1
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Cui G, Botuyan MV, Drané P, Hu Q, Bragantini B, Thompson JR, Schuller DJ, Detappe A, Perfetti MT, James LI, Frye SV, Chowdhury D, Mer G. An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering. Nat Commun 2023; 14:6091. [PMID: 37773238 PMCID: PMC10541411 DOI: 10.1038/s41467-023-41821-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023] Open
Abstract
The recruitment of 53BP1 to chromatin, mediated by its recognition of histone H4 dimethylated at lysine 20 (H4K20me2), is important for DNA double-strand break repair. Using a series of small molecule antagonists, we demonstrate a conformational equilibrium between an open and a pre-existing lowly populated closed state of 53BP1 in which the H4K20me2 binding surface is buried at the interface between two interacting 53BP1 molecules. In cells, these antagonists inhibit the chromatin recruitment of wild type 53BP1, but do not affect 53BP1 variants unable to access the closed conformation despite preservation of the H4K20me2 binding site. Thus, this inhibition operates by shifting the conformational equilibrium toward the closed state. Our work therefore identifies an auto-associated form of 53BP1-autoinhibited for chromatin binding-that can be stabilized by small molecule ligands encapsulated between two 53BP1 protomers. Such ligands are valuable research tools to study the function of 53BP1 and have the potential to facilitate the development of new drugs for cancer therapy.
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Affiliation(s)
- Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - Pascal Drané
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Benoît Bragantini
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - David J Schuller
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY, USA
| | | | - Michael T Perfetti
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
- Department of Cancer Biology, Mayo Clinic, Rochester, MN, USA.
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2
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Yin S, Liu L, Gan W. PRMT1 and PRMT5: on the road of homologous recombination and non-homologous end joining. GENOME INSTABILITY & DISEASE 2023; 4:197-209. [PMID: 37663901 PMCID: PMC10470524 DOI: 10.1007/s42764-022-00095-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/28/2022] [Indexed: 09/05/2023]
Abstract
DNA double-strand breaks (DSBs) are widely accepted to be the most deleterious form of DNA lesions that pose a severe threat to genome integrity. Two predominant pathways are responsible for repair of DSBs, homologous recombination (HR) and non-homologous end-joining (NHEJ). HR relies on a template to faithfully repair breaks, while NHEJ is a template-independent and error-prone repair mechanism. Multiple layers of regulation have been documented to dictate the balance between HR and NHEJ, such as cell cycle and post-translational modifications (PTMs). Arginine methylation is one of the most common PTMs, which is catalyzed by protein arginine methyltransferases (PRMTs). PRMT1 and PRMT5 are the predominate PRMTs that promote asymmetric dimethylarginine and symmetric dimethylarginine, respectively. They have emerged to be crucial regulators of DNA damage repair. In this review, we summarize current understanding and unaddressed questions of PRMT1 and PRMT5 in regulation of HR and NHEJ, providing insights into their roles in DSB repair pathway choice and the potential of targeting them for cancer therapy.
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Affiliation(s)
- Shasha Yin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Liu Liu
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Wenjian Gan
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
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3
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Cui G, Botuyan MV, Drané P, Hu Q, Bragantini B, Thompson JR, Schuller DJ, Detappe A, Perfetti MT, James LI, Frye SV, Chowdhury D, Mer G. An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.534960. [PMID: 37131705 PMCID: PMC10153216 DOI: 10.1101/2023.04.20.534960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The recruitment of 53BP1 to chromatin, mediated by its recognition of histone H4 dimethylated at lysine 20 (H4K20me2), is important for DNA double-strand break repair. Using a series of small molecule antagonists, we demonstrate a conformational equilibrium between an open and a pre-existing lowly populated closed state of 53BP1 in which the H4K20me2 binding surface is buried at the interface between two interacting 53BP1 molecules. In cells, these antagonists inhibit the chromatin recruitment of wild type 53BP1, but do not affect 53BP1 variants unable to access the closed conformation despite preservation of the H4K20me2 binding site. Thus, this inhibition operates by shifting the conformational equilibrium toward the closed state. Our work therefore identifies an auto-associated form of 53BP1 - autoinhibited for chromatin binding - that can be stabilized by small molecule ligands encapsulated between two 53BP1 protomers. Such ligands are valuable research tools to study the function of 53BP1 and have the potential to facilitate the development of new drugs for cancer therapy.
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4
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Jeong A, Cho Y, Cho M, Bae GU, Song DG, Kim SN, Kim YK. PRMT7 Inhibitor SGC8158 Enhances Doxorubicin-Induced DNA Damage and Its Cytotoxicity. Int J Mol Sci 2022; 23:ijms232012323. [PMID: 36293180 PMCID: PMC9604017 DOI: 10.3390/ijms232012323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/09/2022] [Accepted: 10/13/2022] [Indexed: 11/07/2022] Open
Abstract
Protein arginine methyltransferase 7 (PRMT7) regulates various cellular responses, including gene expression, cell migration, stress responses, and stemness. In this study, we investigated the biological role of PRMT7 in cell cycle progression and DNA damage response (DDR) by inhibiting PRMT7 activity with either SGC8158 treatment or its specific siRNA transfection. Suppression of PRMT7 caused cell cycle arrest at the G1 phase, resulting from the stabilization and subsequent accumulation of p21 protein. In addition, PRMT7 activity is closely associated with DNA repair pathways, including both homologous recombination and non-homologous end-joining. Interestingly, SGC8158, in combination with doxorubicin, led to a synergistic increase in both DNA damage and cytotoxicity in MCF7 cells. Taken together, our data demonstrate that PRMT7 is a critical modulator of cell growth and DDR, indicating that it is a promising target for cancer treatment.
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Affiliation(s)
- Ahyeon Jeong
- Muscle Physiome Research Center and Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea
| | - Yena Cho
- Muscle Physiome Research Center and Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea
| | - Minkyeong Cho
- Muscle Physiome Research Center and Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea
| | - Gyu-Un Bae
- Muscle Physiome Research Center and Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea
| | - Dae-Geun Song
- Natural Products Research Institute, KIST Gangneung, Gangneung 25451, Korea
| | - Su-Nam Kim
- Natural Products Research Institute, KIST Gangneung, Gangneung 25451, Korea
- Division of Bio-Medical Science and Technology, University of Science and Technology KIST School, Seoul 02792, Korea
- Correspondence: (S.-N.K.); (Y.K.K.); Tel.: +82-33-650-3503 (S.-N.K.); +82-2-2077-7688 (Y.K.K.)
| | - Yong Kee Kim
- Muscle Physiome Research Center and Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea
- Correspondence: (S.-N.K.); (Y.K.K.); Tel.: +82-33-650-3503 (S.-N.K.); +82-2-2077-7688 (Y.K.K.)
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5
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Furia L, Pelicci S, Scanarini M, Pelicci PG, Faretta M. From Double-Strand Break Recognition to Cell-Cycle Checkpoint Activation: High Content and Resolution Image Cytometry Unmasks 53BP1 Multiple Roles in DNA Damage Response and p53 Action. Int J Mol Sci 2022; 23:ijms231710193. [PMID: 36077590 PMCID: PMC9456172 DOI: 10.3390/ijms231710193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/25/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
53BP1 protein has been isolated in-vitro as a putative p53 interactor. From the discovery of its engagement in the DNA-Damage Response (DDR), its role in sustaining the activity of the p53-regulated transcriptional program has been frequently under-evaluated, even in the case of a specific response to numerous DNA Double-Strand Breaks (DSBs), i.e., exposure to ionizing radiation. The localization of 53BP1 protein constitutes a key to decipher the network of activities exerted in response to stress. We present here an automated-microscopy for image cytometry protocol to analyze the evolution of the DDR, and to demonstrate how 53BP1 moved from damaged sites, where the well-known interaction with the DSB marker γH2A.X takes place, to nucleoplasm, interacting with p53, and enhancing the transcriptional regulation of the guardian of the genome protein. Molecular interactions have been quantitatively described and spatiotemporally localized at the highest spatial resolution by a simultaneous analysis of the impairment of the cell-cycle progression. Thanks to the high statistical sampling of the presented protocol, we provide a detailed quantitative description of the molecular events following the DSBs formation. Single-Molecule Localization Microscopy (SMLM) Analysis finally confirmed the p53–53BP1 interaction on the tens of nanometers scale during the distinct phases of the response.
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Affiliation(s)
- Laura Furia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Simone Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Mirco Scanarini
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
- Correspondence:
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6
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Su PR, You L, Beerens C, Bezstarosti K, Demmers J, Pabst M, Kanaar R, Hsu CC, Chien MP. Microscopy-based single-cell proteomic profiling reveals heterogeneity in DNA damage response dynamics. CELL REPORTS METHODS 2022; 2:100237. [PMID: 35784653 PMCID: PMC9243628 DOI: 10.1016/j.crmeth.2022.100237] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 04/03/2022] [Accepted: 05/23/2022] [Indexed: 11/01/2022]
Abstract
Single-cell proteomics has the potential to decipher tumor heterogeneity, and a method like single-cell proteomics by mass spectrometry (SCoPE-MS) allows profiling several tens of single cells for >1,000 proteins per cell. This method, however, cannot link the proteome of individual cells with phenotypes of interest. Here, we developed a microscopy-based functional single-cell proteomic-profiling technology, called FUNpro, to address this. FUNpro enables screening, identification, and isolation of single cells of interest in a real-time fashion, even if the phenotypes are dynamic or the cells of interest are rare. We applied FUNpro to proteomically profile a newly identified small subpopulation of U2OS osteosarcoma cells displaying an abnormal, prolonged DNA damage response (DDR) after ionizing radiation (IR). With this, we identified the PDS5A protein contributing to the abnormal DDR dynamics and helping the cells survive after IR.
