51
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Yang KS, Kohler RH, Landon M, Giedt R, Weissleder R. Single cell resolution in vivo imaging of DNA damage following PARP inhibition. Sci Rep 2015; 5:10129. [PMID: 25984718 PMCID: PMC4434991 DOI: 10.1038/srep10129] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 03/24/2015] [Indexed: 11/17/2022] Open
Abstract
Targeting DNA repair pathways is a powerful strategy to treat cancers. To gauge efficacy in vivo, typical response markers include late stage effects such as tumor shrinkage, progression free survival, or invasive repeat biopsies. These approaches are often difficult to answer critical questions such as how a given drug affects single cell populations as a function of dose and time, distance from microvessels or how drug concentration (pharmacokinetics) correlates with DNA damage (pharmacodynamics). Here, we established a single-cell in vivo pharmacodynamic imaging read-out based on a truncated 53BP1 double-strand break reporter to determine whether or not poly(ADP-ribose) polymerase (PARP) inhibitor treatment leads to accumulation of DNA damage. Using this reporter, we show that not all PARP inhibitor treated tumors incur an increase in DNA damage. The method provides a framework for single cell analysis of cancer therapeutics in vivo.
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Affiliation(s)
- Katherine S Yang
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Rainer H Kohler
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Matthieu Landon
- 1] Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114 [2] Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115
| | - Randy Giedt
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Ralph Weissleder
- 1] Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114 [2] Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115
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The ubiquitin ligases RNF8 and RNF168 display rapid but distinct dynamics at DNA repair foci in living cells. Int J Biochem Cell Biol 2014; 57:27-34. [PMID: 25304081 DOI: 10.1016/j.biocel.2014.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/25/2014] [Accepted: 09/30/2014] [Indexed: 01/15/2023]
Abstract
Rapid assembly of DNA damage response (DDR) proteins at nuclear "repair" foci is a hallmark response of ionizing radiation (IR)-treated cells. The ubiquitin E3 ligases RNF8 and RNF168 are critical for foci formation, and here we aim to determine their dynamic mobility and abundance at individual foci in living cells. To this end, YFP-tagged RNF8 and RNF168 were expressed at physiological levels in MCF-7 cells, then analyzed by fluorescence recovery after photobleaching (FRAP) assays, nuclear retention measurement, and virus-like particles (VLPs)-based quantification. The results showed that RNF8 and RNF168 were both highly dynamic at IR-induced foci. Intriguingly, RNF8 displayed remarkably faster in vivo association/dissociation rates than RNF168, and RNF8-positive IR-foci were less resistant to detergent extraction. In addition, copy number assay revealed that RNF168 was two-fold more abundant than RNF8 at foci. Collectively, we show for the first time that RNF8 moves on-and-off nuclear DNA repair foci more than six-fold as quickly as RNF168. The faster kinetics of RNF8 recruitment explains why RNF8 is generally observed at DNA-breaks prior to RNF168. Moreover, our finding that RNF8 is less abundant than RNF168 identifies RNF8 as a rate-limiting determinant of focal repair complex assembly.
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53
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Dutertre M, Lambert S, Carreira A, Amor-Guéret M, Vagner S. DNA damage: RNA-binding proteins protect from near and far. Trends Biochem Sci 2014; 39:141-9. [DOI: 10.1016/j.tibs.2014.01.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/20/2014] [Accepted: 01/20/2014] [Indexed: 12/14/2022]
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54
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Date H, Wakui K, Sasaki K, Kato T, Nishioka T. A formulation of cell surviving fraction after radiation exposure. Radiol Phys Technol 2013; 7:148-57. [PMID: 24288163 DOI: 10.1007/s12194-013-0244-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 11/11/2013] [Accepted: 11/11/2013] [Indexed: 10/26/2022]
Abstract
Local energy transfer from electrons generated in biotissues that are exposed to ionizing radiation is fundamental to cell damage. Our aim in this investigation was to quantify the probability of cell mortality associated with the damage by electrons and the repair processes in the cell nucleus, envisaging a new interpretation of the cell surviving fraction (SF). We introduced a SF formula for cells exposed to X-rays, which is given as a linear combination of the Poisson distributions about the number of long-lived lesions per nucleus and their "non-lethal probabilities", to show the non-linearity of log SF as a function of dose. The model selection was rated by a statistical index, Akaike's information criterion (AIC). It was shown that the new formula is suitable for describing cell survival and explicitly takes account of the non-lethality in damage-processing pathways of the cells.
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Affiliation(s)
- Hiroyuki Date
- Faculty of Health Sciences, Hokkaido University, Kita-12, Nishi-5, Kita-ku, Sapporo, 060-0812, Japan,
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55
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d'Adda di Fagagna F. A direct role for small non-coding RNAs in DNA damage response. Trends Cell Biol 2013; 24:171-8. [PMID: 24156824 DOI: 10.1016/j.tcb.2013.09.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 09/16/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
Abstract
Historically, the role of cellular RNA has been subordinate and ancillary to DNA. Protein-coding mRNA conveys the information content of DNA, and transfer RNAs and ribosomal RNAs allow the polymerization of amino acids into proteins. The discovery of non-protein-coding RNAs (ncRNAs) provided an additional role for RNA in finely tuning DNA expression. However, it has recently become apparent that the safeguard of DNA integrity depends on small ncRNAs acting at the site of DNA lesions to signal the presence of DNA damage in the cell, and on the genes involved in their biogenesis to achieve accurate DNA repair. I review here evidence supporting a role for small ncRNAs, termed DNA damage-response RNAs (DDRNAs) or double-strand break (DSB)-induced RNAs (diRNAs), that are generated at sites of DNA damage and control the DNA damage response (DDR). I also discuss their biogenesis, potential mechanisms of action, and their relevance in cancer.
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Affiliation(s)
- Fabrizio d'Adda di Fagagna
- Istituto Firc di Oncologia Molecolare (IFOM) Foundation - Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy; Istituto di Genetica Molecolare - Consiglio Nazionale delle Ricerche, Via Abbiategrasso 207, 27100 Pavia, Italy.
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56
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Ohsawa R, Seol JH, Tyler JK. At the intersection of non-coding transcription, DNA repair, chromatin structure, and cellular senescence. Front Genet 2013; 4:136. [PMID: 23967007 PMCID: PMC3744812 DOI: 10.3389/fgene.2013.00136] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 06/26/2013] [Indexed: 01/23/2023] Open
Abstract
It is well accepted that non-coding RNAs play a critical role in regulating gene expression. Recent paradigm-setting studies are now revealing that non-coding RNAs, other than microRNAs, also play intriguing roles in the maintenance of chromatin structure, in the DNA damage response, and in adult human stem cell aging. In this review, we will discuss the complex inter-dependent relationships among non-coding RNA transcription, maintenance of genomic stability, chromatin structure, and adult stem cell senescence. DNA damage-induced non-coding RNAs transcribed in the vicinity of the DNA break regulate recruitment of the DNA damage machinery and DNA repair efficiency. We will discuss the correlation between non-coding RNAs and DNA damage repair efficiency and the potential role of changing chromatin structures around double-strand break sites. On the other hand, induction of non-coding RNA transcription from the repetitive Alu elements occurs during human stem cell aging and hinders efficient DNA repair causing entry into senescence. We will discuss how this fine balance between transcription and genomic instability may be regulated by the dramatic changes to chromatin structure that accompany cellular senescence.
