1
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Ciaccia PN, Liang Z, Schweitzer AY, Metzner E, Isaacs FJ. Enhanced eMAGE applied to identify genetic factors of nuclear hormone receptor dysfunction via combinatorial gene editing. Nat Commun 2024; 15:5218. [PMID: 38890276 PMCID: PMC11189492 DOI: 10.1038/s41467-024-49365-z] [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: 09/09/2020] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Technologies that generate precise combinatorial genome modifications are well suited to dissect the polygenic basis of complex phenotypes and engineer synthetic genomes. Genome modifications with engineered nucleases can lead to undesirable repair outcomes through imprecise homology-directed repair, requiring non-cleavable gene editing strategies. Eukaryotic multiplex genome engineering (eMAGE) generates precise combinatorial genome modifications in Saccharomyces cerevisiae without generating DNA breaks or using engineered nucleases. Here, we systematically optimize eMAGE to achieve 90% editing frequency, reduce workflow time, and extend editing distance to 20 kb. We further engineer an inducible dominant negative mismatch repair system, allowing for high-efficiency editing via eMAGE while suppressing the elevated background mutation rate 17-fold resulting from mismatch repair inactivation. We apply these advances to construct a library of cancer-associated mutations in the ligand-binding domains of human estrogen receptor alpha and progesterone receptor to understand their impact on ligand-independent autoactivation. We validate that this yeast model captures autoactivation mutations characterized in human breast cancer models and further leads to the discovery of several previously uncharacterized autoactivating mutations. This work demonstrates the development and optimization of a cleavage-free method of genome editing well suited for applications requiring efficient multiplex editing with minimal background mutations.
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Affiliation(s)
- Peter N Ciaccia
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT, 06516, USA
- Physical and Engineering Biology, Yale University, New Haven, CT, 06520, USA
| | - Zhuobin Liang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA.
- Systems Biology Institute, Yale University, West Haven, CT, 06516, USA.
- ZL: Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
| | - Anabel Y Schweitzer
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Eli Metzner
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Farren J Isaacs
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA.
- Systems Biology Institute, Yale University, West Haven, CT, 06516, USA.
- Physical and Engineering Biology, Yale University, New Haven, CT, 06520, USA.
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA.
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2
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Saito S, Adachi N. Characterization and regulation of cell cycle-independent noncanonical gene targeting. Nat Commun 2024; 15:5044. [PMID: 38890315 PMCID: PMC11189520 DOI: 10.1038/s41467-024-49385-9] [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: 11/22/2023] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Homology-dependent targeted DNA integration, generally referred to as gene targeting, provides a powerful tool for precise genome modification; however, its fundamental mechanisms remain poorly understood in human cells. Here we reveal a noncanonical gene targeting mechanism that does not rely on the homologous recombination (HR) protein Rad51. This mechanism is suppressed by Rad52 inhibition, suggesting the involvement of single-strand annealing (SSA). The SSA-mediated gene targeting becomes prominent when DSB repair by HR or end-joining pathways is defective and does not require isogenic DNA, permitting 5% sequence divergence. Intriguingly, loss of Msh2, loss of BLM, and induction of a target-site DNA break all significantly and synergistically enhance SSA-mediated targeted integration. Most notably, SSA-mediated integration is cell cycle-independent, occurring in the G1 phase as well. Our findings provide unequivocal evidence for Rad51-independent targeted integration and unveil multiple mechanisms to regulate SSA-mediated targeted as well as random integration.
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Affiliation(s)
- Shinta Saito
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027, Japan
| | - Noritaka Adachi
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027, Japan.