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Affiliation(s)
- Pin-Rui Su
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Li You
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Cecile Beerens
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Karel Bezstarosti
- Proteomics Core Facility, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jeroen Demmers
- Proteomics Core Facility, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Miao-Ping Chien
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
- Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
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7
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Lee H, Choi S, Ha S, Yoon S, Kim WY. ARL2 is required for homologous recombination repair and colon cancer stem cell survival. FEBS Open Bio 2022; 12:1523-1533. [PMID: 35567502 PMCID: PMC9340879 DOI: 10.1002/2211-5463.13438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/16/2022] [Accepted: 05/12/2022] [Indexed: 11/10/2022] Open
Abstract
ARL2 regulates the dynamics of cytological components and is highly expressed in colon cancer tissues. Here, we report novel roles of ARL2 in the cell nucleus and colon cancer stem cells (CSCs). ARL2 is expressed at relatively low levels in K‐RAS active colon cancer cells, but its expression is induced in CSCs. Depletion of ARL2 results in M phase arrest exclusively in non‐CSC cultured cells; in addition, DNA break stress accumulates in CSCs leading to apoptosis. ARL2 expression is positively associated with the expression of all six RAD51 family genes, which are essential for homologous recombination repair (HRR). Furthermore, ARL2 is required for HRR and detected within chromatin compartments. These results demonstrate the requirement of ARL2 in colon CSC maintenance, which possibly occurs through mediating double‐strand break DNA repair in the nucleus.
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Affiliation(s)
- Hani Lee
- College of Pharmacy, Sookmyung Women's University, Cheongparo 47 gil, Yongsangu, Seoul, 04312, Korea
| | - SeokGyeong Choi
- College of Pharmacy, Sookmyung Women's University, Cheongparo 47 gil, Yongsangu, Seoul, 04312, Korea
| | - Sojung Ha
- College of Pharmacy, Sookmyung Women's University, Cheongparo 47 gil, Yongsangu, Seoul, 04312, Korea
| | - Sukjoon Yoon
- Department of Biological Sciences, Sookmyung Women's University, Cheongparo 47 gil, Yongsangu, Seoul, 04312, Korea
| | - Woo-Young Kim
- College of Pharmacy, Sookmyung Women's University, Cheongparo 47 gil, Yongsangu, Seoul, 04312, Korea.,Research Institute of Pharmacal Research, Sookmyung Women's University, Cheongparo 47 gil, Yongsangu, Seoul, 04312, Korea
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8
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Chen D, Gervai JZ, Póti Á, Németh E, Szeltner Z, Szikriszt B, Gyüre Z, Zámborszky J, Ceccon M, d'Adda di Fagagna F, Szallasi Z, Richardson AL, Szüts D. BRCA1 deficiency specific base substitution mutagenesis is dependent on translesion synthesis and regulated by 53BP1. Nat Commun 2022; 13:226. [PMID: 35017534 PMCID: PMC8752635 DOI: 10.1038/s41467-021-27872-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 12/15/2021] [Indexed: 12/25/2022] Open
Abstract
Defects in BRCA1, BRCA2 and other genes of the homology-dependent DNA repair (HR) pathway cause an elevated rate of mutagenesis, eliciting specific mutation patterns including COSMIC signature SBS3. Using genome sequencing of knock-out cell lines we show that Y family translesion synthesis (TLS) polymerases contribute to the spontaneous generation of base substitution and short insertion/deletion mutations in BRCA1 deficient cells, and that TLS on DNA adducts is increased in BRCA1 and BRCA2 mutants. The inactivation of 53BP1 in BRCA1 mutant cells markedly reduces TLS-specific mutagenesis, and rescues the deficiency of template switch-mediated gene conversions in the immunoglobulin V locus of BRCA1 mutant chicken DT40 cells. 53BP1 also promotes TLS in human cellular extracts in vitro. Our results show that HR deficiency-specific mutagenesis is largely caused by TLS, and suggest a function for 53BP1 in regulating the choice between TLS and error-free template switching in replicative DNA damage bypass.
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Affiliation(s)
- Dan Chen
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Judit Z Gervai
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Doctoral School of Molecular Medicine, Semmelweis University, Budapest, H-1085, Hungary
| | - Judit Zámborszky
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Marta Ceccon
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139, Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139, Milan, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Zoltan Szallasi
- Computational Health Informatics Program (CHIP), Boston Children's Hospital and Harvard Medical School, Boston, MA, 02215, USA
- Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
- SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, Budapest, H-1092, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary.
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9
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Annor GK, Elshabassy N, Lundine D, Conde DG, Xiao G, Ellison V, Bargonetti J. Oligomerization of Mutant p53 R273H is not Required for Gain-of-Function Chromatin Associated Activities. Front Cell Dev Biol 2021; 9:772315. [PMID: 34881245 PMCID: PMC8645790 DOI: 10.3389/fcell.2021.772315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/28/2021] [Indexed: 01/11/2023] Open
Abstract
The TP53 gene is often mutated in cancer, with missense mutations found in the central DNA binding domain, and less often in the C-terminal oligomerization domain (OD). These types of mutations are found in patients with the rare inherited cancer predisposition disorder called Li-Fraumeni syndrome. We previously found that mutant p53 (mtp53) R273H associates with replicating DNA and promotes the chromatin association of replication-associated proteins mini-chromosome maintenance 2 (MCM2), and poly ADP-ribose polymerase 1(PARP1). Herein, we created dual mutants in order to test if the oligomerization state of mtp53 R273H played a role in chromatin binding oncogenic gain-of-function (GOF) activities. We used site-directed mutagenesis to introduce point mutations in the OD in wild-type p53 (wtp53), and mtp53 R273H expressing plasmids. The glutaraldehyde crosslinking assay revealed that both wtp53 and mtp53 R273H formed predominantly tetramers, while the single OD mutant A347D, and the dual mtp53 R273H-A347D, formed predominantly dimers. The R337C, L344P, mtp53 R273H-R337C, and mtp53 R273H-L344P proteins formed predominantly monomers. Wtp53 was able to activate the cyclin-dependent kinase gene p21/waf and the p53 feedback regulator MDM2. As expected, the transactivation activity was lost for all the single mutants, as well as the mtp53 R273H-dual mutants. Importantly, mtp53 R273H and the dual oligomerization mutants, R273H-A347D, R273H-R337C, and R273H-L344P were able to interact with chromatin. Additionally, the dual oligomerization mutants, R273H-A347D, R273H-R337C, and R273H-L344P, maintained strong interactions with MCM2 and PARP1. Our findings suggest that while mtp53 R273H can form tetramers, tetramer formation is not required for the GOF associated chromatin interactions.
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Affiliation(s)
- George K Annor
- The Department of Biological Sciences Hunter College, Belfer Research Building, City University of New York, New York, NY, United States.,The Graduate Center Biology and Biochemistry Programs of City University of New York, New York, NY, United States
| | - Nour Elshabassy
- The Department of Biological Sciences Hunter College, Belfer Research Building, City University of New York, New York, NY, United States
| | - Devon Lundine
- The Department of Biological Sciences Hunter College, Belfer Research Building, City University of New York, New York, NY, United States.,The Graduate Center Biology and Biochemistry Programs of City University of New York, New York, NY, United States
| | - Don-Gerard Conde
- The Department of Biological Sciences Hunter College, Belfer Research Building, City University of New York, New York, NY, United States
| | - Gu Xiao
- The Department of Biological Sciences Hunter College, Belfer Research Building, City University of New York, New York, NY, United States
| | - Viola Ellison
- The Department of Biological Sciences Hunter College, Belfer Research Building, City University of New York, New York, NY, United States
| | - Jill Bargonetti
- The Department of Biological Sciences Hunter College, Belfer Research Building, City University of New York, New York, NY, United States.,The Graduate Center Biology and Biochemistry Programs of City University of New York, New York, NY, United States.,Department of Cell and Developmental Biology, Weill Cornell Medical College, New York City, NY, United States
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10
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Zhang F, Gong Z. Regulation of DNA double-strand break repair pathway choice: a new focus on 53BP1. J Zhejiang Univ Sci B 2021; 22:38-46. [PMID: 33448186 DOI: 10.1631/jzus.b2000306] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Maintenance of cellular homeostasis and genome integrity is a critical responsibility of DNA double-strand break (DSB) signaling. P53-binding protein 1 (53BP1) plays a critical role in coordinating the DSB repair pathway choice and promotes the non-homologous end-joining (NHEJ)-mediated DSB repair pathway that rejoins DSB ends. New insights have been gained into a basic molecular mechanism that is involved in 53BP1 recruitment to the DNA lesion and how 53BP1 then recruits the DNA break-responsive effectors that promote NHEJ-mediated DSB repair while inhibiting homologous recombination (HR) signaling. This review focuses on the up- and downstream pathways of 53BP1 and how 53BP1 promotes NHEJ-mediated DSB repair, which in turn promotes the sensitivity of poly(ADP-ribose) polymerase inhibitor (PARPi) in BRCA1-deficient cancers and consequently provides an avenue for improving cancer therapy strategies.
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Affiliation(s)
- Fan Zhang
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Zihua Gong
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA.
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11
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The role of protein arginine methyltransferases in kidney diseases. Clin Sci (Lond) 2020; 134:2037-2051. [PMID: 32766778 DOI: 10.1042/cs20200680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 12/16/2022]
Abstract
The methylation of arginine residues by protein arginine methyltransferases (PRMTs) is a crucial post-translational modification for many biological processes, including DNA repair, RNA processing, and transduction of intra- and extracellular signaling. Previous studies have reported that PRMTs are extensively involved in various pathologic states, including cancer, inflammation, and oxidative stress reaction. However, the role of PRMTs has not been well described in kidney diseases. Recent studies have shown that aberrant function of PRMTs and its metabolic products-symmetric dimethylarginine (SDMA) and asymmetric dimethylarginine (ADMA)-are involved in several renal pathological processes, including renal fibrosis, acute kidney injury (AKI), diabetic nephropathy (DN), hypertension, graft rejection and renal tumors. We aim in this review to elucidate the possible roles of PRMTs in normal renal function and various kidney diseases.
