1
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Xie B, Sanford EJ, Hung SH, Wagner M, Heyer WD, Smolka MB. Multi-step control of homologous recombination via Mec1/ATR suppresses chromosomal rearrangements. EMBO J 2024; 43:3027-3043. [PMID: 38839993 PMCID: PMC11251156 DOI: 10.1038/s44318-024-00139-9] [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: 12/04/2023] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024] Open
Abstract
The Mec1/ATR kinase is crucial for genome stability, yet the mechanism by which it prevents gross chromosomal rearrangements (GCRs) remains unknown. Here we find that in cells with deficient Mec1 signaling, GCRs accumulate due to the deregulation of multiple steps in homologous recombination (HR). Mec1 primarily suppresses GCRs through its role in activating the canonical checkpoint kinase Rad53, which ensures the proper control of DNA end resection. Upon loss of Rad53 signaling and resection control, Mec1 becomes hyperactivated and triggers a salvage pathway in which the Sgs1 helicase is recruited to sites of DNA lesions via the 911-Dpb11 scaffolds and phosphorylated by Mec1 to favor heteroduplex rejection and limit HR-driven GCR accumulation. Fusing an ssDNA recognition domain to Sgs1 bypasses the requirement of Mec1 signaling for GCR suppression and nearly eliminates D-loop formation, thus preventing non-allelic recombination events. We propose that Mec1 regulates multiple steps of HR to prevent GCRs while ensuring balanced HR usage when needed for promoting tolerance to replication stress.
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Affiliation(s)
- Bokun Xie
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Shih-Hsun Hung
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Mateusz Wagner
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
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2
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Xie B, Sanford EJ, Hung SH, Wagner MM, Heyer WD, Smolka MB. Multi-Step Control of Homologous Recombination by Mec1/ATR Ensures Robust Suppression of Gross Chromosomal Rearrangements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568146. [PMID: 38045423 PMCID: PMC10690203 DOI: 10.1101/2023.11.21.568146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The Mec1/ATR kinase is crucial for genome stability, yet the mechanism by which it prevents gross chromosomal rearrangements (GCRs) remains unknown. Here we find that in cells with deficient Mec1 signaling, GCRs accumulate due to the deregulation of multiple steps in homologous recombination (HR). Mec1 primarily suppresses GCRs through its role in activating the canonical checkpoint kinase Rad53, which ensures the proper control of DNA end resection. Upon loss of Rad53 signaling and resection control, Mec1 becomes hyperactivated and triggers a salvage pathway in which the Sgs1 helicase is recruited to sites of DNA lesions via the 911-Dpb11 scaffolds to favor heteroduplex rejection and limit HR-driven GCR accumulation. Fusing an ssDNA recognition domain to Sgs1 bypasses the requirement of Mec1 signaling for GCR suppression and nearly eliminates D-loop formation, thus preventing non-allelic recombination events. We propose that Mec1 regulates multiple steps of HR to prevent GCRs while ensuring balanced HR usage when needed for promoting tolerance to replication stress.
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Affiliation(s)
- Bokun Xie
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Shih-Hsun Hung
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Mateusz Maciej Wagner
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Marcus B. Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
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3
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Reitz D, Djeghmoum Y, Watson RA, Rajput P, Argueso JL, Heyer WD, Piazza A. Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability. Genes Dev 2023; 37:621-639. [PMID: 37541760 PMCID: PMC10499017 DOI: 10.1101/gad.350618.123] [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: 03/10/2023] [Accepted: 07/14/2023] [Indexed: 08/06/2023]
Abstract
Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR subpathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology and results in sequence insertion without additional breaks or SVs. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Polδ-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.