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3
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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 2024:10.1038/s44318-024-00139-9. [PMID: 38839993 DOI: 10.1038/s44318-024-00139-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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4
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Papp D, Hernandez LA, Mai TA, Haanen TJ, O’Donnell MA, Duran AT, Hernandez SM, Narvanto JE, Arguello B, Onwukwe MO, Mirkin SM, Kim JC. Massive contractions of myotonic dystrophy type 2-associated CCTG tetranucleotide repeats occur via double-strand break repair with distinct requirements for DNA helicases. G3 (BETHESDA, MD.) 2024; 14:jkad257. [PMID: 37950892 PMCID: PMC10849350 DOI: 10.1093/g3journal/jkad257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/06/2023] [Accepted: 10/19/2023] [Indexed: 11/13/2023]
Abstract
Myotonic dystrophy type 2 (DM2) is a genetic disease caused by expanded CCTG DNA repeats in the first intron of CNBP. The number of CCTG repeats in DM2 patients ranges from 75 to 11,000, yet little is known about the molecular mechanisms responsible for repeat expansions or contractions. We developed an experimental system in Saccharomyces cerevisiae that enables the selection of large-scale contractions of (CCTG)100 within the intron of a reporter gene and subsequent genetic analysis. Contractions exceeded 80 repeat units, causing the final repetitive tract to be well below the threshold for disease. We found that Rad51 and Rad52 are involved in these massive contractions, indicating a mechanism that uses homologous recombination. Srs2 helicase was shown previously to stabilize CTG, CAG, and CGG repeats. Loss of Srs2 did not significantly affect CCTG contraction rates in unperturbed conditions. In contrast, loss of the RecQ helicase Sgs1 resulted in a 6-fold decrease in contraction rate with specific evidence that helicase activity is required for large-scale contractions. Using a genetic assay to evaluate chromosome arm loss, we determined that CCTG and reverse complementary CAGG repeats elevate the rate of chromosomal fragility compared to a short-track control. Overall, our results demonstrate that the genetic control of CCTG repeat contractions is notably distinct among disease-causing microsatellite repeat sequences.
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Affiliation(s)
- David Papp
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Luis A Hernandez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Theresa A Mai
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Terrance J Haanen
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Meghan A O’Donnell
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Ariel T Duran
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Sophia M Hernandez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Jenni E Narvanto
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Berenice Arguello
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Marvin O Onwukwe
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Jane C Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
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5
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Sapède E, Sugawara N, Tyers RG, Nakajima Y, Afreen MF, Romero Escobar J, Haber JE. Nonhomologous tails direct heteroduplex rejection and mismatch correction during single-strand annealing in Saccharomyces cerevisiae. PLoS Genet 2024; 20:e1010527. [PMID: 38315739 PMCID: PMC10868807 DOI: 10.1371/journal.pgen.1010527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/15/2024] [Accepted: 12/28/2023] [Indexed: 02/07/2024] Open
Abstract
Single-strand annealing (SSA) is initiated when a double strand break (DSB) occurs between two flanking repeated sequences, resulting in a deletion that leaves a single copy of the repeat. We studied budding yeast strains carrying two 200-bp URA3 sequences separated by 2.6 kb of spacer DNA (phage lambda) in which a site-specific DSB can be created by HO or Cas9 endonucleases. Repeat-mediated deletion requires removal of long 3'-ended single-stranded tails (flaps) by Rad1-Rad10 with the assistance of Msh2-Msh3, Saw1 and Slx4. A natural 3% divergence of unequally spaced heterologies between these repeats (designated F and A) causes a significant reduction in the frequency of SSA repair. This decrease is caused by heteroduplex rejection in which mismatches (MMs) in the annealed intermediate are recognized by the MutS (Msh2 and Msh6) components of the MM repair (MMR) pathway coupled to unwinding of the duplex by the Sgs1-Rmi1-Top3 helicase. MutL homologs, Mlh1-Pms1 (MutL), are not required for rejection but play their expected role in mismatch correction. Remarkably, heteroduplex rejection is very low in strains where the divergent repeats were immediately adjacent (Tailless strains) and the DSB was induced by Cas9. These results suggest that the presence of nonhomologous tails strongly stimulates heteroduplex rejection in SSA. DNA sequencing analysis of SSA products from the FA Tailed strain showed a gradient of correction favoring the sequence opposite each 3' end of the annealed strand. Mismatches located in the center of the repair intermediate were corrected by Msh2-Msh6 mediated mismatch correction, while correction of MMs at the extremity of the SSA intermediate often appears to use a different mechanism, possibly by 3' nonhomologous tail removal that includes part of the homologous sequence. In contrast, in FA Tailless strains there was a uniform repair of the MMs across the repeat. A distinctive pattern of correction was found in the absence of MSH2, in both Tailed and Tailless strains, different from the spectrum seen in a msh3Δ msh6Δ double mutant. Previous work has shown that SSA is Rad51-independent but dependent on the strand annealing activity of Rad52. However Rad52 becomes dispensable in a Tailless construct where the DSB is induced by Cas9 or in transformation of a plasmid where SSA occurs in the absence of nonhomologous tails.