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12
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Ting X, Xia L, Yang J, He L, Si W, Shang Y, Sun L. USP11 acts as a histone deubiquitinase functioning in chromatin reorganization during DNA repair. Nucleic Acids Res 2019; 47:9721-9740. [PMID: 31504778 PMCID: PMC6765148 DOI: 10.1093/nar/gkz726] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 08/03/2019] [Accepted: 08/19/2019] [Indexed: 12/27/2022] Open
Abstract
How chromatin dynamics is regulated to ensure efficient DNA repair remains to be understood. Here, we report that the ubiquitin-specific protease USP11 acts as a histone deubiquitinase to catalyze H2AK119 and H2BK120 deubiquitination. We showed that USP11 is physically associated with the chromatin remodeling NuRD complex and functionally involved in DNA repair process. We demonstrated that USP11-mediated histone deubiquitination and NuRD-associated histone deacetylation coordinate to allow timely termination of DNA repair and reorganization of the chromatin structure. As such, USP11 is involved in chromatin condensation, genomic stability, and cell survival. Together, these observations indicate that USP11 is a chromatin modifier critically involved in DNA damage response and the maintenance of genomic stability.
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Affiliation(s)
- Xia Ting
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lu Xia
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Wenzhe Si
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Yongfeng Shang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Luyang Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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13
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Cao Z, Goyal D, Meiler SE, Zhou Y, Dynan WS. Platforms for delivery of macromolecules to sites of DNA double-strand break repair. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:2196-2204. [PMID: 31159605 DOI: 10.1080/21691401.2019.1622553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Zhen Cao
- Institute of Molecular Medicine and Genetics, Georgia Health Sciences University, Augusta, Georgia, USA
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P. R. China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P. R. China
- Hubei Cancer Clinical Study Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Deepika Goyal
- Institute of Molecular Medicine and Genetics, Georgia Health Sciences University, Augusta, Georgia, USA
| | - Steffen E. Meiler
- Department of Anesthesiology and Perioperative Medicine, Georgia Health Sciences University, Augusta, Georgia, USA
| | - Yunfeng Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P. R. China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P. R. China
- Hubei Cancer Clinical Study Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - William S. Dynan
- Institute of Molecular Medicine and Genetics, Georgia Health Sciences University, Augusta, Georgia, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
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14
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Becker JR, Cuella-Martin R, Barazas M, Liu R, Oliveira C, Oliver AW, Bilham K, Holt AB, Blackford AN, Heierhorst J, Jonkers J, Rottenberg S, Chapman JR. The ASCIZ-DYNLL1 axis promotes 53BP1-dependent non-homologous end joining and PARP inhibitor sensitivity. Nat Commun 2018; 9:5406. [PMID: 30559443 PMCID: PMC6297349 DOI: 10.1038/s41467-018-07855-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
53BP1 controls a specialized non-homologous end joining (NHEJ) pathway that is essential for adaptive immunity, yet oncogenic in BRCA1 mutant cancers. Intra-chromosomal DNA double-strand break (DSB) joining events during immunoglobulin class switch recombination (CSR) require 53BP1. However, in BRCA1 mutant cells, 53BP1 blocks homologous recombination (HR) and promotes toxic NHEJ, resulting in genomic instability. Here, we identify the protein dimerization hub-DYNLL1-as an organizer of multimeric 53BP1 complexes. DYNLL1 binding stimulates 53BP1 oligomerization, and promotes 53BP1's recruitment to, and interaction with, DSB-associated chromatin. Consequently, DYNLL1 regulates 53BP1-dependent NHEJ: CSR is compromised upon deletion of Dynll1 or its transcriptional regulator Asciz, or by mutation of DYNLL1 binding motifs in 53BP1; furthermore, Brca1 mutant cells and tumours are rendered resistant to poly-ADP ribose polymerase (PARP) inhibitor treatments upon deletion of Dynll1 or Asciz. Thus, our results reveal a mechanism that regulates 53BP1-dependent NHEJ and the therapeutic response of BRCA1-deficient cancers.
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Affiliation(s)
- Jordan R Becker
- Genome Integrity Laboratory, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Raquel Cuella-Martin
- Genome Integrity Laboratory, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Marco Barazas
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Rui Liu
- St. Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
| | - Catarina Oliveira
- Genome Integrity Laboratory, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
| | - Kirstin Bilham
- Genome Integrity Laboratory, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Abbey B Holt
- MRC Brain Network Dynamics Unit, Department of Pharmacology, University of Oxford, Oxford, OX1 3TH, UK
| | - Andrew N Blackford
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Jörg Heierhorst
- St. Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
- Department of Medicine at St. Vincent's Hospital, Melbourne Medical School, The University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Sven Rottenberg
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, 3012, Switzerland
| | - J Ross Chapman
- Genome Integrity Laboratory, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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15
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Otsuka K, Tomita M. Concurrent live imaging of DNA double-strand break repair and cell-cycle progression by CRISPR/Cas9-mediated knock-in of a tricistronic vector. Sci Rep 2018; 8:17309. [PMID: 30470841 PMCID: PMC6251881 DOI: 10.1038/s41598-018-35642-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 11/08/2018] [Indexed: 12/31/2022] Open
Abstract
Cell-cycle progression can be arrested by ionizing radiation-induced DNA double-strand breaks (DSBs). Although DSBs are patched by DSB repair systems, which comprise proteins such as p53-binding protein 1 (53BP1), the relationship between DSB repair progression and cell-cycle status in living cells is unclear. The probe FUCCI (fluorescent ubiquitination-based cell-cycle indicator) was previously developed for visualizing cell-cycle status. Here, we established novel live-imaging probes based on custom-designed plasmids designated “Focicles” harboring a tricistronic compartment encoding distinct fluorescent proteins ligated to the murine 53BP1 foci-forming region (FFR) and two cell-cycle indicators that are known components of FUCCI (hCdt1 and hGmnn). We used CRISPR/Cas9-mediated genome editing to obtain Focicle knock-in cell lines in NIH3T3 cells, which were subject to X-ray irradiation that induced comparable numbers of Focicle and endogenous-53BP1 foci. In addition, the Focicle probes enabled the kinetic analysis of both DSB repair and cell-cycle arrest/progression after irradiation, demonstrating that the Focicle knock-in cells progressed to cell division after DNA damage elimination. These newly developed probes can help to gain a better understanding of the dynamics of DSB repair and cell-cycle control to in turn guide cancer treatment development and cancer-risk assessments.
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Affiliation(s)
- Kensuke Otsuka
- Radiation Safety Research Center, Nuclear Technology Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), Tokyo, 201-8511, Japan.
| | - Masanori Tomita
- Radiation Safety Research Center, Nuclear Technology Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), Tokyo, 201-8511, Japan
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16
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Weaver TM, Morrison EA, Musselman CA. Reading More than Histones: The Prevalence of Nucleic Acid Binding among Reader Domains. Molecules 2018; 23:molecules23102614. [PMID: 30322003 PMCID: PMC6222470 DOI: 10.3390/molecules23102614] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/02/2018] [Accepted: 10/07/2018] [Indexed: 01/09/2023] Open
Abstract
The eukaryotic genome is packaged into the cell nucleus in the form of chromatin, a complex of genomic DNA and histone proteins. Chromatin structure regulation is critical for all DNA templated processes and involves, among many things, extensive post-translational modification of the histone proteins. These modifications can be “read out” by histone binding subdomains known as histone reader domains. A large number of reader domains have been identified and found to selectively recognize an array of histone post-translational modifications in order to target, retain, or regulate chromatin-modifying and remodeling complexes at their substrates. Interestingly, an increasing number of these histone reader domains are being identified as also harboring nucleic acid binding activity. In this review, we present a summary of the histone reader domains currently known to bind nucleic acids, with a focus on the molecular mechanisms of binding and the interplay between DNA and histone recognition. Additionally, we highlight the functional implications of nucleic acid binding in chromatin association and regulation. We propose that nucleic acid binding is as functionally important as histone binding, and that a significant portion of the as yet untested reader domains will emerge to have nucleic acid binding capabilities.
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Affiliation(s)
- Tyler M Weaver
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Emma A Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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17
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Wang J, Yuan Z, Cui Y, Xie R, Yang G, Kassab MA, Wang M, Ma Y, Wu C, Yu X, Liu X. Molecular basis for the inhibition of the methyl-lysine binding function of 53BP1 by TIRR. Nat Commun 2018; 9:2689. [PMID: 30002377 PMCID: PMC6043480 DOI: 10.1038/s41467-018-05174-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/14/2018] [Indexed: 11/09/2022] Open
Abstract
53BP1 performs essential functions in DNA double-strand break (DSB) repair and it was recently reported that Tudor interacting repair regulator (TIRR) negatively regulates 53BP1 during DSB repair. Here, we present the crystal structure of the 53BP1 tandem Tudor domain (TTD) in complex with TIRR. Our results show that three loops from TIRR interact with 53BP1 TTD and mask the methylated lysine-binding pocket in TTD. Thus, TIRR competes with histone H4K20 methylation for 53BP1 binding. We map key interaction residues in 53BP1 TTD and TIRR, whose mutation abolishes complex formation. Moreover, TIRR suppresses the relocation of 53BP1 to DNA lesions and 53BP1-dependent DNA damage repair. Finally, despite the high-sequence homology between TIRR and NUDT16, NUDT16 does not directly interact with 53BP1 due to the absence of key residues required for binding. Taken together, our study provides insights into the molecular mechanism underlying TIRR-mediated suppression of 53BP1-dependent DNA damage repair.
