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Jimeno S, Prados-Carvajal R, Fernández-Ávila MJ, Silva S, Silvestris DA, Endara-Coll M, Rodríguez-Real G, Domingo-Prim J, Mejías-Navarro F, Romero-Franco A, Jimeno-González S, Barroso S, Cesarini V, Aguilera A, Gallo A, Visa N, Huertas P. ADAR-mediated RNA editing of DNA:RNA hybrids is required for DNA double strand break repair. Nat Commun 2021; 12:5512. [PMID: 34535666 PMCID: PMC8448848 DOI: 10.1038/s41467-021-25790-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/23/2021] [Indexed: 02/08/2023] Open
Abstract
The maintenance of genomic stability requires the coordination of multiple cellular tasks upon the appearance of DNA lesions. RNA editing, the post-transcriptional sequence alteration of RNA, has a profound effect on cell homeostasis, but its implication in the response to DNA damage was not previously explored. Here we show that, in response to DNA breaks, an overall change of the Adenosine-to-Inosine RNA editing is observed, a phenomenon we call the RNA Editing DAmage Response (REDAR). REDAR relies on the checkpoint kinase ATR and the recombination factor CtIP. Moreover, depletion of the RNA editing enzyme ADAR2 renders cells hypersensitive to genotoxic agents, increases genomic instability and hampers homologous recombination by impairing DNA resection. Such a role of ADAR2 in DNA repair goes beyond the recoding of specific transcripts, but depends on ADAR2 editing DNA:RNA hybrids to ease their dissolution.
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Affiliation(s)
- Sonia Jimeno
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain.
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain.
| | - Rosario Prados-Carvajal
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - María Jesús Fernández-Ávila
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Sonia Silva
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Domenico Alessandro Silvestris
- RNA Editing Lab, Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Viale San Paolo 15, 00146, Rome, Italy
| | - Martín Endara-Coll
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Guillermo Rodríguez-Real
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Judit Domingo-Prim
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
- Moirai Biodesign SL, Parc Científic de Barcelona, 08028, Barcelona, Spain
| | - Fernando Mejías-Navarro
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Amador Romero-Franco
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Silvia Jimeno-González
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Sonia Barroso
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Valeriana Cesarini
- RNA Editing Lab, Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Viale San Paolo 15, 00146, Rome, Italy
| | - Andrés Aguilera
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Angela Gallo
- RNA Editing Lab, Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Viale San Paolo 15, 00146, Rome, Italy
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Pablo Huertas
- Departamento de Genética, Universidad de Sevilla, Sevilla, 41080, Spain.
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, 41092, Spain.
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López-Saavedra A, Gómez-Cabello D, Domínguez-Sánchez MS, Mejías-Navarro F, Fernández-Ávila MJ, Dinant C, Martínez-Macías MI, Bartek J, Huertas P. A genome-wide screening uncovers the role of CCAR2 as an antagonist of DNA end resection. Nat Commun 2016; 7:12364. [PMID: 27503537 PMCID: PMC4980490 DOI: 10.1038/ncomms12364] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/27/2016] [Indexed: 01/29/2023] Open
Abstract
There are two major and alternative pathways to repair DNA double-strand breaks: non-homologous end-joining and homologous recombination. Here we identify and characterize novel factors involved in choosing between these pathways; in this study we took advantage of the SeeSaw Reporter, in which the repair of double-strand breaks by homology-independent or -dependent mechanisms is distinguished by the accumulation of green or red fluorescence, respectively. Using a genome-wide human esiRNA (endoribonuclease-prepared siRNA) library, we isolate genes that control the recombination/end-joining ratio. Here we report that two distinct sets of genes are involved in the control of the balance between NHEJ and HR: those that are required to facilitate recombination and those that favour NHEJ. This last category includes CCAR2/DBC1, which we show inhibits recombination by limiting the initiation and the extent of DNA end resection, thereby acting as an antagonist of CtIP. A DNA double strand break can be repaired through either the non-homologous end-joining or the homologous recombination pathways. Here the authors conduct a genome-wide screen and identify a role for CCAR2 in pathway choice by regulating DNA end resection by CtIP.
