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Kinzig CG, Zakusilo G, Takai KK, Myler LR, de Lange T. ATR blocks telomerase from converting DNA breaks into telomeres. Science 2024; 383:763-770. [PMID: 38359122 DOI: 10.1126/science.adg3224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 12/13/2023] [Indexed: 02/17/2024]
Abstract
Telomerase, the enzyme that maintains telomeres at natural chromosome ends, should be repressed at double-strand breaks (DSBs), where neotelomere formation can cause terminal truncations. We developed an assay to detect neotelomere formation at Cas9- or I-SceI-induced DSBs in human cells. Telomerase added telomeric repeats to DSBs, leading to interstitial telomeric repeat insertions or the formation of functional neotelomeres accompanied by terminal deletions. The threat that telomerase poses to genome integrity was minimized by ataxia telangiectasia and Rad3-related (ATR) kinase signaling, which inhibited telomerase at resected DSBs. In addition to acting at resected DSBs, telomerase used the extruded strand in the Cas9 enzyme-product complex as a primer for neotelomere formation. We propose that although neotelomere formation is detrimental in normal human cells, it may allow cancer cells to escape from breakage-fusion-bridge cycles.
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Affiliation(s)
- Charles G Kinzig
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD/PhD Program, New York, NY 10065, USA
| | - George Zakusilo
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD/PhD Program, New York, NY 10065, USA
| | - Kaori K Takai
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Logan R Myler
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
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2
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Myler LR, Toia B, Vaughan CK, Takai K, Matei AM, Wu P, Paull TT, de Lange T, Lottersberger F. DNA-PK and the TRF2 iDDR inhibit MRN-initiated resection at leading-end telomeres. Nat Struct Mol Biol 2023; 30:1346-1356. [PMID: 37653239 PMCID: PMC10497418 DOI: 10.1038/s41594-023-01072-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
Telomeres replicated by leading-strand synthesis lack the 3' overhang required for telomere protection. Surprisingly, resection of these blunt telomeres is initiated by the telomere-specific 5' exonuclease Apollo rather than the Mre11-Rad50-Nbs1 (MRN) complex, the nuclease that acts at DNA breaks. Without Apollo, leading-end telomeres undergo fusion, which, as demonstrated here, is mediated by alternative end joining. Here, we show that DNA-PK and TRF2 coordinate the repression of MRN at blunt mouse telomeres. DNA-PK represses an MRN-dependent long-range resection, while the endonuclease activity of MRN-CtIP, which could cleave DNA-PK off of blunt telomere ends, is inhibited in vitro and in vivo by the iDDR of TRF2. AlphaFold-Multimer predicts a conserved association of the iDDR with Rad50, potentially interfering with CtIP binding and MRN endonuclease activation. We propose that repression of MRN-mediated resection is a conserved aspect of telomere maintenance and represents an ancient feature of DNA-PK and the iDDR.
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Affiliation(s)
- Logan R Myler
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA
| | - Beatrice Toia
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Cara K Vaughan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Kaori Takai
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA
| | - Andreea M Matei
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Peng Wu
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA.
| | - Francisca Lottersberger
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
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3
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Abstract
In this study, Myler et al. investigated the evolutionary origins of shelterin complex, which is comprised of TRF1, TRF2, Rap1, TIN2, TPP1, and POT1; blocks the DNA damage response at chromosome ends; and interacts with telomerase and the CST complex to regulate telomere length. They describe the evolution of metazoan shelterin, showing that TRF1 emerged in vertebrates upon duplication of a TRF2-like ancestor, and providing insights into the biology of shelterin and its evolution from ancestral telomeric DNA-binding proteins. The mammalian telomeric shelterin complex—comprised of TRF1, TRF2, Rap1, TIN2, TPP1, and POT1—blocks the DNA damage response at chromosome ends and interacts with telomerase and the CST complex to regulate telomere length. The evolutionary origins of shelterin are unclear, partly because unicellular organisms have distinct telomeric proteins. Here, we describe the evolution of metazoan shelterin, showing that TRF1 emerged in vertebrates upon duplication of a TRF2-like ancestor. TRF1 and TRF2 diverged rapidly during vertebrate evolution through the acquisition of new domains and interacting factors. Vertebrate shelterin is also distinguished by the presence of an HJRL domain in the split C-terminal OB fold of POT1, whereas invertebrate POT1s carry inserts of variable nature. Importantly, the data reveal that, apart from the primate and rodent POT1 orthologs, all metazoan POT1s are predicted to have a fourth OB fold at their N termini. Therefore, we propose that POT1 arose from a four-OB-fold ancestor, most likely an RPA70-like protein. This analysis provides insights into the biology of shelterin and its evolution from ancestral telomeric DNA-binding proteins.