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Affiliation(s)
- Elena Sapède
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Neal Sugawara
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Randall G. Tyers
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Yuko Nakajima
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Mosammat Faria Afreen
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jesselin Romero Escobar
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - James E. Haber
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
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6
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Medina-Rivera M, Phelps S, Sridharan M, Becker J, Lamb N, Kumar C, Sutton M, Bielinsky A, Balakrishnan L, Surtees J. Elevated MSH2 MSH3 expression interferes with DNA metabolism in vivo. Nucleic Acids Res 2023; 51:12185-12206. [PMID: 37930834 PMCID: PMC10711559 DOI: 10.1093/nar/gkad934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023] Open
Abstract
The Msh2-Msh3 mismatch repair (MMR) complex in Saccharomyces cerevisiae recognizes and directs repair of insertion/deletion loops (IDLs) up to ∼17 nucleotides. Msh2-Msh3 also recognizes and binds distinct looped and branched DNA structures with varying affinities, thereby contributing to genome stability outside post-replicative MMR through homologous recombination, double-strand break repair (DSBR) and the DNA damage response. In contrast, Msh2-Msh3 promotes genome instability through trinucleotide repeat (TNR) expansions, presumably by binding structures that form from single-stranded (ss) TNR sequences. We previously demonstrated that Msh2-Msh3 binding to 5' ssDNA flap structures interfered with Rad27 (Fen1 in humans)-mediated Okazaki fragment maturation (OFM) in vitro. Here we demonstrate that elevated Msh2-Msh3 levels interfere with DNA replication and base excision repair in vivo. Elevated Msh2-Msh3 also induced a cell cycle arrest that was dependent on RAD9 and ELG1 and led to PCNA modification. These phenotypes also required Msh2-Msh3 ATPase activity and downstream MMR proteins, indicating an active mechanism that is not simply a result of Msh2-Msh3 DNA-binding activity. This study provides new mechanistic details regarding how excess Msh2-Msh3 can disrupt DNA replication and repair and highlights the role of Msh2-Msh3 protein abundance in Msh2-Msh3-mediated genomic instability.
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Affiliation(s)
- Melisa Medina-Rivera
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Samantha Phelps
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Madhumita Sridharan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jordan Becker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Natalie A Lamb
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Charanya Kumar
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Mark D Sutton
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Anja Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jennifer A Surtees
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
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7
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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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8
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Dluzewska J, Dziegielewski W, Szymanska-Lejman M, Gazecka M, Henderson IR, Higgins JD, Ziolkowski PA. MSH2 stimulates interfering and inhibits non-interfering crossovers in response to genetic polymorphism. Nat Commun 2023; 14:6716. [PMID: 37872134 PMCID: PMC10593791 DOI: 10.1038/s41467-023-42511-z] [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: 04/17/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Meiotic crossovers can be formed through the interfering pathway, in which one crossover prevents another from forming nearby, or by an independent non-interfering pathway. In Arabidopsis, local sequence polymorphism between homologs can stimulate interfering crossovers in a MSH2-dependent manner. To understand how MSH2 regulates crossovers formed by the two pathways, we combined Arabidopsis mutants that elevate non-interfering crossovers with msh2 mutants. We demonstrate that MSH2 blocks non-interfering crossovers at polymorphic loci, which is the opposite effect to interfering crossovers. We also observe MSH2-independent crossover inhibition at highly polymorphic sites. We measure recombination along the chromosome arms in lines differing in patterns of heterozygosity and observe a MSH2-dependent crossover increase at the boundaries between heterozygous and homozygous regions. Here, we show that MSH2 is a master regulator of meiotic DSB repair in Arabidopsis, with antagonistic effects on interfering and non-interfering crossovers, which shapes the crossover landscape in relation to interhomolog polymorphism.
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Affiliation(s)
- Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Wojciech Dziegielewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Monika Gazecka
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
- Department of Molecular Virology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.
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Lavi ES, Lin ZP, Ratner ES. Gene expression of non-homologous end-joining pathways in the prognosis of ovarian cancer. iScience 2023; 26:107934. [PMID: 37810216 PMCID: PMC10558711 DOI: 10.1016/j.isci.2023.107934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/04/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Ovarian cancer is the deadliest gynecologic malignancy in women, with a 46% five-year overall survival rate. The objective of the study was to investigate the effects of non-homologous end-joining (NHEJ) genes on clinical outcomes of ovarian cancer patients. To determine if these genes act as prognostic biomarkers of mortality and disease progression, the expression profiles of 48 NHEJ-associated genes were analyzed using an array of statistical and machine learning techniques: logistic regression models, decision trees, naive-Bayes, two sample t-tests, support vector machines, hierarchical clustering, principal component analysis, and neural networks. In this process, the correlation of genes with patient survival and disease progression and recurrence was noted. Also, multiple features from the gene set were found to have significant predictive capabilities. APTX, BRCA1, PAXX, LIG1, and TP53 were identified as most important out of all the candidate genes for predicting clinical outcomes of ovarian cancer patients.