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Affiliation(s)
- Diedre Reitz
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Yasmina Djeghmoum
- Laboratory of Biology and Modelling of the Cell (UMR5239), Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Ruth A Watson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Pallavi Rajput
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA;
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, USA
| | - Aurèle Piazza
- Laboratory of Biology and Modelling of the Cell (UMR5239), Ecole Normale Supérieure de Lyon, 69007 Lyon, France;
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4
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Reitz D, Djeghmoum Y, Watson RA, Rajput P, Argueso JL, Heyer WD, Piazza A. Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532751. [PMID: 36993162 PMCID: PMC10055120 DOI: 10.1101/2023.03.15.532751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide sequencing approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis, and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR sub-pathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology, and results in sequence insertion without additional break or SV. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Polδ-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.
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Affiliation(s)
- Diedre Reitz
- Department of Microbiology and Molecular Genetics, One Shields Ave, University of California, Davis, CA 95616, USA
| | - Yasmina Djeghmoum
- Univ Lyon, ENS, UCBL, CNRS, INSERM, Laboratory of Biology and Modelling of the Cell, UMR5239, U 1210, F-69364, Lyon, France
| | - Ruth A. Watson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523
| | - Pallavi Rajput
- Department of Microbiology and Molecular Genetics, One Shields Ave, University of California, Davis, CA 95616, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, One Shields Ave, University of California, Davis, CA 95616, USA
- Department of Molecular and Cellular Biology, One Shields Ave, University of California, Davis, CA 95616, USA
| | - Aurèle Piazza
- Univ Lyon, ENS, UCBL, CNRS, INSERM, Laboratory of Biology and Modelling of the Cell, UMR5239, U 1210, F-69364, Lyon, France
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5
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Reitz D, Savocco J, Piazza A, Heyer WD. Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae. J Vis Exp 2022:10.3791/64240. [PMID: 36155960 PMCID: PMC10205173 DOI: 10.3791/64240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
DNA damage, including DNA double-stranded breaks and inter-strand cross-links, incurred during the S and G2 phases of the cell cycle can be repaired by homologous recombination (HR). In addition, HR represents an important mechanism of replication fork rescue following stalling or collapse. The regulation of the many reversible and irreversible steps of this complex pathway promotes its fidelity. The physical analysis of the recombination intermediates formed during HR enables the characterization of these controls by various nucleoprotein factors and their interactors. Though there are well-established methods to assay specific events and intermediates in the recombination pathway, the detection of D-loop formation and extension, two critical steps in this pathway, has proved challenging until recently. Here, efficient methods for detecting key events in the HR pathway, namely DNA double-stranded break formation, D-loop formation, D-loop extension, and the formation of products via break-induced replication (BIR) in Saccharomyces cerevisiae are described. These assays detect their relevant recombination intermediates and products with high sensitivity and are independent of cellular viability. The detection of D-loops, D-loop extension, and the BIR product is based on proximity ligation. Together, these assays allow for the study of the kinetics of HR at the population level to finely address the functions of HR proteins and regulators at significant steps in the pathway.
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Affiliation(s)
- Diedre Reitz
- Department of Microbiology & Molecular Genetics, University of California, Davis
| | - Jérôme Savocco
- Laboratory of Biology & Modeling of the Cell, École Normale Supérieure de Lyon
| | - Aurèle Piazza
- Laboratory of Biology & Modeling of the Cell, École Normale Supérieure de Lyon;
| | - Wolf-Dietrich Heyer
- Department of Microbiology & Molecular Genetics, University of California, Davis; Department of Molecular & Cellular Biology, University of California, Davis;
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6
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Break-induced replication: unraveling each step. Trends Genet 2022; 38:752-765. [PMID: 35459559 DOI: 10.1016/j.tig.2022.03.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 10/18/2022]
Abstract
Break-induced replication (BIR) repairs one-ended double-strand DNA breaks through invasion into a homologous template followed by DNA synthesis. Different from S-phase replication, BIR copies the template DNA in a migrating displacement loop (D-loop) and results in conservative inheritance of newly synthesized DNA. This unusual mode of DNA synthesis makes BIR a source of various genetic instabilities like those associated with cancer in humans. This review focuses on recent progress in delineating the mechanism of Rad51-dependent BIR in budding yeast. In addition, we discuss new data that describe changes in BIR efficiency and fidelity on encountering replication obstacles as well as the implications of these findings for BIR-dependent processes such as telomere maintenance and the repair of collapsed replication forks.