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Affiliation(s)
- Logan R Myler
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10021, USA
| | - Charles G Kinzig
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10021, USA
| | - Nanda K Sasi
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10021, USA
| | - George Zakusilo
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10021, USA
| | - Sarah W Cai
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10021, USA
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10021, USA
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4
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Deshpande RA, Myler LR, Soniat MM, Makharashvili N, Lee L, Lees-Miller SP, Finkelstein IJ, Paull TT. DNA-dependent protein kinase promotes DNA end processing by MRN and CtIP. Sci Adv 2020; 6:eaay0922. [PMID: 31934630 PMCID: PMC6949041 DOI: 10.1126/sciadv.aay0922] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
The repair of DNA double-strand breaks occurs through nonhomologous end joining or homologous recombination in vertebrate cells-a choice that is thought to be decided by a competition between DNA-dependent protein kinase (DNA-PK) and the Mre11/Rad50/Nbs1 (MRN) complex but is not well understood. Using ensemble biochemistry and single-molecule approaches, here, we show that the MRN complex is dependent on DNA-PK and phosphorylated CtIP to perform efficient processing and resection of DNA ends in physiological conditions, thus eliminating the competition model. Endonucleolytic removal of DNA-PK-bound DNA ends is also observed at double-strand break sites in human cells. The involvement of DNA-PK in MRN-mediated end processing promotes an efficient and sequential transition from nonhomologous end joining to homologous recombination by facilitating DNA-PK removal.
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Affiliation(s)
- Rajashree A. Deshpande
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan R. Myler
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY 10065, USA
| | - Michael M. Soniat
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Nodar Makharashvili
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Linda Lee
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Susan P. Lees-Miller
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T. Paull
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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5
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Caron MC, Sharma AK, O'Sullivan J, Myler LR, Ferreira MT, Rodrigue A, Coulombe Y, Ethier C, Gagné JP, Langelier MF, Pascal JM, Finkelstein IJ, Hendzel MJ, Poirier GG, Masson JY. Poly(ADP-ribose) polymerase-1 antagonizes DNA resection at double-strand breaks. Nat Commun 2019; 10:2954. [PMID: 31273204 PMCID: PMC6609622 DOI: 10.1038/s41467-019-10741-9] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [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: 09/23/2018] [Accepted: 05/29/2019] [Indexed: 12/20/2022] Open
Abstract
PARP-1 is rapidly recruited and activated by DNA double-strand breaks (DSBs). Upon activation, PARP-1 synthesizes a structurally complex polymer composed of ADP-ribose units that facilitates local chromatin relaxation and the recruitment of DNA repair factors. Here, we identify a function for PARP-1 in DNA DSB resection. Remarkably, inhibition of PARP-1 leads to hyperresected DNA DSBs. We show that loss of PARP-1 and hyperresection are associated with loss of Ku, 53BP1 and RIF1 resection inhibitors from the break site. DNA curtains analysis show that EXO1-mediated resection is blocked by PARP-1. Furthermore, PARP-1 abrogation leads to increased DNA resection tracks and an increase of homologous recombination in cellulo. Our results, therefore, place PARP-1 activation as a critical early event for DNA DSB repair activation and regulation of resection. Hence, our work has direct implications for the clinical use and effectiveness of PARP inhibition, which is prescribed for the treatment of various malignancies. Poly(ADP-ribose) polymerase-1 (PARP-1) facilitates local chromatin relaxation and the recruitment of DNA repair factors at double strand breaks site (DSBs). Here the authors reveal that PARP-1 acts as a critical regulator of DNA end resection of DSBs.