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Affiliation(s)
- Ryosuke Ohsawa
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center Houston, TX, USA
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57
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Fradet-Turcotte A, Canny MD, Escribano-Díaz C, Orthwein A, Leung CCY, Huang H, Landry MC, Kitevski-LeBlanc J, Noordermeer SM, Sicheri F, Durocher D. 53BP1 is a reader of the DNA-damage-induced H2A Lys 15 ubiquitin mark. Nature 2013; 499:50-4. [PMID: 23760478 PMCID: PMC3955401 DOI: 10.1038/nature12318] [Citation(s) in RCA: 516] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 05/24/2013] [Indexed: 12/18/2022]
Abstract
53BP1 (TP53BP1) is a chromatin-associated factor that promotes immunoglobulin class switching and DNA double-strand break (DSB) repair by non-homologous end joining. To accomplish its function in DNA repair, 53BP1 accumulates at DSB sites downstream of the RNF168 ubiquitin ligase. How ubiquitin recruits 53BP1 to break sites remains enigmatic since its relocalization involves recognition of H4 Lys20 (H4K20) methylation by its Tudor domain. Here we elucidate how 53BP1 is recruited to the chromatin that flanks DSB sites. We show that 53BP1 recognizes mono-nucleosomes containing dimethylated H4K20 (H4K20me2) and H2A ubiquitylated on Lys15 (H2AK15ub), the latter being a product of RNF168 action on chromatin. 53BP1 binds to nucleosomes minimally as a dimer using its previously characterized methyl-lysine-binding Tudor domain and a C-terminal extension, termed the ubiquitylation-dependent recruitment (UDR) motif, which interacts with the epitope formed by H2AK15ub and its surrounding residues on the H2A tail. 53BP1 is therefore a bivalent histone modification reader that recognizes a histone “code” produced by DSB signaling.
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Affiliation(s)
- Amélie Fradet-Turcotte
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
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58
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Sharma V, Misteli T. Non-coding RNAs in DNA damage and repair. FEBS Lett 2013; 587:1832-9. [PMID: 23684639 DOI: 10.1016/j.febslet.2013.05.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 02/07/2023]
Abstract
Non-coding RNAs (ncRNAs) are increasingly recognized as central players in diverse biological processes. Upon DNA damage, the DNA damage response (DDR) elicits a complex signaling cascade, which includes the induction of multiple ncRNA species. Recent studies indicate that DNA-damage induced ncRNAs contribute to regulation of cell cycle, apoptosis and DNA repair, and thus play a key role in maintaining genome stability. This review summarizes the emerging role of ncRNAs in DNA damage and repair.
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Affiliation(s)
- Vivek Sharma
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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59
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Abstract
Ubiquitylation and sumoylation, the covalent attachment of the polypeptides ubiquitin and SUMO, respectively, to target proteins, are pervasive mechanisms for controlling cellular functions. Here, we summarize the key steps and enzymes involved in ubiquitin and SUMO conjugation and provide an overview of how they are crucial for maintaining genome stability. Specifically, we review research that has revealed how ubiquitylation and sumoylation regulate and coordinate various pathways of DNA damage recognition, signaling, and repair at the biochemical, cellular, and whole-organism levels. In addition to providing key insights into the control and importance of DNA repair and associated processes, such work has established paradigms for regulatory control that are likely to extend to other cellular processes and that may provide opportunities for better understanding and treatment of human disease.
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Affiliation(s)
- Stephen P Jackson
- The Gurdon Institute and the Department of Biochemistry, University of Cambridge, Cambridge, UK.
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60
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Chowdhury D, Choi YE, Brault ME. Charity begins at home: non-coding RNA functions in DNA repair. Nat Rev Mol Cell Biol 2013; 14:181-9. [PMID: 23385724 DOI: 10.1038/nrm3523] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During the past decade, evolutionarily conserved microRNAs (miRNAs) have been characterized as regulators of almost every cellular process and signalling pathway. There is now emerging evidence that this new class of regulators also impinges on the DNA damage response (DDR). Both miRNAs and other small non-coding RNAs (ncRNAs) are induced at DNA breaks and mediate the repair process. These intriguing observations raise the possibility that crosstalk between ncRNAs and the DDR might provide a means of efficient and accurate DNA repair and facilitate the maintenance of genomic stability.
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Affiliation(s)
- Dipanjan Chowdhury
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.
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61
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Gandhi M, Evdokimova VN, Cuenco KT, Bakkenist CJ, Nikiforov YE. Homologous chromosomes move and rapidly initiate contact at the sites of double-strand breaks in genes in G₀-phase human cells. Cell Cycle 2013; 12:547-52. [PMID: 23370393 PMCID: PMC3594255 DOI: 10.4161/cc.23754] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We recently reported that homologous chromosomes make contact at the sites of double-strand breaks (DSBs) induced by ionizing radiation (IR) and the restriction endonuclease I-PpoI in G₀/G₁-phase somatic human cells. The contact involves short segments of homologous chromosomes and is centered on a DSB that occurs in a gene; contact does not occur at a DSB in intergenic DNA. Contact between homologous chromosomes is abrogated by inhibition of transcription and requires the kinase activity of ATM, but not DNA-PK. Here, we report additional insights into the mechanism underlying this novel phenomenon. We identify four patterns of homologous chromosome contact, and show that contact between homologous arms, but not centrosomes, is induced by IR. Significantly, we demonstrate that contact is induced by IR in non-proliferating, G₀-phase human cells derived from tissue explants. Finally, we show that contact between homologous chromosomes is detectable as early as 5 min after IR. These results point to the existence of a mechanism that rapidly localizes homologous chromosome arms at sites of DSBs in genes in G₀-phase human cells.
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Affiliation(s)
- Manoj Gandhi
- Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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62
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Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature 2012; 488:231-5. [PMID: 22722852 PMCID: PMC3442236 DOI: 10.1038/nature11179] [Citation(s) in RCA: 405] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 05/04/2012] [Indexed: 01/07/2023]
Abstract
Non-coding RNAs (ncRNAs) are involved in an increasing number of cellular events1. Some ncRNAs are processed by DICER and DROSHA ribonucleases to give rise to small double-stranded RNAs involved in RNA interference (RNAi)2. The DNA-damage response (DDR) is a signaling pathway that originates from the DNA lesion and arrests cell proliferation3. So far, DICER or DROSHA RNA products have not been reported to control DDR activation. Here we show that DICER and DROSHA, but not downstream elements of the RNAi pathway, are necessary to activate DDR upon oncogene-induced genotoxic stress and exogenous DNA damage, as studied also by DDR foci formation in mammalian cells and zebrafish and by checkpoint assays. DDR foci are sensitive to RNase A treatment, and DICER- and DROSHA-dependent RNA products are required to restore DDR foci in treated cells. Through RNA deep sequencing and studies of DDR activation at an inducible unique DNA double-strand break (DSB), we demonstrate that DDR foci formation requires site-specific DICER- and DROSHA-dependent small RNAs, named DDRNAs, which act in a MRE11-RAD50-NBS1 (MRN) complex-dependent manner. Chemically synthesized or in vitro-generated by DICER cleavage, DDRNAs are sufficient to restore DDR in RNase A-treated cells, also in the absence of other cellular RNAs. Our results describe an unanticipated direct role of a novel class of ncRNAs in the control of DDR activation at sites of DNA damage.
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63
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Mok MT, Henderson BR. The in vivo dynamic interplay of MDC1 and 53BP1 at DNA damage-induced nuclear foci. Int J Biochem Cell Biol 2012; 44:1398-409. [DOI: 10.1016/j.biocel.2012.05.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 05/28/2012] [Accepted: 05/29/2012] [Indexed: 11/16/2022]
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64
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Puthiyaveetil AG, Caudell DL. Non homologous end joining-mediated DNA break repair is impaired in B lymphocytes of aging mice. Mol Immunol 2012; 53:79-87. [PMID: 22878140 DOI: 10.1016/j.molimm.2012.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 07/02/2012] [Accepted: 07/02/2012] [Indexed: 01/10/2023]
Abstract
Aging is an irreversible physiological process characterized by increased risk of diseases, reduced effectiveness of vaccines, and decreased immune responses. One of the most prominent paradigms of aging and age related conditions is the progressive accumulation of un-repaired DNA breaks leading to apoptosis and exhaustion of stem cells. Here we hypothesized that B lymphocytes from old mice have reduced DNA repair mechanisms as a contributing factor for DNA break accumulation. We analyzed class switch recombination (CSR) of naïve B lymphocytes from old and adult mice to delineate the DNA double strand repair mechanisms during aging. In vitro CSR assays and DNA break analysis by labeling phosphorylated histone H2AX showed that old mice had significantly reduced DNA repair efficiency following DNA breaks. Functional efficiency analysis of DNA break repairs using plasmid ligation method showed that B lymphocytes from old mice had poor repair efficiency and increased misrepair of linear plasmid. Diminished DNA repair in old age can contribute to reduced immune cell repertoire and impaired immunity; increased occurrence of cancer; and reduced stem cell reserve.