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Affiliation(s)
- Jiaxu Wang
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, Shandong, China
| | - Yaqi Cui
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Rong Xie
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Guang Yang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Muzaffer A Kassab
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Mengxi Wang
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
| | - Yinliang Ma
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Chen Wu
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
| | - Xiuhua Liu
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China.
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18
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Paquin KL, Howlett NG. Understanding the Histone DNA Repair Code: H4K20me2 Makes Its Mark. Mol Cancer Res 2018; 16:1335-1345. [PMID: 29858375 DOI: 10.1158/1541-7786.mcr-17-0688] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/28/2018] [Accepted: 05/22/2018] [Indexed: 12/11/2022]
Abstract
Chromatin is a highly compact structure that must be rapidly rearranged in order for DNA repair proteins to access sites of damage and facilitate timely and efficient repair. Chromatin plasticity is achieved through multiple processes, including the posttranslational modification of histone tails. In recent years, the impact of histone posttranslational modification on the DNA damage response has become increasingly well recognized, and chromatin plasticity has been firmly linked to efficient DNA repair. One particularly important histone posttranslational modification process is methylation. Here, we focus on the regulation and function of H4K20 methylation (H4K20me) in the DNA damage response and describe the writers, erasers, and readers of this important chromatin mark as well as the combinatorial histone posttranslational modifications that modulate H4K20me recognition. Finally, we discuss the central role of H4K20me in determining if DNA double-strand breaks (DSB) are repaired by the error-prone, nonhomologous DNA end joining pathway or the error-free, homologous recombination pathway. This review article discusses the regulation and function of H4K20me2 in DNA DSB repair and outlines the components and modifications that modulate this important chromatin mark and its fundamental impact on DSB repair pathway choice. Mol Cancer Res; 16(9); 1335-45. ©2018 AACR.
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Affiliation(s)
- Karissa L Paquin
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island
| | - Niall G Howlett
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island.
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19
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Wang H, Peng B, Pandita RK, Engler DA, Matsunami RK, Xu X, Hegde PM, Butler BE, Pandita TK, Mitra S, Xu B, Hegde ML. Aurora kinase B dependent phosphorylation of 53BP1 is required for resolving merotelic kinetochore-microtubule attachment errors during mitosis. Oncotarget 2018; 8:48671-48687. [PMID: 28415769 PMCID: PMC5564716 DOI: 10.18632/oncotarget.16225] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 01/11/2023] Open
Abstract
Defects in resolving kinetochore-microtubule attachment mistakes during mitosis is linked to chromosome instability associated with carcinogenesis as well as resistance to cancer therapy. Here we report for the first time that tumor suppressor p53-binding protein 1 (53BP1) is phosphorylated at serine 1342 (S1342) by Aurora kinase B both in vitro and in human cells, which is required for optimal recruitment of 53BP1 at kinetochores. Furthermore, 53BP1 staining normally localized on the outer kinetochore, extended to the whole kinetochore when it is merotelically-attached, in concert with mitotic centromere-associated kinesin. Kinetochore-binding of pS1342-53BP1 is essential for efficient resolving of merotelic attachment, a spontaneous kinetochore-microtubule connection error that usually causes aneuploidy. Consistently, loss of 53BP1 results in significant increase in lagging chromosome events, micronuclei formation and aneuploidy, due to the unresolved merotely in both cancer and primary cells, which is prevented by ectopic wild type 53BP1 but not by the nonphophorylable S1342A mutant. We thus document a novel DNA damage-independent function of 53BP1 in maintaining faithful chromosome segregation during mitosis.
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Affiliation(s)
- Haibo Wang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Houston Methodist Neurological Institute, Houston, TX, USA
| | - Bin Peng
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Raj K Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - David A Engler
- Proteomics Programmatic Core Laboratory, Houston Methodist Research Institute, Houston, TX, USA
| | - Risë K Matsunami
- Proteomics Programmatic Core Laboratory, Houston Methodist Research Institute, Houston, TX, USA
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Pavana M Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Brian E Butler
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Tej K Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Weill Medical College of Cornell University, New York, NY, USA
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Weill Medical College of Cornell University, New York, NY, USA
| | - Bo Xu
- Department of Oncology, Southern Research Institute, Birmingham, AL, USA
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA.,Houston Methodist Neurological Institute, Houston, TX, USA.,Weill Medical College of Cornell University, New York, NY, USA
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20
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Wilson MD, Durocher D. Reading chromatin signatures after DNA double-strand breaks. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0280. [PMID: 28847817 DOI: 10.1098/rstb.2016.0280] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2017] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are DNA lesions that must be accurately repaired in order to preserve genomic integrity and cellular viability. The response to DSBs reshapes the local chromatin environment and is largely orchestrated by the deposition, removal and detection of a complex set of chromatin-associated post-translational modifications. In particular, the nucleosome acts as a central signalling hub and landing platform in this process by organizing the recruitment of repair and signalling factors, while at the same time coordinating repair with other DNA-based cellular processes. While current research has provided a descriptive overview of which histone marks affect DSB repair, we are only beginning to understand how these marks are interpreted to foster an efficient DSB response. Here we review how the modified chromatin surrounding DSBs is read, with a focus on the insights gleaned from structural and biochemical studies.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Marcus D Wilson
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Daniel Durocher
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
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21
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Abstract
Dna2 is a nuclease and helicase that functions redundantly with other proteins in Okazaki fragment processing, double-strand break resection, and checkpoint kinase activation. Dna2 is an essential enzyme, required for yeast and mammalian cell viability. Here, we report that numerous mutations affecting the DNA damage checkpoint suppress dna2∆ lethality in Saccharomyces cerevisiaedna2∆ cells are also suppressed by deletion of helicases PIF1 and MPH1, and by deletion of POL32, a subunit of DNA polymerase δ. All dna2∆ cells are temperature sensitive, have telomere length defects, and low levels of telomeric 3' single-stranded DNA (ssDNA). Interestingly, Rfa1, a subunit of the major ssDNA binding protein RPA, and the telomere-specific ssDNA binding protein Cdc13, often colocalize in dna2∆ cells. This suggests that telomeric defects often occur in dna2∆ cells. There are several plausible explanations for why the most critical function of Dna2 is at telomeres. Telomeres modulate the DNA damage response at chromosome ends, inhibiting resection, ligation, and cell-cycle arrest. We suggest that Dna2 nuclease activity contributes to modulating the DNA damage response at telomeres by removing telomeric C-rich ssDNA and thus preventing checkpoint activation.
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22
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He J, Feng X, Hua J, Wei L, Lu Z, Wei W, Cai H, Wang B, Shi W, Ding N, Li H, Zhang Y, Wang J. miR-300 regulates cellular radiosensitivity through targeting p53 and apaf1 in human lung cancer cells. Cell Cycle 2017; 16:1943-1953. [PMID: 28895780 DOI: 10.1080/15384101.2017.1367070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
microRNAs (miRNAs) play a crucial role in mediation of the cellular sensitivity to ionizing radiation (IR). Previous studies revealed that miR-300 was involved in the cellular response to IR or chemotherapy drug. However, whether miR-300 could regulate the DNA damage responses induced by extrinsic genotoxic stress in human lung cancer and the underlying mechanism remain unknown. In this study, the expression of miR-300 was examined in lung cancer cells treated with IR, and the effects of miR-300 on DNA damage repair, cell cycle arrest, apoptosis and senescence induced by IR were investigated. It was found that IR induced upregulation of endogenous miR-300, and ectopic expression of miR-300 by transfected with miR-300 mimics not only greatly enhanced the cellular DNA damage repair ability but also substantially abrogated the G2 cell cycle arrest and apoptosis induced by IR. Bioinformatic analysis predicted that p53 and apaf1 were potential targets of miR-300, and the luciferase reporter assay showed that miR-300 significantly suppressed the luciferase activity through binding to the 3'-UTR of p53 or apaf1 mRNA. In addition, overexpression of miR-300 significantly reduced p53/apaf1 and/or IR-induced p53/apaf1 protein expression levels. Flow cytomertry analysis and colony formation assay showed that miR-300 desensitized lung cancer cells to IR by suppressing p53-dependent G2 cell cycle arrest, apoptosis and senescence. These data demonstrate that miR-300 regulates the cellular sensitivity to IR through targeting p53 and apaf1 in lung cancer cells.