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Affiliation(s)
- Marie-Christine Caron
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Ajit K Sharma
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AL, T6G 1Z2, Canada
| | - Julia O'Sullivan
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Logan R Myler
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Maria Tedim Ferreira
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada.,CHU de Québec Research Center, CHUL Pavilion, Oncology Division, 2705 Boulevard Laurier, Québec City, QC, G1V 4G2, Canada
| | - Amélie Rodrigue
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Yan Coulombe
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Chantal Ethier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada.,CHU de Québec Research Center, CHUL Pavilion, Oncology Division, 2705 Boulevard Laurier, Québec City, QC, G1V 4G2, Canada
| | - Jean-Philippe Gagné
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada.,CHU de Québec Research Center, CHUL Pavilion, Oncology Division, 2705 Boulevard Laurier, Québec City, QC, G1V 4G2, Canada
| | - Marie-France Langelier
- Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Pavillon Roger-Gaudry, Montréal, QC, H3T 1J4, Canada
| | - John M Pascal
- Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Pavillon Roger-Gaudry, Montréal, QC, H3T 1J4, Canada
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AL, T6G 1Z2, Canada.
| | - Guy G Poirier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada. .,CHU de Québec Research Center, CHUL Pavilion, Oncology Division, 2705 Boulevard Laurier, Québec City, QC, G1V 4G2, Canada.
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada. .,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada.
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6
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Soniat MM, Myler LR, Kuo HC, Paull TT, Finkelstein IJ. RPA Phosphorylation Inhibits DNA Resection. Mol Cell 2019; 75:145-153.e5. [PMID: 31153714 DOI: 10.1016/j.molcel.2019.05.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/26/2019] [Accepted: 05/01/2019] [Indexed: 01/20/2023]
Abstract
Genetic recombination in all kingdoms of life initiates when helicases and nucleases process (resect) the free DNA ends to expose single-stranded DNA (ssDNA) overhangs. Resection regulation in bacteria is programmed by a DNA sequence, but a general mechanism limiting resection in eukaryotes has remained elusive. Using single-molecule imaging of reconstituted human DNA repair factors, we identify phosphorylated RPA (pRPA) as a negative resection regulator. Bloom's syndrome (BLM) helicase together with exonuclease 1 (EXO1) and DNA2 nucleases catalyze kilobase-length DNA resection on nucleosome-coated DNA. The resulting ssDNA is rapidly bound by RPA, which further stimulates DNA resection. RPA is phosphorylated during resection as part of the DNA damage response (DDR). Remarkably, pRPA inhibits DNA resection in cellular assays and in vitro via inhibition of BLM helicase. pRPA suppresses BLM initiation at DNA ends and promotes the intrinsic helicase strand-switching activity. These findings establish that pRPA provides a feedback loop between DNA resection and the DDR.
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Affiliation(s)
- Michael M Soniat
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Logan R Myler
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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7
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Abstract
The Mre11-Rad50-Nbs1 (MRN) complex coordinates the repair of DNA double-strand breaks, replication fork restart, meiosis, class-switch recombination, and telomere maintenance. As such, MRN is an essential molecular machine that has homologs in all organisms of life, from bacteriophage to humans. In human cells, MRN is a >500 kDa multifunctional complex that encodes DNA binding, ATPase, and both endonuclease and exonuclease activities. MRN also forms larger assemblies and interacts with multiple DNA repair and replication factors. The enzymatic properties of MRN have been the subject of intense research for over 20 years, and more recently, single-molecule biophysics studies are beginning to probe its many biochemical activities. Here, we describe the methods used to overexpress, fluorescently label, and visualize MRN and its activities on single molecules of DNA.
