O-6-methylguanine-DNA methyltransferase ,DNA ,Methyltransferases ,Cell Biology ,General Medicine ,Base excision repair ,Molecular biology ,Phenotype ,Cell killing ,chemistry ,DNA glycosylase ,Mutation ,DNA Damage ,Plasmids ,Transcription Factors - Abstract
An Indian muntjac cell line, SVM, is unusually sensitive to cell killing induced by a range of alkylating agents. Cells transfected with the Escherichia coli ada gene or human genomic DNA have allowed the response of SVM to alkylating agents to be dissociated into two distinct components. Thus, in SVM, which expresses very low levels of alkyltransferase (AT), O6-alkylguanine appears to be the major cytotoxic, clastogenic, and recombinogenic lesion following exposure to agents such as methylnitrosourea (MNU). However, SVM is also very sensitive to agents such as dimethylsulfate (DMS), which produce only very low levels of O6-methylguanine damage. Sensitivity to DMS resides in an inability to complete base excision repair, with the appearance of persistent single-strand DNA breaks (SSBs), and does not appear to involve defects in glycosylase, apurinic/apyrimidinic endonuclease, or DNA ligase activities. Another, possibly related, phenotypic trait in SVM is its limited ability to ligate transfected linear plasmid DNA. Transfectants of SVM, harboring human DNA sequences, show a significant correction of DMS-induced cytotoxicity and clastogenicity and a reduction in the levels of DMS-induced DNA SSBs. The DMS-resistant transfectants have an increased ability to ligate linear plasmid DNA, and also express AT, making these lines resistant to alkylating agents such as MNU. These results suggest that cells possess a mechanism that regulates AT expression, plasmid break-joining ability, and certain aspects of base excision repair. Transfectants of SVM containing human DNA provide a means to isolate genes involved in a coordinate response to alkylation damage.
- Published
- 1992
- Full Text
- View/download PDF
25. Human CtIP promotes DNA end resection
- Author
-
Shuang Fu, Julia Coates, Richard Baer, Stephen P. Jackson, Claudia Lukas, Jiri Lukas, Alessandro A. Sartori, Jiri Bartek, Martin Mistrik, University of Zurich, and Jackson, S P
- Subjects
G2 Phase ,Saccharomyces cerevisiae Proteins ,DNA Repair ,DNA repair ,genetic processes ,DNA, Single-Stranded ,Cell Cycle Proteins ,Ataxia Telangiectasia Mutated Proteins ,Biology ,Protein Serine-Threonine Kinases ,Article ,Replication fork protection ,S Phase ,Evolution, Molecular ,MRE11 Homologue Protein ,Cell Line, Tumor ,Humans ,DNA Breaks, Double-Stranded ,Replication protein A ,Conserved Sequence ,Genetics ,Recombination, Genetic ,1000 Multidisciplinary ,Multidisciplinary ,Endodeoxyribonucleases ,10061 Institute of Molecular Cancer Research ,fungi ,Nuclear Proteins ,DNA ,Endonucleases ,Cell biology ,DNA-Binding Proteins ,enzymes and coenzymes (carbohydrates) ,Microhomology-mediated end joining ,MRN complex ,Rad50 ,health occupations ,570 Life sciences ,biology ,biological phenomena, cell phenomena, and immunity ,Homologous recombination ,Carrier Proteins - Abstract
In the S and G2 phases of the cell cycle, DNA double-strand breaks (DSBs) are processed into single-stranded DNA, triggering ATR-dependent checkpoint signalling and DSB repair by homologous recombination. Previous work has implicated the MRE11 complex in such DSB-processing events. Here, we show that the human CtIP (RBBP8) protein confers resistance to DSB-inducing agents and is recruited to DSBs exclusively in the S and G2 cell-cycle phases. Moreover, we reveal that CtIP is required for DSB resection, and thereby for recruitment of replication protein A (RPA) and the protein kinase ATR to DSBs, and for the ensuing ATR activation. Furthermore, we establish that CtIP physically and functionally interacts with the MRE11 complex, and that both CtIP and MRE11 are required for efficient homologous recombination. Finally, we reveal that CtIP has sequence homology with Sae2, which is involved in MRE11-dependent DSB processing in yeast. These findings establish evolutionarily conserved roles for CtIP-like proteins in controlling DSB resection, checkpoint signalling and homologous recombination.