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Affiliation(s)
- Jinpeng He
- a Key Laboratory of Space Radiobiology of Gansu Province & Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics , Chinese Academy of Sciences , Lanzhou , China
| | - Xiu Feng
- a Key Laboratory of Space Radiobiology of Gansu Province & Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics , Chinese Academy of Sciences , Lanzhou , China.,b School of Pharmacy , Lanzhou University , Lanzhou , China
| | - Junrui Hua
- a Key Laboratory of Space Radiobiology of Gansu Province & Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics , Chinese Academy of Sciences , Lanzhou , China
| | - Li Wei
- c Clinical Lab & General Surgery Department , Gansu Provincial Hospital , Lanzhou , China
| | - Zhiwei Lu
- d Major Disease Prevention and Control of Molecular Medicine and Traditional Chinese Medicine Research in Gansu Provincial Key Laboratory , Gansu University of Chinese Medicine , Lanzhou , China
| | - Wenjun Wei
- a Key Laboratory of Space Radiobiology of Gansu Province & Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics , Chinese Academy of Sciences , Lanzhou , China.,e University of Chinese Academy of Sciences , Beijing , China
| | - Hui Cai
- c Clinical Lab & General Surgery Department , Gansu Provincial Hospital , Lanzhou , China
| | - Bing Wang
- a Key Laboratory of Space Radiobiology of Gansu Province & Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics , Chinese Academy of Sciences , Lanzhou , China.,e University of Chinese Academy of Sciences , Beijing , China
| | - Wengui Shi
- a Key Laboratory of Space Radiobiology of Gansu Province & Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics , Chinese Academy of Sciences , Lanzhou , China.,e University of Chinese Academy of Sciences , Beijing , China
| | - Nan Ding
- a Key Laboratory of Space Radiobiology of Gansu Province & Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics , Chinese Academy of Sciences , Lanzhou , China
| | - He Li
- a Key Laboratory of Space Radiobiology of Gansu Province & Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics , Chinese Academy of Sciences , Lanzhou , China.,e University of Chinese Academy of Sciences , Beijing , China
| | - Yanan Zhang
- a Key Laboratory of Space Radiobiology of Gansu Province & Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics , Chinese Academy of Sciences , Lanzhou , China
| | - Jufang Wang
- a Key Laboratory of Space Radiobiology of Gansu Province & Key Laboratory of Heavy Ion Radiation Biology and Medicine, Institute of Modern Physics , Chinese Academy of Sciences , Lanzhou , China
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23
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Teske KA, Hadden MK. Methyllysine binding domains: Structural insight and small molecule probe development. Eur J Med Chem 2017; 136:14-35. [DOI: 10.1016/j.ejmech.2017.04.047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/14/2017] [Accepted: 04/19/2017] [Indexed: 12/19/2022]
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24
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Martinez AR, Kaul Z, Parvin JD, Groden J. Differential requirements for DNA repair proteins in immortalized cell lines using alternative lengthening of telomere mechanisms. Genes Chromosomes Cancer 2017; 56:617-631. [PMID: 28398700 DOI: 10.1002/gcc.22465] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 12/28/2022] Open
Abstract
Cancer cells require telomere maintenance to enable uncontrolled growth. Most often telomerase is activated, although a subset of human cancers are telomerase-negative and depend on recombination-based mechanisms known as ALT (Alternative Lengthening of Telomeres). ALT depends on proteins that are essential for homologous recombination, including BLM and the MRN complex, to extend telomeres. This study surveyed the requirement for requisite homologous recombination proteins, yet to be studied in human ALT cell lines, by protein depletion using RNA interference. Effects on ALT were evaluated by measuring C-circle abundance, a marker of ALT. Surprisingly, several proteins essential for homologous recombination, BARD1, BRCA2, and WRN, were dispensable for C-circle production, while PALB2 had varying effects on C-circles among ALT cell lines. Depletion of homologous recombination proteins BRCA1 and BLM, which have been previously studied in ALT, decreased C-circles in all ALT cell lines. Depletion of the non-homologous end joining proteins 53BP1 and LIG4 had no effect on C-circles in any ALT cell line. Proteins such as chromatin modifiers that recruit double-strand break proteins, RNF8 and RNF168, and other proteins loosely grouped into excision DNA repair processes, XPA, MSH2, and MPG, reduced C-circles in some ALT cell lines. MSH2 depletion also reduced recombination at telomeres as measured by intertelomeric exchanges. Collectively, the requirement for DNA repair proteins varied between the ALT cell lines compared. In sum, our study suggests that ALT proceeds by multiple mechanisms that differ between cell lines and that some of these depend on DNA repair proteins not associated with homologous recombination pathways.
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Affiliation(s)
- Alaina R Martinez
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, Ohio
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Zeenia Kaul
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Jeffrey D Parvin
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Joanna Groden
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
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25
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Drané P, Brault ME, Cui G, Meghani K, Chaubey S, Detappe A, Parnandi N, He Y, Zheng XF, Botuyan MV, Kalousi A, Yewdell WT, Münch C, Harper JW, Chaudhuri J, Soutoglou E, Mer G, Chowdhury D. TIRR regulates 53BP1 by masking its histone methyl-lysine binding function. Nature 2017; 543:211-216. [PMID: 28241136 PMCID: PMC5441565 DOI: 10.1038/nature21358] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/03/2017] [Indexed: 01/13/2023]
Abstract
P53-binding protein 1 (53BP1) is a multi-functional double-strand break repair protein that is essential for class switch recombination in B lymphocytes and for sensitizing BRCA1-deficient tumours to poly-ADP-ribose polymerase-1 (PARP) inhibitors. Central to all 53BP1 activities is its recruitment to double-strand breaks via the interaction of the tandem Tudor domain with dimethylated lysine 20 of histone H4 (H4K20me2). Here we identify an uncharacterized protein, Tudor interacting repair regulator (TIRR), that directly binds the tandem Tudor domain and masks its H4K20me2 binding motif. Upon DNA damage, the protein kinase ataxia-telangiectasia mutated (ATM) phosphorylates 53BP1 and recruits RAP1-interacting factor 1 (RIF1) to dissociate the 53BP1-TIRR complex. However, overexpression of TIRR impedes 53BP1 function by blocking its localization to double-strand breaks. Depletion of TIRR destabilizes 53BP1 in the nuclear-soluble fraction and alters the double-strand break-induced protein complex centring 53BP1. These findings identify TIRR as a new factor that influences double-strand break repair using a unique mechanism of masking the histone methyl-lysine binding function of 53BP1.
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Affiliation(s)
- Pascal Drané
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Marie-Eve Brault
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905
| | - Khyati Meghani
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Shweta Chaubey
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Alexandre Detappe
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Nishita Parnandi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Yizhou He
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Xiao-Feng Zheng
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | | | - Alkmini Kalousi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - William T Yewdell
- Immunology Program, Memorial Sloan-Kettering Cancer Center, Gerstner Sloan-Kettering Graduate School, New York, NY 10065; and Immunology and Microbial Pathogenesis Program, Weill-Cornell Medical School, New York, NY 10065
| | - Christian Münch
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan-Kettering Cancer Center, Gerstner Sloan-Kettering Graduate School, New York, NY 10065; and Immunology and Microbial Pathogenesis Program, Weill-Cornell Medical School, New York, NY 10065
| | - Evi Soutoglou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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26
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Structural aspects of small-molecule inhibition of methyllysine reader proteins. Future Med Chem 2016; 8:1681-702. [PMID: 27577975 DOI: 10.4155/fmc-2016-0082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Methyl reader proteins recognize and bind to post-translationally methylated residues. They execute the commands issued by protein methyltransferases and play functional roles in diverse cellular processes including gene regulation, development and oncogenesis. Efforts to inhibit these proteins are relatively new. Only a small number of methyl reader proteins belonging to the chromodomain, malignant brain tumor domain, plant homeodomain finger and Tudor domain families have been targeted by chemical inhibitors. This review summarizes inhibitors that have been reported to date, and provides a perspective for future progress. Structural determinants for methyl reader inhibition will be presented, along with an analysis of the molecular interactions that control potency and selectivity for inhibitors of each family.
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27
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Kocyłowski MK, Rey AJ, Stewart GS, Halazonetis TD. Ubiquitin-H2AX fusions render 53BP1 recruitment to DNA damage sites independent of RNF8 or RNF168. Cell Cycle 2016; 14:1748-58. [PMID: 25695757 PMCID: PMC4615105 DOI: 10.1080/15384101.2015.1010918] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The mammalian E3 ubiquitin ligases RNF8 and RNF168 facilitate recruitment of the DNA damage response protein 53BP1 to sites of DNA double-strand breaks (DSBs). The mechanism involves recruitment of RNF8, followed by recruitment of RNF168, which ubiquitinates histones H2A/H2AX on K15. 53BP1 then binds to nucleosomes at sites of DNA DSBs by recognizing, in addition to methyl marks, histone H2A/H2AX ubiquitinated on K15. We report here that expressing H2AX fusion proteins with N-terminal bulky moieties can rescue 53BP1 recruitment to sites of DNA DSBs in cells lacking RNF8 or RNF168 or in cells treated with proteasome inhibitors, in which histone ubiquitination at sites of DNA DSBs is compromised. The rescue required S139 at the C-terminus of the H2AX fusion protein and was occasionally accompanied by partial rescue of ubiquitination at sites of DNA DSBs. We conclude that recruitment of 53BP1 to sites of DNA DSBs is possible in the absence of RNF8 or RNF168, but still dependent on chromatin ubiquitination.
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Affiliation(s)
- Maciej K Kocyłowski
- a Department of Molecular Biology; University of Geneva ; Geneva , Switzerland
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28
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Katsura M, Cyou-Nakamine H, Zen Q, Zen Y, Nansai H, Amagasa S, Kanki Y, Inoue T, Kaneki K, Taguchi A, Kobayashi M, Kaji T, Kodama T, Miyagawa K, Wada Y, Akimitsu N, Sone H. Effects of Chronic Low-Dose Radiation on Human Neural Progenitor Cells. Sci Rep 2016; 6:20027. [PMID: 26795421 PMCID: PMC4726121 DOI: 10.1038/srep20027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/19/2015] [Indexed: 12/24/2022] Open
Abstract
The effects of chronic low-dose radiation on human health have not been well established. Recent studies have revealed that neural progenitor cells are present not only in the fetal brain but also in the adult brain. Since immature cells are generally more radiosensitive, here we investigated the effects of chronic low-dose radiation on cultured human neural progenitor cells (hNPCs) derived from embryonic stem cells. Radiation at low doses of 31, 124 and 496 mGy per 72 h was administered to hNPCs. The effects were estimated by gene expression profiling with microarray analysis as well as morphological analysis. Gene expression was dose-dependently changed by radiation. By thirty-one mGy of radiation, inflammatory pathways involving interferon signaling and cell junctions were altered. DNA repair and cell adhesion molecules were affected by 124 mGy of radiation while DNA synthesis, apoptosis, metabolism, and neural differentiation were all affected by 496 mGy of radiation. These in vitro results suggest that 496 mGy radiation affects the development of neuronal progenitor cells while altered gene expression was observed at a radiation dose lower than 100 mGy. This study would contribute to the elucidation of the clinical and subclinical phenotypes of impaired neuronal development induced by chronic low-dose radiation.