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Affiliation(s)
- Logan R Myler
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Michael M Soniat
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Xiaoming Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
- The Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX, USA
| | - Rajashree A Deshpande
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
- The Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX, USA
| | - Tanya T Paull
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
- The Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
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8
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Dillard KE, Brown MW, Johnson NV, Xiao Y, Dolan A, Hernandez E, Dahlhauser SD, Kim Y, Myler LR, Anslyn EV, Ke A, Finkelstein IJ. Assembly and Translocation of a CRISPR-Cas Primed Acquisition Complex. Cell 2018; 175:934-946.e15. [PMID: 30343903 DOI: 10.1016/j.cell.2018.09.039] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/20/2018] [Accepted: 09/18/2018] [Indexed: 12/18/2022]
Abstract
CRISPR-Cas systems confer an adaptive immunity against viruses. Following viral injection, Cas1-Cas2 integrates segments of the viral genome (spacers) into the CRISPR locus. In type I CRISPR-Cas systems, efficient "primed" spacer acquisition and viral degradation (interference) require both the Cascade complex and the Cas3 helicase/nuclease. Here, we present single-molecule characterization of the Thermobifida fusca (Tfu) primed acquisition complex (PAC). We show that TfuCascade rapidly samples non-specific DNA via facilitated one-dimensional diffusion. Cas3 loads at target-bound Cascade and the Cascade/Cas3 complex translocates via a looped DNA intermediate. Cascade/Cas3 complexes stall at diverse protein roadblocks, resulting in a double strand break at the stall site. In contrast, Cas1-Cas2 samples DNA transiently via 3D collisions. Moreover, Cas1-Cas2 associates with Cascade and translocates with Cascade/Cas3, forming the PAC. PACs can displace different protein roadblocks, suggesting a mechanism for long-range spacer acquisition. This work provides a molecular basis for the coordinated steps in CRISPR-based adaptive immunity.
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Affiliation(s)
- Kaylee E Dillard
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Maxwell W Brown
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Adam Dolan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Erik Hernandez
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Samuel D Dahlhauser
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Yoori Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan R Myler
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA.
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9
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Johnson TE, Lee JH, Myler LR, Zhou Y, Mosley TJ, Yang SH, Uprety N, Kim J, Paull TT. Homeodomain Proteins Directly Regulate ATM Kinase Activity. Cell Rep 2018; 24:1471-1483. [PMID: 30089259 PMCID: PMC6127865 DOI: 10.1016/j.celrep.2018.06.089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 01/01/2018] [Revised: 04/18/2018] [Accepted: 06/20/2018] [Indexed: 12/17/2022] Open
Abstract
Ataxia-telangiectasia mutated (ATM) is a serine/threonine kinase that coordinates the response to DNA double-strand breaks and oxidative stress. NKX3.1, a prostate-specific transcription factor, was recently shown to directly stimulate ATM kinase activity through its highly conserved homeodomain. Here, we show that other members of the homeodomain family can also regulate ATM kinase activity. We found that six representative homeodomain proteins (NKX3.1, NKX2.2, TTF1, NKX2.5, HOXB7, and CDX2) physically and functionally interact with ATM and with the Mre11-Rad50-Nbs1 (MRN) complex that activates ATM in combination with DNA double-strand breaks. The binding between homeodomain proteins and ATM stimulates oxidation-induced ATM activation in vitro but inhibits ATM kinase activity in the presence of MRN and DNA and in human cells. These findings suggest that many tissue-specific homeodomain proteins may regulate ATM activity during development and differentiation and that this is a unique mechanism for the control of the DNA damage response.
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Affiliation(s)
- Tanya E Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ji-Hoon Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Logan R Myler
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yi Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Trenell J Mosley
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Soo-Hyun Yang
- College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nadima Uprety
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA.