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Affiliation(s)
- Ethan S. Lavi
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Z. Ping Lin
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Elena S. Ratner
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
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10
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Gupta SV, Campos L, Schmidt KH. Mitochondrial superoxide dismutase Sod2 suppresses nuclear genome instability during oxidative stress. Genetics 2023; 225:iyad147. [PMID: 37638880 PMCID: PMC10550321 DOI: 10.1093/genetics/iyad147] [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: 02/24/2023] [Accepted: 07/14/2023] [Indexed: 08/29/2023] Open
Abstract
Oxidative stress can damage DNA and thereby contribute to genome instability. To avoid an imbalance or overaccumulation of reactive oxygen species (ROS), cells are equipped with antioxidant enzymes that scavenge excess ROS. Cells lacking the RecQ-family DNA helicase Sgs1, which contributes to homology-dependent DNA break repair and chromosome stability, are known to accumulate ROS, but the origin and consequences of this oxidative stress phenotype are not fully understood. Here, we show that the sgs1 mutant exhibits elevated mitochondrial superoxide, increased mitochondrial mass, and accumulation of recombinogenic DNA lesions that can be suppressed by antioxidants. Increased mitochondrial mass in the sgs1Δ mutant is accompanied by increased mitochondrial branching, which was also inducible in wildtype cells by replication stress. Superoxide dismutase Sod2 genetically interacts with Sgs1 in the suppression of nuclear chromosomal rearrangements under paraquat (PQ)-induced oxidative stress. PQ-induced chromosome rearrangements in the absence of Sod2 are promoted by Rad51 recombinase and the polymerase subunit Pol32. Finally, the dependence of chromosomal rearrangements on the Rev1/Pol ζ mutasome suggests that under oxidative stress successful DNA synthesis during DNA break repair depends on translesion DNA synthesis.
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Affiliation(s)
- Sonia Vidushi Gupta
- Department of Molecular Biosciences, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Lillian Campos
- Department of Molecular Biosciences, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Kristina Hildegard Schmidt
- Department of Molecular Biosciences, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
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11
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Papp D, Hernandez LA, Mai TA, Haanen TJ, O’Donnell MA, Duran AT, Hernandez SM, Narvanto JE, Arguello B, Onwukwe MO, Kolar K, Mirkin SM, Kim JC. Massive contractions of Myotonic Dystrophy Type 2-associated CCTG tetranucleotide repeats occur via double strand break repair with distinct requirements for helicases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548036. [PMID: 37461657 PMCID: PMC10350092 DOI: 10.1101/2023.07.06.548036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Myotonic Dystrophy Type 2 (DM2) is a genetic disease caused by expanded CCTG DNA repeats in the first intron of CNBP. The number of CCTG repeats in DM2 patients ranges from 75-11,000, yet little is known about the molecular mechanisms responsible for repeat expansions or contractions. We developed an experimental system in Saccharomyces cerevisiae that enables selection of large-scale contractions of (CCTG)100 within the intron of a reporter gene and subsequent genetic analysis. Contractions exceeded 80 repeat units, causing the final repetitive tract to be well below the threshold for disease. We found that Rad51 and Rad52 are required for these massive contractions, indicating a mechanism that involves homologous recombination. Srs2 helicase was shown previously to stabilize CTG, CAG, and CGG repeats. Loss of Srs2 did not significantly affect CCTG contraction rates in unperturbed conditions. In contrast, loss of the RecQ helicase Sgs1 resulted in a 6-fold decrease in contraction rate with specific evidence that helicase activity is required for large-scale contractions. Using a genetic assay to evaluate chromosome arm loss, we determined that CCTG and reverse complementary CAGG repeats elevate the rate of chromosomal fragility compared to a low-repeat control. Overall, our results demonstrate that the genetic control of CCTG repeat contractions is notably distinct among disease-causing microsatellite repeat sequences.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Kara Kolar
- Department of Biology, Tufts University, Medford, MA 02155
| | | | - Jane C. Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078