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7
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Liu L, Sugawara N, Malkova A, Haber JE. Determining the kinetics of break-induced replication (BIR) by the assay for monitoring BIR elongation rate (AMBER). Methods Enzymol 2021; 661:139-154. [PMID: 34776210 DOI: 10.1016/bs.mie.2021.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A detailed understanding of how homologous recombination proceeds at the molecular level in vivo requires the ability to detect in real time the appearance of specific intermediates of DNA repair. The most detailed analysis of double-strand break (DSB) repair in eukaryotes has come from the study of budding yeast, using an inducible site-specific HO endonuclease to initiate recombination synchronously in nearly all cells of the population. Polymerase chain reaction (PCR) and chromatin immunoprecipitation (ChIP) methods have been used to visualize the timing of the DSB, its resection by 5' to 3' exonucleases, the binding of the Rad51 recombinase and the pairing of the Rad51 filament with a homologous donor sequence. PCR has also been used to identify the next key step: the initiation of new DNA synthesis to extend the invading stand and copy the donor template. In break-induced replication (BIR), there appears to be a very long delay between strand invasion and this primer extension step. Here we describe an alternative method, an assay for monitoring BIR elongation rate (AMBER) based on digital droplet PCR that yields a much earlier time of initial DNA synthesis. We suggest that previous methods have failed to recover the initial long, single-stranded primer extension product that is readily detected by AMBER.
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Affiliation(s)
- Liping Liu
- Department of Biology, University of Iowa, Iowa City, IA, United States
| | - Neal Sugawara
- Department of Biology, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, United States
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA, United States.
| | - James E Haber
- Department of Biology, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, United States.
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8
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Piazza A, Rajput P, Heyer WD. Physical and Genetic Assays for the Study of DNA Joint Molecules Metabolism and Multi-invasion-Induced Rearrangements in S. cerevisiae. Methods Mol Biol 2021; 2153:535-554. [PMID: 32840803 DOI: 10.1007/978-1-0716-0644-5_36] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA double-strand breaks (DSBs) are genotoxic lesions that can be repaired in a templated fashion by homologous recombination (HR). HR is a complex pathway that involves the formation of DNA joint molecules (JMs) containing heteroduplex DNA. Various types of JMs are formed throughout the pathway, including displacement loops (D-loops), multi-invasions (MI), and double Holliday junction intermediates. Dysregulation of JM metabolism in various mutant contexts revealed the propensity of HR to generate repeat-mediated chromosomal rearrangements. Specifically, we recently identified MI-induced rearrangements (MIR), a tripartite recombination mechanism initiated by one end of a DSB that exploits repeated regions to generate rearrangements between intact chromosomal regions. MIR occurs upon MI-JM processing by endonucleases and is suppressed by JM disruption activities. Here, we detail two assays: a physical assay for JM detection in Saccharomyces cerevisiae cells and genetic assays to determine the frequency of MIR in various chromosomal contexts. These assays enable studying the regulation of the HR pathway and the consequences of their defects for genomic instability by MIR.
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Affiliation(s)
- Aurèle Piazza
- Spatial Regulation of Genomes, Institut Pasteur, UMR3525 CNRS, Paris, France.,Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA.,Univ Lyon, ENS, UCBL, CNRS, INSERM, Laboratory of Biology and Modelling of the Cell, UMR5239, Lyon, France
| | - Pallavi Rajput
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA. .,Department of Molecular and Cellular Biology, University of California, Davis, CA, USA.