- Published
- 2007
26. Becoming Indian: The Struggle over Cherokee Identity in the Twenty-First Century Circe Sturm. Santa Fe: School for Advanced Research Press, 2011. 280 pp
- Author
-
Julia Coates
- Subjects
History ,Arts and Humanities (miscellaneous) ,Cherokee ,Anthropology ,language ,Twenty-First Century ,Identity (social science) ,language.human_language - Published
- 2013
- Full Text
- View/download PDF
27. Conserved modes of recruitment of ATM, ATR and DNA-PKcs to sites of DNA damage
- Author
-
Stephen P. Jackson, Jacob Falck, and Julia Coates
- Subjects
DNA damage ,DNA repair ,Amino Acid Motifs ,Molecular Sequence Data ,Cell Cycle Proteins ,Ataxia Telangiectasia Mutated Proteins ,DNA-Activated Protein Kinase ,Biology ,Protein Serine-Threonine Kinases ,Phosphatidylinositol 3-Kinases ,Cricetinae ,Animals ,Humans ,CHEK1 ,Amino Acid Sequence ,Phosphorylation ,Ku Autoantigen ,DNA-PKcs ,Conserved Sequence ,Multidisciplinary ,Binding Sites ,Tumor Suppressor Proteins ,DNA replication ,Nuclear Proteins ,Antigens, Nuclear ,DNA ,MDC1 ,Cell biology ,DNA-Binding Proteins ,enzymes and coenzymes (carbohydrates) ,Protein Transport ,MRN complex ,Biochemistry ,biological phenomena, cell phenomena, and immunity ,Ataxia telangiectasia and Rad3 related ,DNA Damage ,Protein Binding ,Signal Transduction - Abstract
Ataxia-telangiectasia mutated (ATM), ataxia-telangiectasia and Rad3-related (ATR) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) are members of the phosphoinositide-3-kinase-related protein kinase (PIKK) family, and are rapidly activated in response to DNA damage. ATM and DNA-PKcs respond mainly to DNA double-strand breaks, whereas ATR is activated by single-stranded DNA and stalled DNA replication forks. In all cases, activation involves their recruitment to the sites of damage. Here we identify related, conserved carboxy-terminal motifs in human Nbs1, ATRIP and Ku80 proteins that are required for their interaction with ATM, ATR and DNA-PKcs, respectively. These motifs are essential not only for efficient recruitment of ATM, ATR and DNA-PKcs to sites of damage, but are also critical for ATM-, ATR- and DNA-PKcs-mediated signalling events that trigger cell cycle checkpoints and DNA repair. Our findings reveal that recruitment of these PIKKs to DNA lesions occurs by common mechanisms through an evolutionarily conserved motif, and provide direct evidence that PIKK recruitment is required for PIKK-dependent DNA-damage signalling.
- Published
- 2004
28. p53 prevents the accumulation of double-strand DNA breaks at stalled-replication forks induced by UV in human cells
- Author
-
Stephen P. Jackson, Lorraine H. Toji, Duncan J. Clarke, Michal Goldberg, Robert T. Johnson, Shoshana Squires, and Julia Coates
- Subjects
Genome instability ,DNA Replication ,Time Factors ,DNA Repair ,Cell Survival ,Ultraviolet Rays ,Dimer ,Cell ,Pyrimidine dimer ,Biology ,medicine.disease_cause ,Models, Biological ,chemistry.chemical_compound ,Multienzyme Complexes ,Cell Line, Tumor ,medicine ,Humans ,Molecular Biology ,Cells, Cultured ,Gel electrophoresis ,Electrophoresis, Agar Gel ,Mutation ,Endodeoxyribonucleases ,Genome, Human ,Chromosome ,Dose-Response Relationship, Radiation ,Cell Biology ,DNA ,Fibroblasts ,Molecular biology ,Cell biology ,enzymes and coenzymes (carbohydrates) ,Kinetics ,medicine.anatomical_structure ,chemistry ,Gamma Rays ,Pyrimidine Dimers ,Tumor Suppressor Protein p53 ,Developmental Biology ,DNA Damage - Abstract
To investigate the mechanism by which UV irradiation causes S-phase-dependent chromosome aberrations and thereby genomic instability, we have developed an assay to study the DNA structure of replication forks (RFs) in UV-irradiated mammalian cells, using pulse-field gel electrophoresis for the DNA analysis. We demonstrate that replication stalling at UV-induced pyrimidine dimers results in the formation of single-strand DNA (ssDNA) regions and incomplete RF structures. In normal and in nucleotide-excision-repair (NER)-defective xeroderma pimentosum (XP) cells, stalling at dimers is rapid and prolonged and recovery depends on dimer repair or bypass. By contrast, XP variant (XPV) cells, defective in replication of a UV-damaged template due to mutation of bypass-polymerase epsilon, fail to arrest at dimers, resulting in a much higher frequency of ssDNA regions in the stalled RFs. We show that the stability of UV-arrested RFs depends directly on functional p53, and indirectly on NER and pol eta. In p53-deficient cells, the stalled sites give rise to double-strand DNA breaks (DSBs), at a frequency inversely correlated with repair capacity of the cell. In normal cells only a fraction of the stalled sites give rise to DSBs, while in XPASV, XPDSV and also XPVSV, all the sites do. XPVSV cells, although repair proficient, accumulate almost double the number of DSBs, suggesting that a high frequency of ssDNA regions in UV-arrested forks cause RF instability. These replication-associated DSBs do not accumulate in p53-proficient human cells. We propose that a major mechanism by which p53 maintains genome stability is the prevention of DSB accumulation at long-lived ssDNA regions in stalled-replication forks.