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Affiliation(s)
- Mari Katsura
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Hiromasa Cyou-Nakamine
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
- Center for Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan
- Faculty of Pharmaceutical Sciences, Department of Pharmacy, Tokyo University of Science, Noda, Japan
| | - Qin Zen
- Center for Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan
| | - Yang Zen
- Center for Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan
| | - Hiroko Nansai
- Center for Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan
| | - Shota Amagasa
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Yasuharu Kanki
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Tsuyoshi Inoue
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyomi Kaneki
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Akashi Taguchi
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Mika Kobayashi
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Toshiyuki Kaji
- Faculty of Pharmaceutical Sciences, Department of Pharmacy, Tokyo University of Science, Noda, Japan
| | - Tatsuhiko Kodama
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Japan
| | - Youichiro Wada
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | | | - Hideko Sone
- Center for Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan
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29
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Abstract
Protein methylation is a common post-translational modification with diverse biological functions. Methyllysine reader proteins are increasingly a focus of epigenetics research and play important roles in regulating many cellular processes. These reader proteins are vital players in development, cell cycle regulation, stress responses, oncogenesis, and other disease pathways. The recent emergence of a small number of chemical inhibitors for methyllysine reader proteins supports the viability of these proteins as targets for drug development. This article introduces the biochemistry and biology of methyllysine reader proteins, provides an overview of functions for those families of readers that have been targeted to date (MBT, PHD, tudor, and chromodomains), and reviews the development of synthetic agents that directly block their methyllysine reading functions.
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Affiliation(s)
- Natalia Milosevich
- Department of Chemistry, University of Victoria , Victoria, British Columbia V8W 3V6, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria , Victoria, British Columbia V8W 3V6, Canada
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30
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Ahmed EA, Scherthan H, de Rooij DG. DNA Double Strand Break Response and Limited Repair Capacity in Mouse Elongated Spermatids. Int J Mol Sci 2015; 16:29923-35. [PMID: 26694360 PMCID: PMC4691157 DOI: 10.3390/ijms161226214] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/14/2015] [Accepted: 12/10/2015] [Indexed: 12/31/2022] Open
Abstract
Spermatids are extremely sensitive to genotoxic exposures since during spermiogenesis only error-prone non homologous end joining (NHEJ) repair pathways are available. Hence, genomic damage may accumulate in sperm and be transmitted to the zygote. Indirect, delayed DNA fragmentation and lesions associated with apoptotic-like processes have been observed during spermatid elongation, 27 days after irradiation. The proliferating spermatogonia and early meiotic prophase cells have been suggested to retain a memory of a radiation insult leading later to this delayed fragmentation. Here, we used meiotic spread preparations to localize phosphorylate histone H2 variant (γ-H2AX) foci marking DNA double strand breaks (DSBs) in elongated spermatids. This technique enabled us to determine the background level of DSB foci in elongated spermatids of RAD54/RAD54B double knockout (dko) mice, severe combined immunodeficiency SCID mice, and poly adenosine diphosphate (ADP)-ribose polymerase 1 (PARP1) inhibitor (DPQ)-treated mice to compare them with the appropriate wild type controls. The repair kinetics data and the protein expression patterns observed indicate that the conventional NHEJ repair pathway is not available for elongated spermatids to repair the programmed and the IR-induced DSBs, reflecting the limited repair capacity of these cells. However, although elongated spermatids express the proteins of the alternative NHEJ, PARP1-inhibition had no effect on the repair kinetics after IR, suggesting that DNA damage may be passed onto sperm. Finally, our genetic mutant analysis suggests that an incomplete or defective meiotic recombinational repair of Spo11-induced DSBs may lead to a carry-over of the DSB damage or induce a delayed nuclear fragmentation during the sensitive programmed chromatin remodeling occurring in elongated spermatids.
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Affiliation(s)
- Emad A Ahmed
- Laboratory of Immunology and Molecular Physiology, Department of Zoology, Faculty of Science, Assiut University, Assiut 71516, Egypt.
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Harry Scherthan
- Institute für Radiobiologie der Bundeswehr in Verb. mit der University, Ulm, Neuherbergstr, 11, Munich D-80937, Germany.
| | - Dirk G de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584CM, The Netherlands.
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31
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Marková E, Somsedíková A, Vasilyev S, Pobijaková M, Lacková A, Lukačko P, Belyaev I. DNA repair foci and late apoptosis/necrosis in peripheral blood lymphocytes of breast cancer patients undergoing radiotherapy. Int J Radiat Biol 2015; 91:934-45. [DOI: 10.3109/09553002.2015.1101498] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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32
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Structures and Functions of the Multiple KOW Domains of Transcription Elongation Factor Spt5. Mol Cell Biol 2015. [PMID: 26217010 DOI: 10.1128/mcb.00520-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The eukaryotic Spt4-Spt5 heterodimer forms a higher-order complex with RNA polymerase II (and I) to regulate transcription elongation. Extensive genetic and functional data have revealed diverse roles of Spt4-Spt5 in coupling elongation with chromatin modification and RNA-processing pathways. A mechanistic understanding of the diverse functions of Spt4-Spt5 is hampered by challenges in resolving the distribution of functions among its structural domains, including the five KOW domains in Spt5, and a lack of their high-resolution structures. We present high-resolution crystallographic results demonstrating that distinct structures are formed by the first through third KOW domains (KOW1-Linker1 [K1L1] and KOW2-KOW3) of Saccharomyces cerevisiae Spt5. The structure reveals that K1L1 displays a positively charged patch (PCP) on its surface, which binds nucleic acids in vitro, as shown in biochemical assays, and is important for in vivo function, as shown in growth assays. Furthermore, assays in yeast have shown that the PCP has a function that partially overlaps that of Spt4. Synthesis of our results with previous evidence suggests a model in which Spt4 and the K1L1 domain of Spt5 form functionally overlapping interactions with nucleic acids upstream of the transcription bubble, and this mechanism may confer robustness on processes associated with transcription elongation.
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33
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Perfetti MT, Baughma BM, Dickson BM, Mu Y, Cui G, Mader P, Dong A, Norris JL, Rothbart SB, Strahl BD, Brown PJ, Janzen WP, Arrowsmith CH, Mer G, McBride KM, James LI, Frye SV. Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1. ACS Chem Biol 2015; 10:1072-81. [PMID: 25590533 PMCID: PMC4402254 DOI: 10.1021/cb500956g] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Improving our understanding of the role of chromatin regulators in the initiation, development, and suppression of cancer and other devastating diseases is critical, as they are integral players in regulating DNA integrity and gene expression. Developing small molecule inhibitors for this target class with cellular activity is a crucial step toward elucidating their specific functions. We specifically targeted the DNA damage response protein, 53BP1, which uses its tandem tudor domain to recognize histone H4 dimethylated on lysine 20 (H4K20me2), a modification related to double-strand DNA breaks. Through a cross-screening approach, we identified UNC2170 (1) as a micromolar ligand of 53BP1, which demonstrates at least 17-fold selectivity for 53BP1 as compared to other methyl-lysine (Kme) binding proteins tested. Structural studies revealed that the tert-butyl amine of UNC2170 anchors the compound in the methyl-lysine (Kme) binding pocket of 53BP1, making it competitive with endogenous Kme substrates. X-ray crystallography also demonstrated that UNC2170 binds at the interface of two tudor domains of a 53BP1 dimer. Importantly, this compound functions as a 53BP1 antagonist in cellular lysates and shows cellular activity by suppressing class switch recombination, a process which requires a functional 53BP1 tudor domain. These results demonstrate that UNC2170 is a functionally active, fragment-like ligand for 53BP1.
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Affiliation(s)
- Michael T. Perfetti
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Brandi M. Baughma
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Bradley M. Dickson
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Yunxiang Mu
- Department of Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Pavel Mader
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada, M5G 1L7
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada, M5G 1L7
| | - Jacqueline L. Norris
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Scott B. Rothbart
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Brian D. Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada, M5G 1L7
| | - William P. Janzen
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada, M5G 1L7
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kevin M. McBride
- Department of Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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34
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Gibbs-Seymour I, Markiewicz E, Bekker-Jensen S, Mailand N, Hutchison CJ. Lamin A/C-dependent interaction with 53BP1 promotes cellular responses to DNA damage. Aging Cell 2015; 14:162-9. [PMID: 25645366 PMCID: PMC4364828 DOI: 10.1111/acel.12258] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2014] [Indexed: 12/22/2022] Open
Abstract
Lamins A/C have been implicated in DNA damage response pathways. We show that the DNA repair protein 53BP1 is a lamin A/C binding protein. In undamaged human dermal fibroblasts (HDF), 53BP1 is a nucleoskeleton protein. 53BP1 binds to lamins A/C via its Tudor domain, and this is abrogated by DNA damage. Lamins A/C regulate 53BP1 levels and consequently lamin A/C-null HDF display a 53BP1 null-like phenotype. Our data favour a model in which lamins A/C maintain a nucleoplasmic pool of 53BP1 in order to facilitate its rapid recruitment to sites of DNA damage and could explain why an absence of lamin A/C accelerates aging.