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Affiliation(s)
- Abdul Gafoor Puthiyaveetil
- Laboratory of Molecular Pathology, Department of Biomedical Sciences & Pathobiology, Center for Molecular Medicine & Infectious Diseases, Virginia Tech, Blacksburg, VA 24061, USA
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65
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Thompson LH. Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: the molecular choreography. Mutat Res 2012; 751:158-246. [PMID: 22743550 DOI: 10.1016/j.mrrev.2012.06.002] [Citation(s) in RCA: 261] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 06/09/2012] [Accepted: 06/16/2012] [Indexed: 12/15/2022]
Abstract
The faithful maintenance of chromosome continuity in human cells during DNA replication and repair is critical for preventing the conversion of normal diploid cells to an oncogenic state. The evolution of higher eukaryotic cells endowed them with a large genetic investment in the molecular machinery that ensures chromosome stability. In mammalian and other vertebrate cells, the elimination of double-strand breaks with minimal nucleotide sequence change involves the spatiotemporal orchestration of a seemingly endless number of proteins ranging in their action from the nucleotide level to nucleosome organization and chromosome architecture. DNA DSBs trigger a myriad of post-translational modifications that alter catalytic activities and the specificity of protein interactions: phosphorylation, acetylation, methylation, ubiquitylation, and SUMOylation, followed by the reversal of these changes as repair is completed. "Superfluous" protein recruitment to damage sites, functional redundancy, and alternative pathways ensure that DSB repair is extremely efficient, both quantitatively and qualitatively. This review strives to integrate the information about the molecular mechanisms of DSB repair that has emerged over the last two decades with a focus on DSBs produced by the prototype agent ionizing radiation (IR). The exponential growth of molecular studies, heavily driven by RNA knockdown technology, now reveals an outline of how many key protein players in genome stability and cancer biology perform their interwoven tasks, e.g. ATM, ATR, DNA-PK, Chk1, Chk2, PARP1/2/3, 53BP1, BRCA1, BRCA2, BLM, RAD51, and the MRE11-RAD50-NBS1 complex. Thus, the nature of the intricate coordination of repair processes with cell cycle progression is becoming apparent. This review also links molecular abnormalities to cellular pathology as much a possible and provides a framework of temporal relationships.
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Affiliation(s)
- Larry H Thompson
- Biology & Biotechnology Division, L452, Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551-0808, United States.
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66
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Zhu Y, Zhao T, Itasaka S, Zeng L, Yeom CJ, Hirota K, Suzuki K, Morinibu A, Shinomiya K, Ou G, Yoshimura M, Hiraoka M, Harada H. Involvement of decreased hypoxia-inducible factor 1 activity and resultant G1-S cell cycle transition in radioresistance of perinecrotic tumor cells. Oncogene 2012; 32:2058-68. [PMID: 22710721 PMCID: PMC3631307 DOI: 10.1038/onc.2012.223] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cancer patients often suffer from local tumor recurrence after radiation therapy. Some intracellular and extracellular factors, such as activity of hypoxia-inducible factor 1 (HIF-1), cell cycle status and oxygen availability, have been suggested to affect DNA damage responses and eventual radioresistant characteristics of cancer cells. But when, where, and how these factors affect one another and induce cellular radioresistance is largely unknown. Here, we analyzed mechanistic and spatio-temporal relationships among them in highly heterogeneous tumor microenvironments. Experiments in vitro demonstrated that a decrease in the glucose concentration reduced the transcriptional activity of HIF-1 and expression of a downstream gene for the cell cycle regulator p27Kip1 even under hypoxic conditions. Then, the proportion of cells in the radioresistant S phase increased, whereas that in the radiosensitive G1 phase decreased, significantly. Immunohistochemical analyses showed that cancer cells in perinecrotic hypoxic regions, which should be under low-glucose conditions, expressed little HIF-1α, and therefore, were mainly in S phase and less damaged by radiation treatment. Continuous administration of glucagon, which increases the blood glucose concentration and so improves glucose availability in perinecrotic hypoxic regions, induced HIF-1α expression and increased radiation-induced DNA damage. Taken all together, these results indicate that cancer cells in perinecrotic regions, which would be under low-glucose and hypoxic conditions, obtain radioresistance by decreasing the level of both HIF-1 activity and p27Kip1 expression, and adjusting their cell cycle to the radioresistant S phase.
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Affiliation(s)
- Y Zhu
- Group of Radiation and Tumor Biology, Career-Path Promotion Unit for Young Life Scientists, Kyoto University, Kyoto, Japan
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67
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Gandhi M, Evdokimova VN, T.Cuenco K, Nikiforova MN, Kelly LM, Stringer JR, Bakkenist CJ, Nikiforov YE. Homologous chromosomes make contact at the sites of double-strand breaks in genes in somatic G0/G1-phase human cells. Proc Natl Acad Sci U S A 2012; 109:9454-9. [PMID: 22645362 PMCID: PMC3386068 DOI: 10.1073/pnas.1205759109] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Double-strand DNA breaks (DSBs) are continuously induced in cells by endogenously generated free radicals and exogenous genotoxic agents such as ionizing radiation. DSBs activate the kinase activity in sensor proteins such as ATM and DNA-PK, initiating a complex DNA damage response that coordinates various DNA repair pathways to restore genomic integrity. In this study, we report the unexpected finding that homologous chromosomes contact each other at the sites of DSBs induced by either radiation or the endonuclease I-PpoI in human somatic cells. Contact involves short segments of homologous chromosomes and is centered on a DSB in active genes but does not occur at I-PpoI sites in intergenic DNA. I-PpoI-induced contact between homologous genes is abrogated by the transcriptional inhibitors actinomycin D and α-amanitin and requires the kinase activity of ATM but not DNA-PK. Our findings provide documentation of a common transcription-related and ATM kinase-dependent mechanism that induces contact between allelic regions of homologous chromosomes at sites of DSBs in human somatic cells.
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Affiliation(s)
- Manoj Gandhi
- Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - Viktoria N. Evdokimova
- Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - Karen T.Cuenco
- Department of Oral Biology, School of Dental Medicine and
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219
| | - Marina N. Nikiforova
- Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - Lindsey M. Kelly
- Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - James R. Stringer
- Department of Molecular Genetics, University of Cincinnati, Cincinnati, OH 45267; and
| | - Christopher J. Bakkenist
- Department of Molecular Genetics, University of Cincinnati, Cincinnati, OH 45267; and
- Departments of Radiation Oncology and Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213
| | - Yuri E. Nikiforov
- Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA 15213
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68
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Uringa EJ, Lisaingo K, Pickett HA, Brind'Amour J, Rohde JH, Zelensky A, Essers J, Lansdorp PM. RTEL1 contributes to DNA replication and repair and telomere maintenance. Mol Biol Cell 2012; 23:2782-92. [PMID: 22593209 PMCID: PMC3395665 DOI: 10.1091/mbc.e12-03-0179] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Telomere maintenance and DNA repair are important processes that protect the genome. The essential helicase mRtel1 functions in homologous recombination repair and replication. In addition, telomeres in mRtel-deficient ES cells appear relatively stable in length, suggesting that mRtel1 is required to allow extension by telomerase. Telomere maintenance and DNA repair are important processes that protect the genome against instability. mRtel1, an essential helicase, is a dominant factor setting telomere length in mice. In addition, mRtel1 is involved in DNA double-strand break repair. The role of mRtel1 in telomere maintenance and genome stability is poorly understood. Therefore we used mRtel1-deficient mouse embryonic stem cells to examine the function of mRtel1 in replication, DNA repair, recombination, and telomere maintenance. mRtel1-deficient mouse embryonic stem cells showed sensitivity to a range of DNA-damaging agents, highlighting its role in replication and genome maintenance. Deletion of mRtel1 increased the frequency of sister chromatid exchange events and suppressed gene replacement, demonstrating the involvement of the protein in homologous recombination. mRtel1 localized transiently at telomeres and is needed for efficient telomere replication. Of interest, in the absence of mRtel1, telomeres in embryonic stem cells appeared relatively stable in length, suggesting that mRtel1 is required to allow extension by telomerase. We propose that mRtel1 is a key protein for DNA replication, recombination, and repair and efficient elongation of telomeres by telomerase.