- Published
- 2004
29. Unearthing Indian Land: Living with the Legacies of Allotment
- Author
-
Julia Coates
- Subjects
Cultural Studies ,History ,Anthropology - Published
- 2012
- Full Text
- View/download PDF
30. New patterns of bulk DNA repair in ultraviolet irradiated mouse embryo carcinoma cells following differentiation
- Author
-
Robert T. Johnson, David L. Mitchell, Julia Coates, Miklós Sántha, Milka Georgieva, István Raskó, K. Burg, and Gabriella Farkas
- Subjects
DNA Repair ,DNA repair ,Ultraviolet Rays ,Cellular differentiation ,Genes, myc ,Biology ,Cyclobutane ,chemistry.chemical_compound ,Deoxyribonuclease (Pyrimidine Dimer) ,Mice ,Viral Proteins ,Cricetinae ,Genetics ,Tumor Cells, Cultured ,Animals ,Bacteriophage T4 ,Humans ,Endodeoxyribonucleases ,Teratoma ,Cell Differentiation ,Cell Biology ,General Medicine ,DNA ,Molecular biology ,Genes, src ,P19 cell ,chemistry ,Cell culture ,Pyrimidine Dimers ,Stem cell ,Nucleotide excision repair - Abstract
Mouse embryocarcinoma stem cells differentiate in culture, given the appropriate induction. We examined whether these cells could provide information about the regulation of nucleotide excision repair in relation to differentiation by measuring the rate-limiting incision step, the removal of cyclobutane dimers and (6-4) photoproducts from the genome as a whole and the effect of the bacteriophage T4 endonuclease (denV) gene on repair in differentiated cells. It was found that differentiation is accompanied by a marked decline in the early incision ability after UV irradiation (sixfold for P19, fourfold for PCC7 and twofold for F9), and we measured, in parallel, the loss of two common UV photoproducts [cyclobutane dimers and (6-4) photoproducts] from P19 cells. After differentiation, the excellent overall cyclobutane dimer repair capacity of proliferating cells (84% removal in 24 h) is lost (no removal in 24 h), while removal of (6-4) photoproducts, although normal at 24 h (94%), is much slower than in undifferentiated P19 at 3 h (no removal versus 64%). The presence of the denV gene greatly stimulates the repair of cyclobutane dimers in undifferentiated P19 cells (94% removal at 3 h versus 40%) and also in differentiated cells (50% removal at 24 h versus no removal). The denV gene also stimulates the early repair of (6-4) photoproducts in both differentiated and undifferentiated cells.
- Published
- 1993
31. Murine radiation myeloid leukaemogenesis: relationship between interstitial telomere-like sequences and chromosome 2 fragile sites
- Author
-
Julia Coates, Roger Cox, Simon Bouffler, David Papworth, and Andy Silver
- Subjects
Cancer Research ,Inverted repeat ,Molecular Sequence Data ,Clone (cell biology) ,Biology ,Mice ,Tandem repeat ,Genetics ,Animals ,Gene ,In Situ Hybridization, Fluorescence ,Repetitive Sequences, Nucleic Acid ,Chromosome Aberrations ,Leukemia, Radiation-Induced ,Base Sequence ,Chromosomal fragile site ,Chromosome Fragile Sites ,Chromosome Fragility ,Breakpoint ,Chromosome ,Telomere ,Molecular biology ,Leukemia, Myeloid ,Acute Disease ,Mice, Inbred CBA - Abstract
While the specific nature of chromosomal fragile sites and their relationship to human leukaemogenesis remain obscure, there is evidence that chromosomal fragility may, in some circumstances, be associated with telomere-like repeat sequences and that chromosome 2 fragility in the mouse is involved in the initiation of myeloid leukaemia by ionising radiation. Here we describe the molecular cloning and characterisation of two murine telomere-like sequences, one having an inverted repeat structure and the other a simple tandem repeat organisation. The inverted telomere repeat clone generates an in situ chromosome 2 hybridisation pattern very similar to the distribution of the radiation-sensitive fragile sites previously found to be associated with leukaemogenic initiation. Furthermore, statistical comparison of the distributions of radiation induced breakpoints and sites of inverted telomere repeat hybridization indicates concordance at all chromosome 2 sites excluding the terminal regions. These data are discussed with respect to mechanisms of radiation-induced, site-specific chromosome 2 rearrangement and their implications for leukaemogenic initiation. © 1993 Wiley-Liss, Inc.
- Published
- 1993
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