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Affiliation(s)
- Ian Gibbs-Seymour
- School of Biological and Biomedical Sciences, Durham UniversityMountjoy Science Park, Durham, DH1 3LE, UK
- Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of CopenhagenCopenhagen, DK-2200, Denmark
| | - Ewa Markiewicz
- School of Biological and Biomedical Sciences, Durham UniversityMountjoy Science Park, Durham, DH1 3LE, UK
| | - Simon Bekker-Jensen
- Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of CopenhagenCopenhagen, DK-2200, Denmark
| | - Niels Mailand
- Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of CopenhagenCopenhagen, DK-2200, Denmark
| | - Christopher J Hutchison
- School of Biological and Biomedical Sciences, Durham UniversityMountjoy Science Park, Durham, DH1 3LE, UK
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35
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Coster G, Goldberg M. The cellular response to DNA damage: A focus on MDC1 and its interacting proteins. Nucleus 2014. [DOI: 10.4161/nucl.11176] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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36
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Regulation of 53BP1 protein stability by RNF8 and RNF168 is important for efficient DNA double-strand break repair. PLoS One 2014; 9:e110522. [PMID: 25337968 PMCID: PMC4206297 DOI: 10.1371/journal.pone.0110522] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/23/2014] [Indexed: 11/19/2022] Open
Abstract
53BP1 regulates DNA double-strand break (DSB) repair. In functional assays for specific DSB repair pathways, we found that 53BP1 was important in the conservative non-homologous end-joining (C-NHEJ) pathway, and this activity was dependent upon RNF8 and RNF168. We observed that 53BP1 protein was diffusely abundant in nuclei, and upon ionizing radiation, 53BP1 was everywhere degraded except at DNA damage sites. Depletion of RNF8 or RNF168 blocked the degradation of the diffusely localized nuclear 53BP1, and ionizing radiation induced foci (IRIF) did not form. Furthermore, when 53BP1 degradation was inhibited, a subset of 53BP1 was bound to DNA damage sites but bulk, unbound 53BP1 remained in the nucleoplasm, and localization of its downstream effector RIF1 at DSBs was abolished. Our data suggest a novel mechanism for responding to DSB that upon ionizing radiation, 53BP1 was divided into two populations, ensuring functional DSB repair: damage site-bound 53BP1 whose binding signal is known to be generated by RNF8 and RNF168; and unbound bulk 53BP1 whose ensuing degradation is regulated by RNF8 and RNF168.
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37
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Lee DH, Acharya SS, Kwon M, Drane P, Guan Y, Adelmant G, Kalev P, Shah J, Pellman D, Marto JA, Chowdhury D. Dephosphorylation enables the recruitment of 53BP1 to double-strand DNA breaks. Mol Cell 2014; 54:512-25. [PMID: 24703952 DOI: 10.1016/j.molcel.2014.03.020] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 02/27/2014] [Accepted: 03/12/2014] [Indexed: 01/01/2023]
Abstract
Excluding 53BP1 from chromatin is required to attenuate the DNA damage response during mitosis, yet the functional relevance and regulation of this exclusion are unclear. Here we show that 53BP1 is phosphorylated during mitosis on two residues, T1609 and S1618, located in its well-conserved ubiquitination-dependent recruitment (UDR) motif. Phosphorylating these sites blocks the interaction of the UDR motif with mononuclesomes containing ubiquitinated histone H2A and impedes binding of 53BP1 to mitotic chromatin. Ectopic recruitment of 53BP1-T1609A/S1618A to mitotic DNA lesions was associated with significant mitotic defects that could be reversed by inhibiting nonhomologous end-joining. We also reveal that protein phosphatase complex PP4C/R3β dephosphorylates T1609 and S1618 to allow the recruitment of 53BP1 to chromatin in G1 phase. Our results identify key sites of 53BP1 phosphorylation during mitosis, identify the counteracting phosphatase complex that restores the potential for DDR during interphase, and establish the physiological importance of this regulation.
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Affiliation(s)
- Dong-Hyun Lee
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Sciences, College of Science, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Sanket S Acharya
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Mijung Kwon
- Department of Cell Biology, Harvard Medical School, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Pascal Drane
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Yinghua Guan
- Department of Systems Biology, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Guillaume Adelmant
- Department of Biological Chemistry Molecular Pharmacology, Harvard Medical School, Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Peter Kalev
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jagesh Shah
- Department of Systems Biology, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - David Pellman
- Department of Cell Biology, Harvard Medical School, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jarrod A Marto
- Department of Biological Chemistry Molecular Pharmacology, Harvard Medical School, Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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USP28 is recruited to sites of DNA damage by the tandem BRCT domains of 53BP1 but plays a minor role in double-strand break metabolism. Mol Cell Biol 2014; 34:2062-74. [PMID: 24687851 DOI: 10.1128/mcb.00197-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The DNA damage response (DDR) is critical for genome stability and the suppression of a wide variety of human malignancies, including neurodevelopmental disorders, immunodeficiency, and cancer. In addition, the efficacy of many chemotherapeutic strategies is dictated by the status of the DDR. Ubiquitin-specific protease 28 (USP28) was reported to govern the stability of multiple factors that are critical for diverse aspects of the DDR. Here, we examined the effects of USP28 depletion on the DDR in cells and in vivo. We found that USP28 is recruited to double-strand breaks in a manner that requires the tandem BRCT domains of the DDR protein 53BP1. However, we observed only minor DDR defects in USP28-depleted cells, and mice lacking USP28 showed normal longevity, immunological development, and radiation responses. Our results thus indicate that USP28 is not a critical factor in double-strand break metabolism and is unlikely to be an attractive target for therapeutic intervention aimed at chemotherapy sensitization.
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39
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Clerici M, Trovesi C, Galbiati A, Lucchini G, Longhese MP. Mec1/ATR regulates the generation of single-stranded DNA that attenuates Tel1/ATM signaling at DNA ends. EMBO J 2013; 33:198-216. [PMID: 24357557 DOI: 10.1002/embj.201386041] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Tel1/ATM and Mec1/ATR checkpoint kinases are activated by DNA double-strand breaks (DSBs). Mec1/ATR recruitment to DSBs requires the formation of RPA-coated single-stranded DNA (ssDNA), which arises from 5'-3' nucleolytic degradation (resection) of DNA ends. Here, we show that Saccharomyces cerevisiae Mec1 regulates resection of the DSB ends. The lack of Mec1 accelerates resection and reduces the loading to DSBs of the checkpoint protein Rad9, which is known to inhibit ssDNA generation. Extensive resection is instead inhibited by the Mec1-ad mutant variant that increases the recruitment near the DSB of Rad9, which in turn blocks DSB resection by both Rad53-dependent and Rad53-independent mechanisms. The mec1-ad resection defect leads to prolonged persistence at DSBs of the MRX complex that causes unscheduled Tel1 activation, which in turn impairs checkpoint switch off. Thus, Mec1 regulates the generation of ssDNA at DSBs, and this control is important to coordinate Mec1 and Tel1 signaling activities at these breaks.
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Affiliation(s)
- Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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40
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Gupta A, Hunt CR, Chakraborty S, Pandita RK, Yordy J, Ramnarain DB, Horikoshi N, Pandita TK. Role of 53BP1 in the regulation of DNA double-strand break repair pathway choice. Radiat Res 2013; 181:1-8. [PMID: 24320053 DOI: 10.1667/rr13572.1] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The p53-binding protein 1 (53BP1) is a well-known DNA damage response (DDR) factor, which is recruited to nuclear structures at the site of DNA damage and forms readily visualized ionizing radiation (IR) induced foci. Depletion of 53BP1 results in cell cycle arrest in G2/M phase as well as genomic instability in human as well as mouse cells. Within the DNA damage response mechanism, 53BP1 is classified as an adaptor/mediator, required for processing of the DNA damage response signal and as a platform for recruitment of other repair factors. More recently, specific 53BP1 contributions to DSB repair pathway choice have been recognized and are being characterized. In this review, we have summarized recent advances in understanding the role of 53BP1 in regulating DNA DSBs repair pathway choice, variable diversity joining [V(D)J] recombination and class-switch recombination (CSR).
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Affiliation(s)
- Arun Gupta
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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41
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RNF168 ubiquitylates 53BP1 and controls its response to DNA double-strand breaks. Proc Natl Acad Sci U S A 2013; 110:20982-7. [PMID: 24324146 DOI: 10.1073/pnas.1320302111] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Defective signaling or repair of DNA double-strand breaks has been associated with developmental defects and human diseases. The E3 ligase RING finger 168 (RNF168), mutated in the human radiosensitivity, immunodeficiency, dysmorphic features, and learning difficulties syndrome, was shown to ubiquitylate H2A-type histones, and this ubiquitylation was proposed to facilitate the recruitment of p53-binding protein 1 (53BP1) to the sites of DNA double-strand breaks. In contrast to more upstream proteins signaling DNA double-strand breaks (e.g., RNF8), deficiency of RNF168 fully prevents both the initial recruitment to and retention of 53BP1 at sites of DNA damage; however, the mechanism for this difference has remained unclear. Here, we identify mechanisms that regulate 53BP1 recruitment to the sites of DNA double-strand breaks and provide evidence that RNF168 plays a central role in the regulation of 53BP1 functions. RNF168 mediates K63-linked ubiquitylation of 53BP1 which is required for the initial recruitment of 53BP1 to sites of DNA double-strand breaks and for its function in DNA damage repair, checkpoint activation, and genomic integrity. Our findings highlight the multistep roles of RNF168 in signaling DNA damage.
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42
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Wei H, Mundade R, Lange K, Lu T. Protein arginine methylation of non-histone proteins and its role in diseases. Cell Cycle 2013; 13:32-41. [PMID: 24296620 PMCID: PMC3925732 DOI: 10.4161/cc.27353] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) are a family of enzymes that can methylate arginine residues on histones and other proteins. PRMTs play a crucial role in influencing various cellular functions, including cellular development and tumorigenesis. Arginine methylation by PRMTs is found on both nuclear and cytoplasmic proteins. Recently, there is increasing evidence regarding post-translational modifications of non-histone proteins by PRMTs, illustrating the previously unknown importance of PRMTs in the regulation of various cellular functions by post-translational modifications. In this review, we present the recent developments in the regulation of non-histone proteins by PRMTs.