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69
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Hnilicová J, Staněk D. Where splicing joins chromatin. Nucleus 2012; 2:182-8. [PMID: 21818411 DOI: 10.4161/nucl.2.3.15876] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 04/18/2011] [Accepted: 04/19/2011] [Indexed: 12/14/2022] Open
Abstract
There are numerous data suggesting that two key steps in gene expression-transcription and splicing influence each other closely. For a long time it was known that chromatin modifications regulate transcription, but only recently it was shown that chromatin and histone modifications play a significant role in pre-mRNA splicing. Here we summarize interactions between splicing machinery and chromatin and discuss their potential functional significance. We focus mainly on histone acetylation and methylation and potential mechanisms of their role in splicing. It seems that whereas histone acetylation acts mainly by alterating the transcription rate, histone methylation can also influence splicing directly by recruiting various splicing components.
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Affiliation(s)
- Jarmila Hnilicová
- Department of RNA Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague
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70
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Mok MT, Henderson BR. The In Vivo Dynamic Organization of BRCA1-A Complex Proteins at DNA Damage-Induced Nuclear Foci. Traffic 2012; 13:800-14. [DOI: 10.1111/j.1600-0854.2012.01355.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 03/13/2012] [Accepted: 03/15/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Myth T.S. Mok
- Westmead Institute for Cancer Research; The University of Sydney, Westmead Millennium Institute at Westmead Hospital; Westmead; NSW; 2145; Australia
| | - Beric R. Henderson
- Westmead Institute for Cancer Research; The University of Sydney, Westmead Millennium Institute at Westmead Hospital; Westmead; NSW; 2145; Australia
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71
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Casafont I, Palanca A, Lafarga V, Berciano MT, Lafarga M. Effect of ionizing radiation in sensory ganglion neurons: organization and dynamics of nuclear compartments of DNA damage/repair and their relationship with transcription and cell cycle. Acta Neuropathol 2011; 122:481-93. [PMID: 21915754 DOI: 10.1007/s00401-011-0869-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 08/31/2011] [Accepted: 09/02/2011] [Indexed: 12/18/2022]
Abstract
Neurons are very sensitive to DNA damage induced by endogenous and exogenous genotoxic agents, as defective DNA repair can lead to neurodevelopmental disorders, brain tumors and neurodegenerative diseases with severe clinical manifestations. Understanding the impact of DNA damage/repair mechanisms on the nuclear organization, particularly on the regulation of transcription and cell cycle, is essential to know the pathophysiology of defective DNA repair syndromes. In this work, we study the nuclear architecture and spatiotemporal organization of chromatin compartments involved in the DNA damage response (DDR) in rat sensory ganglion neurons exposed to X-ray irradiation (IR). We demonstrate that the neuronal DDR involves the formation of two categories of DNA-damage processing chromatin compartments: transient, disappearing within the 1 day post-IR, and persistent, where unrepaired DNA is accumulated. Both compartments concentrate components of the DDR pathway, including γH2AX, pATM and 53BP1. Furthermore, DNA damage does not induce neuronal apoptosis but triggers the G0-G1 cell cycle phase transition, which is mediated by the activation of the ATM-p53 pathway and increased protein levels of p21 and cyclin D1. Moreover, the run on transcription assay reveals a severe inhibition of transcription at 0.5 h post-IR, followed by its rapid recovery over the 1 day post-IR in parallel with the progression of DNA repair. Therefore, the response of healthy neurons to DNA damage involves a transcription- and cell cycle-dependent but apoptosis-independent process. Furthermore, we propose that the segregation of unrepaired DNA in a few persistent chromatin compartments preserves genomic stability of undamaged DNA and the global transcription rate in neurons.
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Affiliation(s)
- Iñigo Casafont
- Departamento de Anatomía y Biología Celular, "Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)", Universidad de Cantabria, IFIMAV, Santander, Spain
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72
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Wang J, Geesman GJ, Hostikka SL, Atallah M, Blackwell B, Lee E, Cook PJ, Pasaniuc B, Shariat G, Halperin E, Dobke M, Rosenfeld MG, Jordan IK, Lunyak VV. Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal. Cell Cycle 2011; 10:3016-30. [PMID: 21862875 PMCID: PMC3218602 DOI: 10.4161/cc.10.17.17543] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 07/28/2011] [Indexed: 01/01/2023] Open
Abstract
Cellular aging is linked to deficiencies in efficient repair of DNA double strand breaks and authentic genome maintenance at the chromatin level. Aging poses a significant threat to adult stem cell function by triggering persistent DNA damage and ultimately cellular senescence. Senescence is often considered to be an irreversible process. Moreover, critical genomic regions engaged in persistent DNA damage accumulation are unknown. Here we report that 65% of naturally occurring repairable DNA damage in self-renewing adult stem cells occurs within transposable elements. Upregulation of Alu retrotransposon transcription upon ex vivo aging causes nuclear cytotoxicity associated with the formation of persistent DNA damage foci and loss of efficient DNA repair in pericentric chromatin. This occurs due to a failure to recruit of condensin I and cohesin complexes. Our results demonstrate that the cytotoxicity of induced Alu repeats is functionally relevant for the human adult stem cell aging. Stable suppression of Alu transcription can reverse the senescent phenotype, reinstating the cells' self-renewing properties and increasing their plasticity by altering so-called "master" pluripotency regulators.
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Affiliation(s)
- Jianrong Wang
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
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73
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Huo Q, Yang Q. P53-Binding protein 1: A new player for tumorigenesis and a new target for breast cancer treatment. Med Hypotheses 2011; 77:359-63. [DOI: 10.1016/j.mehy.2011.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 04/16/2011] [Accepted: 05/11/2011] [Indexed: 12/21/2022]
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74
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Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation. PLoS One 2010; 5:e14152. [PMID: 21152398 PMCID: PMC2994767 DOI: 10.1371/journal.pone.0014152] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 10/25/2010] [Indexed: 12/26/2022] Open
Abstract
Background High doses of ionizing radiation result in biological damage; however, the precise relationships between long-term health effects, including cancer, and low-dose exposures remain poorly understood and are currently extrapolated using high-dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose-dependent responses to radiation. Principal Findings We have identified 7117 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts 1 h post-exposure. Semi-quantitative label-free analyses were performed to identify phosphopeptides that are apparently altered by radiation exposure. This screen identified phosphorylation sites on proteins with known roles in radiation responses including TP53BP1 as well as previously unidentified radiation-responsive proteins such as the candidate tumor suppressor SASH1. Bioinformatic analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role for MAP kinase and protein kinase A (PKA) signaling in the radiation response as well as differential regulation of p53 networks at low and high doses of radiation. Conclusions Our results represent the most comprehensive analysis of the phosphoproteomes of human primary fibroblasts exposed to multiple doses of ionizing radiation published to date and provide a basis for the systems-level identification of biological processes, molecular pathways and individual proteins regulated in a dose dependent manner by ionizing radiation. Further study of these modified proteins and affected networks should help to define the molecular mechanisms that regulate biological responses to radiation at different radiation doses and elucidate the impact of low-dose radiation exposure on human health.