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10
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Myler LR, Gallardo IF, Soniat MM, Deshpande RA, Gonzalez XB, Kim Y, Paull TT, Finkelstein IJ. Single-Molecule Imaging Reveals How Mre11-Rad50-Nbs1 Initiates DNA Break Repair. Mol Cell 2017; 67:891-898.e4. [PMID: 28867292 PMCID: PMC5609712 DOI: 10.1016/j.molcel.2017.08.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/07/2017] [Accepted: 08/04/2017] [Indexed: 11/21/2022]
Abstract
DNA double-strand break (DSB) repair is essential for maintaining our genomes. Mre11-Rad50-Nbs1 (MRN) and Ku70-Ku80 (Ku) direct distinct DSB repair pathways, but the interplay between these complexes at a DSB remains unclear. Here, we use high-throughput single-molecule microscopy to show that MRN searches for free DNA ends by one-dimensional facilitated diffusion, even on nucleosome-coated DNA. Rad50 binds homoduplex DNA and promotes facilitated diffusion, whereas Mre11 is required for DNA end recognition and nuclease activities. MRN gains access to occluded DNA ends by removing Ku or other DNA adducts via an Mre11-dependent nucleolytic reaction. Next, MRN loads exonuclease 1 (Exo1) onto the free DNA ends to initiate DNA resection. In the presence of replication protein A (RPA), MRN acts as a processivity factor for Exo1, retaining the exonuclease on DNA for long-range resection. Our results provide a mechanism for how MRN promotes homologous recombination on nucleosome-coated DNA.
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Affiliation(s)
- Logan R Myler
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ignacio F Gallardo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Michael M Soniat
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Rajashree A Deshpande
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xenia B Gonzalez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yoori Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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Myler LR, Finkelstein IJ. Eukaryotic resectosomes: A single-molecule perspective. Prog Biophys Mol Biol 2016; 127:119-129. [PMID: 27498169 DOI: 10.1016/j.pbiomolbio.2016.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/02/2016] [Indexed: 12/13/2022]
Abstract
DNA double-strand breaks (DSBs) disrupt the physical and genetic continuity of the genome. If unrepaired, DSBs can lead to cellular dysfunction and malignant transformation. Homologous recombination (HR) is a universally conserved DSB repair mechanism that employs the information in a sister chromatid to catalyze error-free DSB repair. To initiate HR, cells assemble the resectosome: a multi-protein complex composed of helicases, nucleases, and regulatory proteins. The resectosome nucleolytically degrades (resects) the free DNA ends for downstream homologous recombination. Several decades of intense research have identified the core resectosome components in eukaryotes, archaea, and bacteria. More recently, these proteins have been characterized via single-molecule approaches. Here, we focus on recent single-molecule studies that have begun to unravel how nucleases, helicases, processivity factors, and other regulatory proteins dictate the extent and efficiency of DNA resection in eukaryotic cells. We conclude with a discussion of outstanding questions that can be addressed via single-molecule approaches.
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Affiliation(s)
- Logan R Myler
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA.
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Abstract
Resveratrol has been widely reported to reduce cancer progression in model systems and to selectively induce cell death in transformed cell lines. Many enzymes have been reported to respond to resveratrol in mammalian cells, including the Ataxia-Telangiectasia Mutated (ATM) protein kinase that acts in DNA damage recognition, signaling, and repair. Here we investigate the responses of ATM to resveratrol exposure in normal and transformed human cell lines and find that ATM autophosphorylation and substrate phosphorylation is stimulated by resveratrol in a manner that is promoted by reactive oxygen species (ROS). We observe direct stimulatory effects of resveratrol on purified ATM in vitro and find that the catalytic efficiency of the kinase on a model substrate is increased by resveratrol. In the purified system we also observe a requirement for oxidation, as the effect of resveratrol on ATM signaling is substantially reduced by agents that prevent disulfide bond formation in ATM. These results demonstrate that resveratrol effects on ATM are direct, and suggest a mechanism by which the oxidizing environment of transformed cells promotes ATM activity and blocks cell proliferation.
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Affiliation(s)
- Ji-Hoon Lee
- The Howard Hughes Medical Institute, The Department of Molecular Biosciences, and the Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Zhi Guo
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, United States of America, and the Department of Genetics, Harvard University Medical School, Boston, Massachusetts, United States of America and the Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Logan R. Myler
- The Howard Hughes Medical Institute, The Department of Molecular Biosciences, and the Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Suting Zheng
- The Howard Hughes Medical Institute, The Department of Molecular Biosciences, and the Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Tanya T. Paull
- The Howard Hughes Medical Institute, The Department of Molecular Biosciences, and the Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
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