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43
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Shahar OD, Gabizon R, Feine O, Alhadeff R, Ganoth A, Argaman L, Shimshoni E, Friedler A, Goldberg M. Acetylation of lysine 382 and phosphorylation of serine 392 in p53 modulate the interaction between p53 and MDC1 in vitro. PLoS One 2013; 8:e78472. [PMID: 24194938 PMCID: PMC3806821 DOI: 10.1371/journal.pone.0078472] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 09/12/2013] [Indexed: 11/18/2022] Open
Abstract
Occurrence of DNA damage in a cell activates the DNA damage response, a survival mechanism that ensures genomics stability. Two key members of the DNA damage response are the tumor suppressor p53, which is the most frequently mutated gene in cancers, and MDC1, which is a central adaptor that recruits many proteins to sites of DNA damage. Here we characterize the in vitro interaction between p53 and MDC1 and demonstrate that p53 and MDC1 directly interact. The p53-MDC1 interaction is mediated by the tandem BRCT domain of MDC1 and the C-terminal domain of p53. We further show that both acetylation of lysine 382 and phosphorylation of serine 392 in p53 enhance the interaction between p53 and MDC1. Additionally, we demonstrate that the p53-MDC1 interaction is augmented upon the induction of DNA damage in human cells. Our data suggests a new role for acetylation of lysine 382 and phosphorylation of serine 392 in p53 in the cellular stress response and offers the first evidence for an interaction involving MDC1 that is modulated by acetylation.
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Affiliation(s)
- Or David Shahar
- The Department of Genetics, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ronen Gabizon
- The Department of Organic Chemistry, the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oren Feine
- The Department of Genetics, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Raphael Alhadeff
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Assaf Ganoth
- The Interdisciplinary Center (IDC), Herzliya, Israel and Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa-Oranim, Tivon, Israel
| | - Liron Argaman
- The Department of Genetics, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Elee Shimshoni
- The Department of Genetics, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Assaf Friedler
- The Department of Organic Chemistry, the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Goldberg
- The Department of Genetics, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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44
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Interplays between ATM/Tel1 and ATR/Mec1 in sensing and signaling DNA double-strand breaks. DNA Repair (Amst) 2013; 12:791-9. [PMID: 23953933 DOI: 10.1016/j.dnarep.2013.07.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 07/23/2013] [Indexed: 01/13/2023]
Abstract
DNA double-strand breaks (DSBs) are highly hazardous for genome integrity because they have the potential to cause mutations, chromosomal rearrangements and genomic instability. The cellular response to DSBs is orchestrated by signal transduction pathways, known as DNA damage checkpoints, which are conserved from yeasts to humans. These pathways can sense DNA damage and transduce this information to specific cellular targets, which in turn regulate cell cycle transitions and DNA repair. The mammalian protein kinases ATM and ATR, as well as their budding yeast corresponding orthologs Tel1 and Mec1, act as master regulators of the checkpoint response to DSBs. Here, we review the early steps of DSB processing and the role of DNA-end structures in activating ATM/Tel1 and ATR/Mec1 in an orderly and reciprocal manner.
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45
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Tsabar M, Haber JE. Chromatin modifications and chromatin remodeling during DNA repair in budding yeast. Curr Opin Genet Dev 2013; 23:166-73. [PMID: 23602331 DOI: 10.1016/j.gde.2012.11.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 11/19/2012] [Indexed: 02/03/2023]
Abstract
Double-strand breaks (DSBs) pose a serious threat to genome integrity. Eukaryotes from yeast to humans respond to DSB damage by activating a complex DNA damage response that includes imposing a block to cell cycle progression and the repair of the DSB by one of several pathways. Many of these processes are accompanied by alterations in chromosome and chromatin structure. In this review we focus on the checkpoint responses and DNA repair in the well-studied model organism, the budding yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Michael Tsabar
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Waltham, MA 02454-9110, United States
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46
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Middle infrared radiation induces G2/M cell cycle arrest in A549 lung cancer cells. PLoS One 2013; 8:e54117. [PMID: 23335992 PMCID: PMC3546001 DOI: 10.1371/journal.pone.0054117] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 12/06/2012] [Indexed: 11/19/2022] Open
Abstract
There were studies investigating the effects of broadband infrared radiation (IR) on cancer cell, while the influences of middle-infrared radiation (MIR) are still unknown. In this study, a MIR emitter with emission wavelength band in the 3-5 µm region was developed to irradiate A549 lung adenocarcinoma cells. It was found that MIR exposure inhibited cell proliferation and induced morphological changes by altering the cellular distribution of cytoskeletal components. Using quantitative PCR, we found that MIR promoted the expression levels of ATM (ataxia telangiectasia mutated), ATR (ataxia-telangiectasia and Rad3-related and Rad3-related), TP53 (tumor protein p53), p21 (CDKN1A, cyclin-dependent kinase inhibitor 1A) and GADD45 (growth arrest and DNA-damage inducible), but decreased the expression levels of cyclin B coding genes, CCNB1 and CCNB2, as well as CDK1 (Cyclin-dependent kinase 1). The reduction of protein expression levels of CDC25C, cyclin B1 and the phosphorylation of CDK1 at Thr-161 altogether suggest G(2)/M arrest occurred in A549 cells by MIR. DNA repair foci formation of DNA double-strand breaks (DSB) marker γ-H2AX and sensor 53BP1 was induced by MIR treatment, it implies the MIR induced G(2)/M cell cycle arrest resulted from DSB. This study illustrates a potential role for the use of MIR in lung cancer therapy by initiating DSB and blocking cell cycle progression.
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47
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Muñoz MC, Laulier C, Gunn A, Cheng A, Robbiani DF, Nussenzweig A, Stark JM. RING finger nuclear factor RNF168 is important for defects in homologous recombination caused by loss of the breast cancer susceptibility factor BRCA1. J Biol Chem 2012; 287:40618-28. [PMID: 23055523 DOI: 10.1074/jbc.m112.410951] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND RNF168 promotes chromosomal break localization of 53BP1 and BRCA1; 53BP1 loss rescues homologous recombination (HR) in BRCA1-deficient cells. RESULTS RNF168 depletion suppresses HR defects caused by BRCA1 silencing; RNF168 influences HR similarly to 53BP1. CONCLUSION RNF168 is important for HR defects caused by BRCA1 loss. SIGNIFICANCE Although RNF168 promotes BRCA1 and 53BP1 localization to chromosomal breaks, RNF168 affects HR similarly to 53BP1. The RING finger nuclear factor RNF168 is required for recruitment of several DNA damage response factors to double strand breaks (DSBs), including 53BP1 and BRCA1. Because 53BP1 and BRCA1 function antagonistically during the DSB repair pathway homologous recombination (HR), the influence of RNF168 on HR has been unclear. We report that RNF168 depletion causes an elevated frequency of two distinct HR pathways (homology-directed repair and single strand annealing), suppresses defects in HR caused by BRCA1 silencing, but does not suppress HR defects caused by disruption of CtIP, RAD50, BRCA2, or RAD51. Furthermore, RNF168-depleted cells can form ionizing radiation-induced foci of the recombinase RAD51 without forming BRCA1 ionizing radiation-induced foci, indicating that this loss of BRCA1 recruitment to DSBs does not reflect a loss of function during HR. Additionally, we find that RNF168 and 53BP1 have a similar influence on HR. We suggest that RNF168 is important for HR defects caused by BRCA1 loss.
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Affiliation(s)
- Meilen C Muñoz
- Department of Radiation Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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48
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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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49
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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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50
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Harding SM, Bristow RG. Discordance between phosphorylation and recruitment of 53BP1 in response to DNA double-strand breaks. Cell Cycle 2012; 11:1432-44. [PMID: 22421153 DOI: 10.4161/cc.19824] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
During the DNA damage response (DDR), chromatin modifications contribute to localization of 53BP1 to sites of DNA double-strand breaks (DSBs). 53BP1 is phosphorylated during the DDR, but it is unclear whether phosphorylation is directly coupled to chromatin binding. In this study, we used human diploid fibroblasts and HCT116 tumor cells to study 53BP1 phosphorylation at Serine-25 and Serine-1778 during endogenous and exogenous DSBs (DNA replication and whole-cell or sub-nuclear microbeam irradiation, respectively). In non-stressed conditions, endogenous DSBs in S-phase cells led to accumulation of 53BP1 and γH2AX into discrete nuclear foci. Only the frank collapse of DNA replication forks following hydroxyurea treatment initiated 53BP1(Ser25) and 53BP1(Ser1778) phosphorylation. In response to exogenous DSBs, 53BP1(Ser25) and 53BP1(Ser1778) phosphoforms localized to sites of initial DSBs in a cell cycle-independent manner. 53BP1 phosphoforms also localized to late residual foci and associated with PML-NBs during IR-induced senescence. Using isogenic cell lines and small-molecule inhibitors, we observed that DDR-induced 53BP1 phosphorylation was dependent on ATM and DNA-PKcs kinase activity but independent of MRE11 sensing or RNF168 chromatin remodeling. However, loss of RNF168 blocked recruitment of phosphorylated 53BP1 to sites of DNA damage. Our results uncouple 53BP1 phosphorylation from DSB localization and support parallel pathways for 53BP1 biology during the DDR. As relative 53BP1 expression may be a biomarker of DNA repair capacity in solid tumors, the tracking of 53BP1 phosphoforms in situ may give unique information regarding different cancer phenotypes or response to cancer treatment.
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Affiliation(s)
- Shane M Harding
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
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