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12
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Oh JM, Kang Y, Park J, Sung Y, Kim D, Seo Y, Lee E, Ra J, Amarsanaa E, Park YU, Lee S, Hwang J, Kim H, Schärer O, Cho S, Lee C, Takata KI, Lee J, Myung K. MSH2-MSH3 promotes DNA end resection during homologous recombination and blocks polymerase theta-mediated end-joining through interaction with SMARCAD1 and EXO1. Nucleic Acids Res 2023; 51:5584-5602. [PMID: 37140056 PMCID: PMC10287916 DOI: 10.1093/nar/gkad308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/04/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
DNA double-strand break (DSB) repair via homologous recombination is initiated by end resection. The extent of DNA end resection determines the choice of the DSB repair pathway. Nucleases for end resection have been extensively studied. However, it is still unclear how the potential DNA structures generated by the initial short resection by MRE11-RAD50-NBS1 are recognized and recruit proteins, such as EXO1, to DSB sites to facilitate long-range resection. We found that the MSH2-MSH3 mismatch repair complex is recruited to DSB sites through interaction with the chromatin remodeling protein SMARCAD1. MSH2-MSH3 facilitates the recruitment of EXO1 for long-range resection and enhances its enzymatic activity. MSH2-MSH3 also inhibits access of POLθ, which promotes polymerase theta-mediated end-joining (TMEJ). Collectively, we present a direct role of MSH2-MSH3 in the initial stages of DSB repair by promoting end resection and influencing the DSB repair pathway by favoring homologous recombination over TMEJ.
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Affiliation(s)
- Jung-Min Oh
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Oral Biochemistry, Dental and Life Science Institute, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea
| | - Yujin Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Jumi Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Yubin Sung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Dayoung Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Yuri Seo
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Eun A Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Enkhzul Amarsanaa
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Young-Un Park
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Seon Young Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Jung Me Hwang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Hongtae Kim
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Orlando Schärer
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Seung Woo Cho
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Changwook Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Kei-ichi Takata
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Ja Yil Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
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13
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Trost H, Merkell A, Lopezcolorado FW, Stark J. Resolution of sequence divergence for repeat-mediated deletions shows a polarity that is mediated by MLH1. Nucleic Acids Res 2023; 51:650-667. [PMID: 36620890 PMCID: PMC9881173 DOI: 10.1093/nar/gkac1240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/07/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
Repeat-mediated deletions (RMDs) are a type of chromosomal rearrangement between two homologous sequences that causes loss of the sequence between the repeats, along with one of the repeats. Sequence divergence between repeats suppresses RMDs; the mechanisms of such suppression and of resolution of the sequence divergence remains poorly understood. We identified RMD regulators using a set of reporter assays in mouse cells that test two key parameters: repeat sequence divergence and the distances between one repeat and the initiating chromosomal break. We found that the mismatch repair factor MLH1 suppresses RMDs with sequence divergence in the same pathway as MSH2 and MSH6, and which is dependent on residues in MLH1 and its binding partner PMS2 that are important for nuclease activity. Additionally, we found that the resolution of sequence divergence in the RMD product has a specific polarity, where divergent bases that are proximal to the chromosomal break end are preferentially removed. Moreover, we found that the domain of MLH1 that forms part of the MLH1-PMS2 endonuclease is important for polarity of resolution of sequence divergence. We also identified distinctions between MLH1 versus TOP3α in regulation of RMDs. We suggest that MLH1 suppresses RMDs with sequence divergence, while also promoting directional resolution of sequence divergence in the RMD product.