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75
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Dynamics of Rad9 chromatin binding and checkpoint function are mediated by its dimerization and are cell cycle-regulated by CDK1 activity. PLoS Genet 2010; 6. [PMID: 20700441 PMCID: PMC2916856 DOI: 10.1371/journal.pgen.1001047] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Accepted: 07/02/2010] [Indexed: 12/21/2022] Open
Abstract
Saccharomyces cerevisiae Rad9 is required for an effective DNA damage response throughout the cell cycle. Assembly of Rad9 on chromatin after DNA damage is promoted by histone modifications that create docking sites for Rad9 recruitment, allowing checkpoint activation. Rad53 phosphorylation is also dependent upon BRCT-directed Rad9 oligomerization; however, the crosstalk between these molecular determinants and their functional significance are poorly understood. Here we report that, in the G1 and M phases of the cell cycle, both constitutive and DNA damage-dependent Rad9 chromatin association require its BRCT domains. In G1 cells, GST or FKBP dimerization motifs can substitute to the BRCT domains for Rad9 chromatin binding and checkpoint function. Conversely, forced Rad9 dimerization in M phase fails to promote its recruitment onto DNA, although it supports Rad9 checkpoint function. In fact, a parallel pathway, independent on histone modifications and governed by CDK1 activity, allows checkpoint activation in the absence of Rad9 chromatin binding. CDK1-dependent phosphorylation of Rad9 on Ser11 leads to specific interaction with Dpb11, allowing Rad53 activation and bypassing the requirement for the histone branch. In response to DNA damage all eukaryotic cells activate a surveillance mechanism, known as the DNA damage checkpoint, which delays cell cycle progression and modulates DNA repair. Yeast RAD9 was the first DNA damage checkpoint gene identified. The genetic tools available in this model system allow to address relevant questions to understand the molecular mechanisms underlying the Rad9 biological function. By chromatin-binding and domain-swapping experiments, we found that Rad9 is recruited into DNA both in unperturbed and in DNA–damaging conditions, and we identified the molecular determinants required for such interaction. Moreover, the extent of chromatin-bound Rad9 is regulated during the cell cycle and influences its role in checkpoint activation. In fact, the checkpoint function of Rad9 in G1 cells is solely mediated by its interaction with modified histones, while in M phase it occurs through an additional scaffold protein, named Dpb11. Productive Rad9-Dpb11 interaction in M phase requires Rad9 phosphorylation by CDK1, and we identified the Ser11 residue as the major CDK1 target. The model of Rad9 action that we are presenting can be extended to other eukaryotic organisms, since Rad9 and Dpb11 have been conserved through evolution from yeast to mammalian cells.
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76
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Efimova EV, Mauceri HJ, Golden DW, Labay E, Bindokas VP, Darga TE, Chakraborty C, Barreto-Andrade JC, Crawley C, Sutton HG, Kron SJ, Weichselbaum RR. Poly(ADP-ribose) polymerase inhibitor induces accelerated senescence in irradiated breast cancer cells and tumors. Cancer Res 2010; 70:6277-82. [PMID: 20610628 DOI: 10.1158/0008-5472.can-09-4224] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Persistent DNA double-strand breaks (DSB) may determine the antitumor effects of ionizing radiation (IR) by inducing apoptosis, necrosis, mitotic catastrophe, or permanent growth arrest. IR induces rapid modification of megabase chromatin domains surrounding DSBs via poly-ADP-ribosylation, phosphorylation, acetylation, and protein assembly. The dynamics of these IR-induced foci (IRIF) have been implicated in DNA damage signaling and DNA repair. As an IRIF reporter, we tracked the relocalization of green fluorescent protein fused to a chromatin binding domain of the checkpoint adapter protein 53BP1 after IR of breast cancer cells and tumors. To block DSB repair in breast cancer cells and tumors, we targeted poly(ADP-ribose) polymerase (PARP) with ABT-888 (veliparib), one of several PARP inhibitors currently in clinical trials. PARP inhibition markedly enhanced IRIF persistence and increased breast cancer cell senescence both in vitro and in vivo, arguing for targeting IRIF resolution as a novel therapeutic strategy.
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Affiliation(s)
- Elena V Efimova
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois 60637, USA
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77
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Yuan J, Adamski R, Chen J. Focus on histone variant H2AX: to be or not to be. FEBS Lett 2010; 584:3717-24. [PMID: 20493860 DOI: 10.1016/j.febslet.2010.05.021] [Citation(s) in RCA: 227] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2010] [Revised: 05/04/2010] [Accepted: 05/11/2010] [Indexed: 12/16/2022]
Abstract
Phosphorylation of histone variant H2AX at serine 139, named gammaH2AX, has been widely used as a sensitive marker for DNA double-strand breaks (DSBs). gammaH2AX is required for the accumulation of many DNA damage response (DDR) proteins at DSBs. Thus it is believed to be the principal signaling protein involved in DDR and to play an important role in DNA repair. However, only mild defects in DNA damage signaling and DNA repair were observed in H2AX-deficient cells and animals. Such findings prompted us and others to explore H2AX-independent mechanisms in DNA damage response. Here, we will review recent advances in our understanding of H2AX-dependent and independent DNA damage signaling and repair pathways in mammalian cells.
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Affiliation(s)
- Jingsong Yuan
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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78
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Cao Z, Kuhne WW, Steeb J, Merkley MA, Zhou Y, Janata J, Dynan WS. Use of a microscope stage-mounted Nickel-63 microirradiator for real-time observation of the DNA double-strand break response. Nucleic Acids Res 2010; 38:e144. [PMID: 20484377 PMCID: PMC2919731 DOI: 10.1093/nar/gkq409] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Eukaryotic cells begin to assemble discrete, nucleoplasmic repair foci within seconds after the onset of exposure to ionizing radiation. Real-time imaging of this assembly has the potential to further our understanding of the effects of medical and environmental radiation exposure. Here, we describe a microirradiation system for targeted delivery of ionizing radiation to individual cells without the need for specialized facilities. The system consists of a 25-micron diameter electroplated Nickel-63 electrode, enveloped in a glass capillary and mounted in a micromanipulator. Because of the low energy of the beta radiation and the minute total amount of isotope present on the tip, the device can be safely handled with minimum precautions. We demonstrate the use of this system for tracking assembly of individual repair foci in real time in live U2OS human osteosarcoma cells. Results indicate that there is a subset of foci that appear and disappear rapidly, before a plateau level is reached ∼30 min post-exposure. This subset of foci would not have been evident without real-time observation. The development of a microirradiation system that is compatible with a standard biomedical laboratory expands the potential for real-time investigation of the biological effects of ionizing radiation.
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Affiliation(s)
- Zhen Cao
- Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, Georgia, USA
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79
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Schettino G, Al Rashid ST, Prise KM. Radiation microbeams as spatial and temporal probes of subcellular and tissue response. Mutat Res 2010; 704:68-77. [PMID: 20079877 DOI: 10.1016/j.mrrev.2010.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 12/22/2009] [Accepted: 01/06/2010] [Indexed: 11/29/2022]
Abstract
Understanding the effects of ionizing radiations are key to determining their optimal use in therapy and assessing risks from exposure. The development of microbeams where radiations can be delivered in a highly temporal and spatially constrained manner has been a major advance. Several different types of radiation microbeams have been developed using X-rays, charged particles and electrons. For charged particles, beams can be targeted with sub-micron accuracy into biological samples and the lowest possible dose of a single particle track can be delivered with high reproducibility. Microbeams have provided powerful tools for understanding the kinetics of DNA damage and formation under conditions of physiological relevance and have significant advantages over other approaches for producing localized DNA damage, such as variable wavelength laser beam approaches. Recent studies have extended their use to probing for radiosensitive sites outside the cell nucleus, and testing for mechanisms underpinning bystander responses where irradiated and non-irradiated cells communicate with each other. Ongoing developments include the ability to locally target regions of 3D tissue models and ultimately to target localized regions in vivo. With future advances in radiation delivery and imaging microbeams will continue to be applied in a range of biological studies.