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Affiliation(s)
- Ana López-Saavedra
- Departamento de Genética, Universidad de Sevilla, 41080 Sevilla, Spain.,Department of Regenerative Medicine, Centro Andaluz de Biología Molecular y Medicina Regenerativa, 41092 Sevilla, Spain
| | - Daniel Gómez-Cabello
- Department of Regenerative Medicine, Centro Andaluz de Biología Molecular y Medicina Regenerativa, 41092 Sevilla, Spain
| | - María Salud Domínguez-Sánchez
- Department of Regenerative Medicine, Centro Andaluz de Biología Molecular y Medicina Regenerativa, 41092 Sevilla, Spain
| | - Fernando Mejías-Navarro
- Departamento de Genética, Universidad de Sevilla, 41080 Sevilla, Spain.,Department of Regenerative Medicine, Centro Andaluz de Biología Molecular y Medicina Regenerativa, 41092 Sevilla, Spain
| | - María Jesús Fernández-Ávila
- Department of Regenerative Medicine, Centro Andaluz de Biología Molecular y Medicina Regenerativa, 41092 Sevilla, Spain
| | - Christoffel Dinant
- Genome Integrity Unit, Danish Cancer Society Research Centre, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - María Isabel Martínez-Macías
- Departamento de Genética, Universidad de Sevilla, 41080 Sevilla, Spain.,Department of Regenerative Medicine, Centro Andaluz de Biología Molecular y Medicina Regenerativa, 41092 Sevilla, Spain
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Centre, Strandboulevarden 49, 2100 Copenhagen, Denmark.,Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Pablo Huertas
- Departamento de Genética, Universidad de Sevilla, 41080 Sevilla, Spain.,Department of Regenerative Medicine, Centro Andaluz de Biología Molecular y Medicina Regenerativa, 41092 Sevilla, Spain
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3
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Meir M, Galanty Y, Kashani L, Blank M, Khosravi R, Fernández-Ávila MJ, Cruz-García A, Star A, Shochot L, Thomas Y, Garrett LJ, Chamovitz DA, Bodine DM, Kurz T, Huertas P, Ziv Y, Shiloh Y. The COP9 signalosome is vital for timely repair of DNA double-strand breaks. Nucleic Acids Res 2015; 43:4517-30. [PMID: 25855810 PMCID: PMC4482063 DOI: 10.1093/nar/gkv270] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/17/2015] [Indexed: 01/07/2023] Open
Abstract
The DNA damage response is vigorously activated by DNA double-strand breaks (DSBs). The chief mobilizer of the DSB response is the ATM protein kinase. We discovered that the COP9 signalosome (CSN) is a crucial player in the DSB response and an ATM target. CSN is a protein complex that regulates the activity of cullin ring ubiquitin ligase (CRL) complexes by removing the ubiquitin-like protein, NEDD8, from their cullin scaffold. We find that the CSN is physically recruited to DSB sites in a neddylation-dependent manner, and is required for timely repair of DSBs, affecting the balance between the two major DSB repair pathways—nonhomologous end-joining and homologous recombination repair (HRR). The CSN is essential for the processivity of deep end-resection—the initial step in HRR. Cullin 4a (CUL4A) is recruited to DSB sites in a CSN- and neddylation-dependent manner, suggesting that CSN partners with CRL4 in this pathway. Furthermore, we found that ATM-mediated phosphorylation of CSN subunit 3 on S410 is critical for proper DSB repair, and that loss of this phosphorylation site alone is sufficient to cause a DDR deficiency phenotype in the mouse. This novel branch of the DSB response thus significantly affects genome stability.