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9
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Prednisone is genotoxic in mice and Drosophila melanogaster. Mutat Res 2021; 865:503334. [PMID: 33865545 DOI: 10.1016/j.mrgentox.2021.503334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
Prednisone (PD) is one of the most commonly used corticosteroids in immunosuppressive therapy for patients with autoimmune diseases and transplants. Chronic use of corticosteroids is associated with several side effects and an increase in neoplasia. Since genotoxic effects are associated with an increased risk of cancer development, this study evaluated the genotoxic and cytotoxic activities of PD using the SMART/wing assay in Drosophila melanogaster and the micronucleus test and comet assay in mouse bone marrow cells. Further, the toxic effects of PD on mouse organ tissues were assessed using histopathological analyses. In the SMART/wing assay, PD showed a significant genotoxic activity at all concentrations tested (0.375, 0.75, 1.5, and 2.0 mg/mL) compared to the negative control (p < 0.05). The micronucleus test and comet assay also showed an elevated genotoxicity of PD at all treatment conditions (24, 48, and 120 h with doses ranging from 0.5 to 1.5 mg/kg) compared to the negative control (p < 0.05). The histopathological analyses did not show toxicity of PD in mouse cells and tissues. Therefore, our results demonstrate that PD is a potent genotoxic immunosuppressant in mice and D. melanogaster cells. Somatic recombination was the primary contributor (46%-82%) to the induced genotoxicity observed in the SMART test.
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10
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Liu L, Yan Z, Osia BA, Twarowski J, Sun L, Kramara J, Lee RS, Kumar S, Elango R, Li H, Dang W, Ira G, Malkova A. Tracking break-induced replication shows that it stalls at roadblocks. Nature 2021; 590:655-659. [PMID: 33473214 PMCID: PMC8219245 DOI: 10.1038/s41586-020-03172-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 12/08/2020] [Indexed: 12/29/2022]
Abstract
Break-induced replication (BIR) repairs one-ended double strand breaks (DSBs) similar to those formed by replication collapse or telomere erosion, and it has been implicated in the initiation of genome instability in cancer and other human disease1,2. Previous studies have defined the enzymes required for BIR1–5; however, understanding of initial and extended BIR synthesis as well as how the migrating D-loop proceeds through known replication roadblocks has been precluded by technical limitations. Here, using a newly developed assay, we demonstrate that BIR synthesis initiates soon after strand invasion and proceeds slower than S-phase replication. Without primase, leading strand synthesis is initiated efficiently, but fails to proceed beyond 30 kb, suggesting that primase is needed for stabilization of the nascent leading strand. DNA synthesis can initiate in the absence of Pif1 or Pol32 but does not proceed efficiently. We demonstrate that interstitial telomeric DNA disrupts and terminates BIR progression. Also, BIR initiation is suppressed by transcription proportionally to the transcription level. Collisions between BIR and transcription lead to mutagenesis and chromosome rearrangements at levels that exceed instabilities induced by transcription during normal replication. Together, these results provide fundamental insights into the mechanism of BIR and on how BIR contributes to genome instability.
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Affiliation(s)
- Liping Liu
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Zhenxin Yan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Beth A Osia
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Jerzy Twarowski
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Luyang Sun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Juraj Kramara
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Rosemary S Lee
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Sandeep Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rajula Elango
- Department of Biology, University of Iowa, Iowa City, IA, USA.,Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Hanzeng Li
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Weiwei Dang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA, USA. .,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA.
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11
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Shah SS, Hartono SR, Chédin F, Heyer WD. Bisulfite treatment and single-molecule real-time sequencing reveal D-loop length, position, and distribution. eLife 2020; 9:59111. [PMID: 33185185 PMCID: PMC7695462 DOI: 10.7554/elife.59111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/27/2020] [Indexed: 01/01/2023] Open
Abstract
Displacement loops (D-loops) are signature intermediates formed during homologous recombination. Numerous factors regulate D-loop formation and disruption, thereby influencing crucial aspects of DNA repair, including donor choice and the possibility of crossover outcome. While D-loop detection methods exist, it is currently unfeasible to assess the relationship between D-loop editors and D-loop characteristics such as length and position. Here, we developed a novel in vitro assay to characterize the length and position of individual D-loops with near base-pair resolution and deep coverage, while also revealing their distribution in a population. Non-denaturing bisulfite treatment modifies the cytosines on the displaced strand of the D-loop to uracil, leaving a permanent signature for the displaced strand. Subsequent single-molecule real-time sequencing uncovers the cytosine conversion patch as a D-loop footprint. The D-loop Mapping Assay is widely applicable with different substrates and donor types and can be used to study factors that influence D-loop properties.