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Affiliation(s)
- Hannah Trost
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Arianna Merkell
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | | - Jeremy M Stark
- To whom correspondence should be addressed. Tel: +1 626 218-6346; Fax: +1 626 218 8892;
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14
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Walens A, Van Alsten SC, Olsson LT, Smith MA, Lockhart A, Gao X, Hamilton AM, Kirk EL, Love MI, Gupta GP, Perou CM, Vaziri C, Hoadley KA, Troester MA. RNA-Based Classification of Homologous Recombination Deficiency in Racially Diverse Patients with Breast Cancer. Cancer Epidemiol Biomarkers Prev 2022; 31:2136-2147. [PMID: 36129803 PMCID: PMC9720427 DOI: 10.1158/1055-9965.epi-22-0590] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/03/2022] [Accepted: 09/14/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Aberrant expression of DNA repair pathways such as homologous recombination (HR) can lead to DNA repair imbalance, genomic instability, and altered chemotherapy response. DNA repair imbalance may predict prognosis, but variation in DNA repair in diverse cohorts of breast cancer patients is understudied. METHODS To identify RNA-based patterns of DNA repair expression, we performed unsupervised clustering on 51 DNA repair-related genes in the Cancer Genome Atlas Breast Cancer [TCGA BRCA (n = 1,094)] and Carolina Breast Cancer Study [CBCS (n = 1,461)]. Using published DNA-based HR deficiency (HRD) scores (high-HRD ≥ 42) from TCGA, we trained an RNA-based supervised classifier. Unsupervised and supervised HRD classifiers were evaluated in association with demographics, tumor characteristics, and clinical outcomes. RESULTS : Unsupervised clustering on DNA repair genes identified four clusters of breast tumors, with one group having high expression of HR genes. Approximately 39.7% of CBCS and 29.3% of TCGA breast tumors had this unsupervised high-HRD (U-HRD) profile. A supervised HRD classifier (S-HRD) trained on TCGA had 84% sensitivity and 73% specificity to detect HRD-high samples. Both U-HRD and S-HRD tumors in CBCS had higher frequency of TP53 mutant-like status (45% and 41% enrichment) and basal-like subtype (63% and 58% enrichment). S-HRD high was more common among black patients. Among chemotherapy-treated participants, recurrence was associated with S-HRD high (HR: 2.38, 95% confidence interval = 1.50-3.78). CONCLUSIONS HRD is associated with poor prognosis and enriched in the tumors of black women. IMPACT RNA-level indicators of HRD are predictive of breast cancer outcomes in diverse populations.
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Affiliation(s)
- Andrea Walens
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Sarah C. Van Alsten
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Linnea T. Olsson
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Markia A. Smith
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Alex Lockhart
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Xiaohua Gao
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Alina M. Hamilton
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Erin L. Kirk
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gaorav P. Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Melissa A. Troester
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
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15
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Choi J, Kong M, Gallagher DN, Li K, Bronk G, Cao Y, Greene EC, Haber JE. Repair of mismatched templates during Rad51-dependent Break-Induced Replication. PLoS Genet 2022; 18:e1010056. [PMID: 36054210 PMCID: PMC9477423 DOI: 10.1371/journal.pgen.1010056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 09/15/2022] [Accepted: 08/10/2022] [Indexed: 12/02/2022] Open
Abstract
Using budding yeast, we have studied Rad51-dependent break-induced replication (BIR), where the invading 3’ end of a site-specific double-strand break (DSB) and a donor template share 108 bp of homology that can be easily altered. BIR still occurs about 10% as often when every 6th base is mismatched as with a perfectly matched donor. Here we explore the tolerance of mismatches in more detail, by examining donor templates that each carry 10 mismatches, each with different spatial arrangements. Although 2 of the 6 arrangements we tested were nearly as efficient as the evenly-spaced reference, 4 were significantly less efficient. A donor with all 10 mismatches clustered at the 3’ invading end of the DSB was not impaired compared to arrangements where mismatches were clustered at the 5’ end. Our data suggest that the efficiency of strand invasion is principally dictated by thermodynamic considerations, i.e., by the total number of base pairs that can be formed; but mismatch position-specific effects are also important. We also addressed an apparent difference between in vitro and in vivo strand exchange assays, where in vitro studies had suggested that at a single contiguous stretch of 8 consecutive bases was needed to be paired for stable strand pairing, while in vivo assays using 108-bp substrates found significant recombination even when every 6th base was mismatched. Now, using substrates of either 90 or 108 nt–the latter being the size of the in vivo templates–we find that in vitro D-loop results are very similar to the in vivo results. However, there are still notable differences between in vivo and in vitro assays that are especially evident with unevenly-distributed mismatches. Mismatches in the donor template are incorporated into the BIR product in a strongly polar fashion up to ~40 nucleotides from the 3’ end. Mismatch incorporation depends on the 3’→ 5’ proofreading exonuclease activity of DNA polymerase δ, with