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Affiliation(s)
- Giuseppe Schettino
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT97BL, UK
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80
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Stavnezer J, Björkman A, Du L, Cagigi A, Pan-Hammarström Q. Mapping of Switch Recombination Junctions, a Tool for Studying DNA Repair Pathways during Immunoglobulin Class Switching. Adv Immunol 2010; 108:45-109. [DOI: 10.1016/b978-0-12-380995-7.00003-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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81
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Ugenskiene R, Prise K, Folkard M, Lekki J, Stachura Z, Zazula M, Stachura J. Dose response and kinetics of foci disappearance following exposure to high- and low-LET ionizing radiation. Int J Radiat Biol 2009. [DOI: 10.1080/09553000903072462] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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82
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Andersson R, Enroth S, Rada-Iglesias A, Wadelius C, Komorowski J. Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res 2009; 19:1732-41. [PMID: 19687145 DOI: 10.1101/gr.092353.109] [Citation(s) in RCA: 257] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The genomes of higher organisms are packaged in nucleosomes with functional histone modifications. Until now, genome-wide nucleosome and histone modification studies have focused on transcription start sites (TSSs) where nucleosomes in RNA polymerase II (RNAPII) occupied genes are well positioned and have histone modifications that are characteristic of expression status. Using public data, we here show that there is a higher nucleosome-positioning signal in internal human exons and that this positioning is independent of expression. We observed a similarly strong nucleosome-positioning signal in internal exons of Caenorhabditis elegans. Among the 38 histone modifications analyzed in man, H3K36me3, H3K79me1, H2BK5me1, H3K27me1, H3K27me2, and H3K27me3 had evidently higher signals in internal exons than in the following introns and were clearly related to exon expression. These observations are suggestive of roles in splicing. Thus, exons are not only characterized by their coding capacity, but also by their nucleosome organization, which seems evolutionarily conserved since it is present in both primates and nematodes.
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Affiliation(s)
- Robin Andersson
- The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
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83
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Asaithamby A, Chen DJ. Cellular responses to DNA double-strand breaks after low-dose gamma-irradiation. Nucleic Acids Res 2009; 37:3912-23. [PMID: 19401436 PMCID: PMC2709554 DOI: 10.1093/nar/gkp237] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are a serious threat to genome stability and cell viability. Although biological effects of low levels of radiation are not clear, the risks of low-dose radiation are of societal importance. Here, we directly monitored induction and repair of single DSBs and quantitatively analyzed the dynamics of interaction of DNA repair proteins at individual DSB sites in living cells using 53BP1 fused to yellow fluorescent protein (YFP-53BP1) as a surrogate marker. The number of DSBs formed was linear with dose from 5 mGy to 1 Gy. The DSBs induced by very low radiation doses (5 mGy) were repaired with efficiency similar to repair of DSBs induced at higher doses. The YFP-53BP1 foci are dynamic structures: 53BP1 rapidly and reversibly interacted at these DSB sites. The time frame of recruitment and affinity of 53BP1 for DSB sites were indistinguishable between low and high doses, providing mechanistic evidence for the similar DSB repair after low- and high-dose radiation. These findings have important implications for estimating the risk associated with low-dose radiation exposure on human health.
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Affiliation(s)
| | - David J. Chen
- *To whom correspondence should be addressed. Tel: +1 214 648 5597; Fax: +1 214 648 5995;
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84
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A mouse PRMT1 null allele defines an essential role for arginine methylation in genome maintenance and cell proliferation. Mol Cell Biol 2009; 29:2982-96. [PMID: 19289494 DOI: 10.1128/mcb.00042-09] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Protein arginine methyltransferase 1 (PRMT1) is the major enzyme that generates monomethylarginine and asymmetrical dimethylarginine. We report here a conditional null allele of PRMT1 in mice and that the loss of PRMT1 expression leads to embryonic lethality. Using the Cre/lox-conditional system, we show that the loss of PRMT1 in mouse embryonic fibroblasts (MEFs) leads to the loss of arginine methylation of substrates harboring a glycine-arginine rich motif, including Sam68 and MRE11. The loss of PRMT1 in MEFs leads to spontaneous DNA damage, cell cycle progression delay, checkpoint defects, aneuploidy, and polyploidy. We show using a 4-hydroxytamoxifen-inducible Cre that the loss of PRMT1 in MEFs leads to a higher incidence of chromosome losses, gains, structural rearrangements, and polyploidy, as documented by spectral karyotyping. Using PRMT1 small interfering RNA in U2OS cells, we further show that PRMT1-deficient cells are hypersensitive to the DNA damaging agent etoposide and exhibit a defect in the recruitment of the homologous recombination RAD51 recombinase to DNA damage foci. Taken together, these data show that PRMT1 is required for genome integrity and cell proliferation. Our findings also suggest that arginine methylation by PRMT1 is a key posttranslational modification in the DNA damage response pathway in proliferating mammalian cells.
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85
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Eliezer Y, Argaman L, Rhie A, Doherty AJ, Goldberg M. The Direct Interaction between 53BP1 and MDC1 Is Required for the Recruitment of 53BP1 to Sites of Damage. J Biol Chem 2009; 284:426-435. [DOI: 10.1074/jbc.m807375200] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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86
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An oligomerized 53BP1 tudor domain suffices for recognition of DNA double-strand breaks. Mol Cell Biol 2008; 29:1050-8. [PMID: 19064641 DOI: 10.1128/mcb.01011-08] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
53BP1, the vertebrate ortholog of the budding yeast Rad9 and fission yeast Crb2/Rhp9 checkpoint proteins, is recruited rapidly to sites of DNA double-strand breaks (DSBs). A tandem tudor domain in human 53BP1 that recognizes methylated residues in the histone core is necessary, but not sufficient, for efficient recruitment. By analysis of deletion mutants, we identify here additional elements in 53BP1 that facilitate recognition of DNA DSBs. The first element corresponds to an independently folding oligomerization domain. Replacement of this domain with heterologous tetramerization domains preserves the ability of 53BP1 to recognize DNA DSBs. A second element is only about 15 amino acids long and appears to be a C-terminal extension of the tudor domain, rather than an independently functioning domain. Recruitment of 53BP1 to sites of DNA DSBs is facilitated by histone H2AX phosphorylation and ubiquitination. However, none of the 53BP1 domains/elements important for recruitment are known to bind phosphopeptides or ubiquitin, suggesting that histone phosphorylation and ubiquitination regulate 53BP1 recruitment to sites of DNA DSBs indirectly.
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87
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Medhurst AL, Warmerdam DO, Akerman I, Verwayen EH, Kanaar R, Smits VAJ, Lakin ND. ATR and Rad17 collaborate in modulating Rad9 localisation at sites of DNA damage. J Cell Sci 2008; 121:3933-40. [DOI: 10.1242/jcs.033688] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The cell cycle checkpoint kinase Chk1 is phosphorylated and activated by ATR in response to DNA damage and is crucial for initiating the DNA damage response. A number of factors act in concert with ATR to facilitate Chk1 phosphorylation, including Rad17-RFC, the Rad9-Rad1-Hus1 complex, TopBP1 and Claspin. Rad17 is required for loading of Rad9-Rad1-Hus1 (9-1-1) onto sites of DNA damage. Although phosphorylation of Rad17 by ATR is required for checkpoint function, how this affects 9-1-1 regulation remains unclear. We report that exposure of cells to DNA damage or replication stress results in Rad17-dependent immobilisation of Rad9 into nuclear foci. Furthermore, expression of mutant Rad17 that cannot be phosphorylated by ATR (Rad17AA), or downregulation of ATR, results in a decreased number of cells that display Rad9 foci. Photobleaching experiments reveal an increase in the dynamic behaviour of Rad9 within remaining foci in the absence of ATR or following expression of Rad17AA. Together, these data suggest a model in which Rad17 and ATR collaborate in regulating Rad9 localisation and association at sites of DNA damage.