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Affiliation(s)
- Shanaya Shital Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - Stella R Hartono
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States.,Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
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12
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Dynamic Processing of Displacement Loops during Recombinational DNA Repair. Mol Cell 2019; 73:1255-1266.e4. [PMID: 30737186 DOI: 10.1016/j.molcel.2019.01.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/08/2018] [Accepted: 01/03/2019] [Indexed: 12/22/2022]
Abstract
Displacement loops (D-loops) are pivotal intermediates of homologous recombination (HR), a universal DNA double strand break (DSB) repair pathway. We developed a versatile assay for the physical detection of D-loops in vivo, which enabled studying the kinetics of their formation and defining the activities controlling their metabolism. Nascent D-loops are detected within 2 h of DSB formation and extended in a delayed fashion in a genetic system designed to preclude downstream repair steps. The majority of nascent D-loops are disrupted by two pathways: one supported by the Srs2 helicase and the other by the Mph1 helicase and the Sgs1-Top3-Rmi1 helicase-topoisomerase complex. Both pathways operate without significant overlap and are delineated by the Rad54 paralog Rdh54 in an ATPase-independent fashion. This study uncovers a layer of quality control of HR relying on nascent D-loop dynamics.
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13
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Muller H, Scolari VF, Agier N, Piazza A, Thierry A, Mercy G, Descorps-Declere S, Lazar-Stefanita L, Espeli O, Llorente B, Fischer G, Mozziconacci J, Koszul R. Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi-C. Mol Syst Biol 2018; 14:e8293. [PMID: 30012718 PMCID: PMC6047084 DOI: 10.15252/msb.20188293] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 12/29/2022] Open
Abstract
In chromosome conformation capture experiments (Hi-C), the accuracy with which contacts are detected varies due to the uneven distribution of restriction sites along genomes. In addition, repeated sequences or homologous regions remain indistinguishable because of the ambiguities they introduce during the alignment of the sequencing reads. We addressed both limitations by designing and engineering 144 kb of a yeast chromosome with regularly spaced restriction sites (Syn-HiC design). In the Syn-HiC region, Hi-C signal-to-noise ratio is enhanced and can be used to measure the shape of an unbiased distribution of contact frequencies, allowing to propose a robust definition of a Hi-C experiment resolution. The redesigned region is also distinguishable from its native homologous counterpart in an otherwise isogenic diploid strain. As a proof of principle, we tracked homologous chromosomes during meiotic prophase in synchronized and pachytene-arrested cells and captured important features of their spatial reorganization, such as chromatin restructuration into arrays of Rec8-delimited loops, centromere declustering, individualization, and pairing. Overall, we illustrate the promises held by redesigning genomic regions to explore complex biological questions.
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Affiliation(s)
- Héloïse Muller
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Vittore F Scolari
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Nicolas Agier
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Aurèle Piazza
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Agnès Thierry
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Guillaume Mercy
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Stéphane Descorps-Declere
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Luciana Lazar-Stefanita
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Olivier Espeli
- Centre Interdisciplinaire de Recherche en Biologie, Collège de France, UMR-CNRS 7241, INSERM U1050, Paris, France
| | - Bertrand Llorente
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Gilles Fischer
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Julien Mozziconacci
- Theoretical Physics for Condensed Matter Lab, CNRS UMR 7600, Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Romain Koszul
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
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