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Affiliation(s)
- Michal Meir
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Yaron Galanty
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Lior Kashani
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Michael Blank
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Rami Khosravi
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - María Jesús Fernández-Ávila
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, 41092, Spain
| | - Andrés Cruz-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, 41092, Spain
| | - Ayelet Star
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Lea Shochot
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Yann Thomas
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - Lisa J Garrett
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel A Chamovitz
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - David M Bodine
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thimo Kurz
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, 41092, Spain
| | - Yael Ziv
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Yosef Shiloh
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
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4
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Jimeno S, Fernández-Ávila MJ, Cruz-García A, Cepeda-García C, Gómez-Cabello D, Huertas P. Neddylation inhibits CtIP-mediated resection and regulates DNA double strand break repair pathway choice. Nucleic Acids Res 2015; 43:987-99. [PMID: 25567988 PMCID: PMC4333419 DOI: 10.1093/nar/gku1384] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
DNA double strand breaks are the most cytotoxic lesions that can occur on the DNA. They can be repaired by different mechanisms and optimal survival requires a tight control between them. Here we uncover protein deneddylation as a major controller of repair pathway choice. Neddylation inhibition changes the normal repair profile toward an increase on homologous recombination. Indeed, RNF111/UBE2M-mediated neddylation acts as an inhibitor of BRCA1 and CtIP-mediated DNA end resection, a key process in repair pathway choice. By controlling the length of ssDNA produced during DNA resection, protein neddylation not only affects the choice between NHEJ and homologous recombination but also controls the balance between different recombination subpathways. Thus, protein neddylation status has a great impact in the way cells respond to DNA breaks.
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Affiliation(s)
- Sonia Jimeno
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), 41092 Sevilla, Spain Departamento de Genética, Universidad de Sevilla, 41080 Sevilla, Spain
| | | | - Andrés Cruz-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), 41092 Sevilla, Spain Departamento de Genética, Universidad de Sevilla, 41080 Sevilla, Spain
| | - Cristina Cepeda-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), 41092 Sevilla, Spain
| | - Daniel Gómez-Cabello
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), 41092 Sevilla, Spain
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), 41092 Sevilla, Spain Departamento de Genética, Universidad de Sevilla, 41080 Sevilla, Spain
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5
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Gomez-Cabello D, Jimeno S, Fernández-Ávila MJ, Huertas P. New tools to study DNA double-strand break repair pathway choice. PLoS One 2013; 8:e77206. [PMID: 24155929 PMCID: PMC3796453 DOI: 10.1371/journal.pone.0077206] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/06/2013] [Indexed: 01/13/2023] Open
Abstract
A broken DNA molecule is difficult to repair, highly mutagenic, and extremely cytotoxic. Such breaks can be repaired by homology-independent or homology-directed mechanisms. Little is known about the network that controls the repair pathway choice except that a licensing step for homology-mediated repair exists, called DNA-end resection. The choice between these two repair pathways is a key event for genomic stability maintenance, and an imbalance of the ratio is directly linked with human diseases, including cancer. Here we present novel reporters to study the balance between both repair options in human cells. In these systems, a double-strand break can be alternatively repaired by homology-independent or -dependent mechanisms, leading to the accumulation of distinct fluorescent proteins. These reporters thus allow the balance between both repair pathways to be analyzed in different experimental setups. We validated the reporters by analyzing the effect of protein downregulation of the DNA end resection and non-homologous end-joining pathways. Finally, we analyzed the role of the DNA damage response on double-strand break (DSB) repair mechanism selection. Our reporters could be used in the future to understand the roles of specific factors, whole pathways, or drugs in DSB repair pathway choice, or for genome-wide screening. Moreover, our findings can be applied to increase gene-targeting efficiency, making it a beneficial tool for a broad audience in the biological sciences.
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Affiliation(s)
- Daniel Gomez-Cabello
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Sevilla, Spain
| | - Sonia Jimeno
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | | | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
- * E-mail:
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