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Affiliation(s)
- Annette L. Medhurst
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QD, UK
| | - Daniël O. Warmerdam
- Department of Cell Biology and Genetics, Cancer Genome Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Ildem Akerman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QD, UK
| | - Edward H. Verwayen
- Department of Cell Biology and Genetics, Cancer Genome Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Cell Biology and Genetics, Cancer Genome Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Veronique A. J. Smits
- Department of Cell Biology and Genetics, Cancer Genome Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Nicholas D. Lakin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QD, UK
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88
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Abstract
DEAD box proteins are a family of putative RNA helicases associated with all aspects of cellular metabolism involving the modification of RNA secondary structure. DDX1 is a member of the DEAD box protein family that is overexpressed in a subset of retinoblastoma and neuroblastoma cell lines and tumors. DDX1 is found primarily in the nucleus, where it forms two to four large aggregates called DDX1 bodies. Here, we report a rapid redistribution of DDX1 in cells exposed to ionizing radiation, resulting in the formation of numerous foci that colocalize with gamma-H2AX and phosphorylated ATM foci at sites of DNA double-strand breaks (DSBs). The formation of DDX1 ionizing-radiation-induced foci (IRIF) is dependent on ATM, which was shown to phosphorylate DDX1 both in vitro and in vivo. The treatment of cells with RNase H prevented the formation of DDX1 IRIF, suggesting that DDX1 is recruited to sites of DNA damage containing RNA-DNA structures. We have shown that DDX1 has RNase activity toward single-stranded RNA, as well as ADP-dependent RNA-DNA- and RNA-RNA-unwinding activities. We propose that DDX1 plays an RNA clearance role at DSB sites, thereby facilitating the template-guided repair of transcriptionally active regions of the genome.
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89
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Abstract
Antibody class switching occurs in mature B cells in response to antigen stimulation and costimulatory signals. It occurs by a unique type of intrachromosomal deletional recombination within special G-rich tandem repeated DNA sequences [called switch, or S, regions located upstream of each of the heavy chain constant (C(H)) region genes, except Cdelta]. The recombination is initiated by the B cell-specific activation-induced cytidine deaminase (AID), which deaminates cytosines in both the donor and acceptor S regions. AID activity converts several dC bases to dU bases in each S region, and the dU bases are then excised by the uracil DNA glycosylase UNG; the resulting abasic sites are nicked by apurinic/apyrimidinic endonuclease (APE). AID attacks both strands of transcriptionally active S regions, but how transcription promotes AID targeting is not entirely clear. Mismatch repair proteins are then involved in converting the resulting single-strand DNA breaks to double-strand breaks with DNA ends appropriate for end-joining recombination. Proteins required for the subsequent S-S recombination include DNA-PK, ATM, Mre11-Rad50-Nbs1, gammaH2AX, 53BP1, Mdc1, and XRCC4-ligase IV. These proteins are important for faithful joining of S regions, and in their absence aberrant recombination and chromosomal translocations involving S regions occur.
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Affiliation(s)
- Janet Stavnezer
- Department of Molecular Genetics and Microbiology, Program in Immunology and Virology, University of Massachusetts Medical School, Worcester, Massachusetts 01655-012, USA.
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90
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Sakasai R, Tibbetts R. RNF8-dependent and RNF8-independent regulation of 53BP1 in response to DNA damage. J Biol Chem 2008; 283:13549-55. [PMID: 18337245 DOI: 10.1074/jbc.m710197200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DNA damage surveillance network orchestrates cellular responses to DNA damage through the recruitment of DNA damage-signaling molecules to DNA damage sites and the concomitant activation of protein phosphorylation cascades controlled by the ATM (ataxia-telangiectasia-mutated) and ATR (ATM-Rad3-related) kinases. Activation of ATM/ATR triggers cell cycle checkpoint activation and adaptive responses to DNA damage. Recent studies suggest that protein ubiquitylation or degradation plays an important role in the DNA damage response. In this study, we examined the potential role of the proteasome in checkpoint activation and ATM/ATR signaling in response to UV light-induced DNA damage. HeLa cells treated with the proteasome inhibitor MG-132 showed delayed phosphorylation of ATM substrates in response to UV light. UV light-induced phosphorylation of 53BP1, as well as its recruitment to DNA damage foci, was strongly suppressed by proteasome inhibition, whereas the recruitment of upstream regulators of 53BP1, including MDC1 and H2AX, was unaffected. The ubiquitin-protein isopeptide ligase RNF8 was critical for 53BP1 focus targeting and phosphorylation in ionizing radiation-damaged cells, whereas UV light-induced 53BP1 phosphorylation and targeting exhibited partial dependence on RNF8 and the ubiquitin-conjugating enzyme UBC13. Suppression of RNF8 or UBC13 also led to subtle defects in UV light-induced G2/M checkpoint activation. These findings are consistent with a model in which RNF8 ubiquitylation pathways are essential for 53BP1 regulation in response to ionizing radiation, whereas RNF8-independent pathways contribute to 53BP1 targeting and phosphorylation in response to UV light and potentially other forms of DNA replication stress.
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Affiliation(s)
- Ryo Sakasai
- Department of Pharmacology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
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91
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Clarke AR, Jones N, Pryde F, Adachi Y, Sansom OJ. 53BP1 deficiency in intestinal enterocytes does not alter the immediate response to ionizing radiation, but leads to increased nuclear area consistent with polyploidy. Oncogene 2007; 26:6349-55. [PMID: 17452983 DOI: 10.1038/sj.onc.1210457] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The p53-binding protein 53BP1 has been implicated in the DNA damage response and genomic instability. Previous reports have highlighted these roles in vivo in haematopoietic lineages. To investigate the importance of 53BP1 to the DNA damage response in epithelial cells in vivo, we have investigated the role of 53BP1 in mediating apoptosis and proliferation within the murine small intestine following gamma-irradiation. 53BP1 deficiency does not affect the immediate response to gamma-irradiation with normal levels of apoptosis, proliferation and p53 and p21 accumulation. However, 48 h post-gamma-irradiation there was a significant accumulation of cells with much larger nuclei marked by p53 and p21 accumulation. These data reflect increases in polyploidy observed 53BP1-/- deficient fibroblasts following gamma-irradiation. At 72 h post-irradiation both the 4N and 8N populations were significantly increased in 53BP1-/- MEFS. Taken together, these results show that following in vivo exposure to gamma-irradiation, 53BP1 is dispensable for signalling apoptosis and cell-cycle arrest in the intestinal epithelium. However, it is important for prevention of genomic instability within this epithelial cell population.
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Affiliation(s)
- A R Clarke
- Institute of Cell Biology, Cardiff School of Biosciences, Cardiff University, Cardiff, UK
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92
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Botuyan MV, Lee J, Ward IM, Kim JE, Thompson JR, Chen J, Mer G. Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair. Cell 2007; 127:1361-73. [PMID: 17190600 PMCID: PMC1804291 DOI: 10.1016/j.cell.2006.10.043] [Citation(s) in RCA: 761] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Revised: 09/22/2006] [Accepted: 10/29/2006] [Indexed: 01/09/2023]
Abstract
Histone lysine methylation has been linked to the recruitment of mammalian DNA repair factor 53BP1 and putative fission yeast homolog Crb2 to DNA double-strand breaks (DSBs), but how histone recognition is achieved has not been established. Here we demonstrate that this link occurs through direct binding of 53BP1 and Crb2 to histone H4. Using X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, we show that, despite low amino acid sequence conservation, both 53BP1 and Crb2 contain tandem tudor domains that interact with histone H4 specifically dimethylated at Lys20 (H4-K20me2). The structure of 53BP1/H4-K20me2 complex uncovers a unique five-residue 53BP1 binding cage, remarkably conserved in the structure of Crb2, that best accommodates a dimethyllysine but excludes a trimethyllysine, thus explaining the methylation state-specific recognition of H4-K20. This study reveals an evolutionarily conserved molecular mechanism of targeting DNA repair proteins to DSBs by direct recognition of H4-K20me2.
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Affiliation(s)
- Maria Victoria Botuyan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Joseph Lee
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Irene M. Ward
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Ja-Eun Kim
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - James R. Thompson
- Department of Physiology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Junjie Chen
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
- *Contact: (J.C.), (G.M.)
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
- *Contact: (J.C.), (G.M.)
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93
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Rogne M, Landsverk HB, Van Eynde A, Beullens M, Bollen M, Collas P, Küntziger T. The KH-Tudor Domain of A-Kinase Anchoring Protein 149 Mediates RNA-Dependent Self-Association. Biochemistry 2006; 45:14980-9. [PMID: 17154535 DOI: 10.1021/bi061418y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A-Kinase anchoring proteins (AKAPs) control the subcellular localization and temporal specificity of protein phosphorylation mediated by cAMP-dependent protein kinase. AKAP149 (AKAP1) is found in mitochondria and in the endoplasmic reticulum-nuclear envelope network where it anchors protein kinases, phosphatases, and a phosphodiesterase. AKAP149 harbors in its COOH-terminal part one KH and one Tudor domain, both known to be involved in RNA binding. We investigated the properties of the COOH-terminal domain of AKAP149. We show here that AKAP149 is a self-associating protein with RNA binding features. The KH domain of AKAP149 is sufficient for self-association in a RNA-dependent manner. The Tudor domain is not necessary for self-association, but it is required together with the KH domain for targeting to well-defined nuclear foci. These foci are spatially closely related to nucleolar subcompartments. We also show that the KH-Tudor-containing domain of AKAP149 binds RNA in vitro and in RNA coprecipitation experiments. AKAP149 emerges as a scaffolding protein involved in the integration of intracellular signals and possibly in RNA metabolism.
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Affiliation(s)
- Marie Rogne
- Institute of Basic Medical Sciences, Department of Biochemistry, Faculty of Medicine, University of Oslo, P.O. Box 1112 Blindern, 0317 Oslo, Norway
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94
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le Maire A, Schiltz M, Stura EA, Pinon-Lataillade G, Couprie J, Moutiez M, Gondry M, Angulo JF, Zinn-Justin S. A tandem of SH3-like domains participates in RNA binding in KIN17, a human protein activated in response to genotoxics. J Mol Biol 2006; 364:764-76. [PMID: 17045609 DOI: 10.1016/j.jmb.2006.09.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Revised: 08/24/2006] [Accepted: 09/11/2006] [Indexed: 10/24/2022]
Abstract
The human KIN17 protein is an essential nuclear protein conserved from yeast to human and expressed ubiquitously in mammals. Suppression of Rts2, the yeast equivalent of gene KIN17, renders the cells unviable, and silencing the human KIN17 gene slows cell growth dramatically. Moreover, the human gene KIN17 is up-regulated following exposure to ionizing radiations and UV light, depending on the integrity of the human global genome repair machinery. Its ectopic over-expression blocks S-phase progression by inhibiting DNA synthesis. The C-terminal region of human KIN17 is crucial for this anti-proliferation effect. Its high-resolution structure, presented here, reveals a tandem of SH3-like subdomains. This domain binds to ribonucleotide homopolymers with the same preferences as the whole protein. Analysis of its structure complexed with tungstate shows structural variability within the domain. The interaction with tungstate is mediated by several lysine residues located within a positively charged groove at the interface between the two subdomains. This groove could be the site of interaction with RNA, since mutagenesis of two of these highly conserved lysine residue weakens RNA binding.
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95
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Valero J, Berciano MT, Weruaga E, Lafarga M, Alonso JR. Pre-neurodegeneration of mitral cells in the pcd mutant mouse is associated with DNA damage, transcriptional repression, and reorganization of nuclear speckles and Cajal bodies. Mol Cell Neurosci 2006; 33:283-95. [PMID: 16978877 DOI: 10.1016/j.mcn.2006.08.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Revised: 07/04/2006] [Accepted: 08/01/2006] [Indexed: 01/01/2023] Open
Abstract
DNA damage and impairment of its repair underlie several neurodegenerative diseases. The Purkinje cell degeneration (pcd) mutation causes the loss of Nna1 expression and is associated with a selective and progressive degeneration of specific neuronal populations, including mitral cells in the olfactory bulb. Using an in situ transcription assay, molecular markers for both nuclear compartments and components of the DNA damage/repair pathway, and ultrastructural analysis, here we demonstrate that the pcd mutation induces the formation of DNA damage/repair foci in mitral cells. Furthermore, this effect is associated with transcriptional inhibition, heterochromatinization, nucleolar segregation and the reorganization of nuclear speckles of splicing factors and Cajal bodies. The most significant cytoplasmic alteration observed was a partial replacement of rough endoplasmic reticulum cisternae by a larger amount of free ribosomes, while other organelles were structurally preserved. The tools employed in this work may be of use for the early detection of predegenerative processes in neurodegenerative disorders and for validating rescue strategies.
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Affiliation(s)
- Jorge Valero
- Laboratorio de Plasticidad Neuronal y Neurorreparación, Instituto de Neurociencias de Castilla y León, Universidad de Salamanca. Avd. Alfonso X el Sabio s/n, E-37007 Salamanca, Spain
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96
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Adams MM, Carpenter PB. Tying the loose ends together in DNA double strand break repair with 53BP1. Cell Div 2006; 1:19. [PMID: 16945145 PMCID: PMC1601952 DOI: 10.1186/1747-1028-1-19] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Accepted: 08/31/2006] [Indexed: 01/08/2023] Open
Abstract
To maintain genomic stability and ensure the fidelity of chromosomal transmission, cells respond to various forms of genotoxic stress, including DNA double-stranded breaks (DSBs), through the activation of DNA damage response signaling networks. In response to DSBs as induced by ionizing radiation (IR), during DNA replication, or through immunoglobulin heavy chain (IgH) rearrangements in B cells of lymphoid origin, the phosphatidyl inositol-like kinase (PIK) kinases ATM (mutated in ataxia telangiectasia), ATR (ATM and Rad3-related kinase), and the DNA-dependent protein kinase (DNA-PK) activate signaling pathways that lead to DSB repair. DSBs are repaired by either of two major, non-mutually exclusive pathways: homologous recombination (HR) that utilizes an undamaged sister chromatid template (or homologous chromosome) and non- homologous end joining (NHEJ), an error prone mechanism that processes and joins broken DNA ends through the coordinated effort of a small set of ubiquitous factors (DNA-PKcs, Ku70, Ku80, artemis, Xrcc4/DNA lig IV, and XLF/Cernunnos). The PIK kinases phosphorylate a variety of effector substrates that propagate the DNA damage signal, ultimately resulting in various biological outputs that influence cell cycle arrest, transcription, DNA repair, and apoptosis. A variety of data has revealed a critical role for p53-binding protein 1 (53BP1) in the cellular response to DSBs including various aspects of p53 function. Importantly, 53BP1 plays a major role in suppressing translocations, particularly in B and T cells. This report will review past experiments and current knowledge regarding the role of 53BP1 in the DNA damage response.
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Affiliation(s)
- Melissa M Adams
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Phillip B Carpenter
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, TX 77030, USA
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97
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Du LL, Nakamura TM, Russell P. Histone modification-dependent and -independent pathways for recruitment of checkpoint protein Crb2 to double-strand breaks. Genes Dev 2006; 20:1583-96. [PMID: 16778077 PMCID: PMC1482479 DOI: 10.1101/gad.1422606] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cellular responses to DNA damage involve the relocalization of checkpoint proteins to DNA double-strand breaks (DSBs). The fission yeast checkpoint mediator protein Crb2, a homolog of mammalian 53BP1, forms ionizing radiation-induced nuclear foci (IRIF). The IRIF formation by Crb2 requires histone H2A C-terminal phosphorylation and H4-K20 methylation. However, the relevance of Crb2 relocalization is uncertain, because neither histone modification is required for a checkpoint response. Here we show that these histone modifications cooperate in the same Crb2 recruitment pathway, which also requires the Tudor and BRCT motifs in Crb2. In the absence of these histone modifications, an alternative recruitment pathway is sufficient for checkpoint activation and accumulation of Crb2 at a persistent DSB generated by HO endonuclease. This parallel pathway requires a cyclin-dependent kinase phosphorylation site in Crb2 that mediates an association with another BRCT protein Cut5 (the TopBP1 homolog), which also accumulates at HO-induced DSBs. We propose that such dual recruitment mechanisms may be a common feature of DNA damage checkpoint mediators.
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Affiliation(s)
- Li-Lin Du
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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98
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Taucher-Scholz G, Jakob B. Ion Irradiation as a Tool to Reveal the Spatiotemporal Dynamics of DNA Damage Response Processes. Genome Integr 2006. [DOI: 10.1007/7050_015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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