little contribution from Msh2/Mlh1 mismatch repair proteins, or from Rad1-Rad10 flap nuclease or the Mph1 helicase. Surprisingly, the probability of a mismatch 27 nt from the 3’ end being replaced by donor sequence was the same whether the preceding 26 nucleotides were mismatched every 6th base or fully homologous. These data suggest that DNA polymerase δ “chews back” the 3’ end of the invading strand without any mismatch-dependent cues from the strand invasion structure. However, there appears to be an alternative way to incorporate a mismatch at the first base at the 3’ end of the donor. DNA double-strand breaks (DSBs) are the most lethal forms of DNA damage and inaccurate repair of these breaks presents a serious threat to genomic integrity and cell viability. Break-induced replication (BIR) is a homologous recombination pathway that results in a nonreciprocal translocation of chromosome ends. We used budding yeast Saccharomyces cerevisiae to investigate Rad51-mediated BIR, where the invading 3’ end of the DSB and a donor template share 108 bp of homology. We examined the tolerance of differently distributed mismatches on a homologous donor template. A donor with all 10 mismatches clustered every 6th base at the 3’ invading end of the DSB was not impaired compared to arrangements where mismatches were clustered at the 5’ end. We also compared the efficiency of in vivo BIR with in vitro D-loop formation and find that for substrates of the same length, the tolerance for mismatches is comparable. However, there are still notable differences between in vivo and in vitro assays that are especially evident in substrates with unevenly-distributed mismatches. Mismatches are incorporated into the BIR product in a strongly polar fashion as far as about 40 nucleotides from the 3’ end, dependent on the 5’ to 3’ proofreading activity of DNA polymerase δ. Pol δ can “chew back” the 3’ end of the invading strand even when the sequences removed have no mismatches for the first 26 nucleotides. However, a mismatch at the first base can be removed from the 3’ end by another, unidentified mechanism.
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Affiliation(s)
- Jihyun Choi
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Muwen Kong
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - Danielle N. Gallagher
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Kevin Li
- Department of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Gabriel Bronk
- Department of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Yiting Cao
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Eric C. Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - James E. Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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16
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Nibau C, Gonzalo A, Evans A, Sweet‐Jones W, Phillips D, Lloyd A. Meiosis in allopolyploid Arabidopsis suecica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1110-1122. [PMID: 35759495 PMCID: PMC9545853 DOI: 10.1111/tpj.15879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 06/01/2023]
Abstract
Polyploidy is a major force shaping eukaryote evolution but poses challenges for meiotic chromosome segregation. As a result, first-generation polyploids often suffer from more meiotic errors and lower fertility than established wild polyploid populations. How established polyploids adapt their meiotic behaviour to ensure genome stability and accurate chromosome segregation remains an active research question. We present here a cytological description of meiosis in the model allopolyploid species Arabidopsis suecica (2n = 4x = 26). In large part meiosis in A. suecica is diploid-like, with normal synaptic progression and no evidence of synaptic partner exchanges. Some abnormalities were seen at low frequency, including univalents at metaphase I, anaphase bridges and aneuploidy at metaphase II; however, we saw no evidence of crossover formation occurring between non-homologous chromosomes. The crossover number in A. suecica is similar to the combined number reported from its diploid parents Arabidopsis thaliana (2n = 2x = 10) and Arabidopsis arenosa (2n = 2x = 16), with an average of approximately 1.75 crossovers per chromosome pair. This contrasts with naturally evolved autotetraploid A. arenosa, where accurate chromosome segregation is achieved by restricting crossovers to approximately 1 per chromosome pair. Although an autotetraploid donor is hypothesized to have contributed the A. arenosa subgenome to A. suecica, A. suecica harbours diploid A. arenosa variants of key meiotic genes. These multiple lines of evidence suggest that meiosis in the recently evolved allopolyploid A. suecica is essentially diploid like, with meiotic adaptation following a very different trajectory to that described for autotetraploid A. arenosa.
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Affiliation(s)
- Candida Nibau
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityPenglaisAberystwythCeredigionSY23 3DAUK
| | - Adrián Gonzalo
- John Innes CentreColney LaneNorwichNR4 7UHUK
- Department of Biology, Institute of Molecular Plant BiologySwiss Federal Institute of Technology (ETH) ZürichZürich8092Switzerland
| | - Aled Evans
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityPenglaisAberystwythCeredigionSY23 3DAUK
| | - William Sweet‐Jones
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityPenglaisAberystwythCeredigionSY23 3DAUK
| | - Dylan Phillips
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityPenglaisAberystwythCeredigionSY23 3DAUK
| | - Andrew Lloyd
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityPenglaisAberystwythCeredigionSY23 3DAUK
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17
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CNOT6: A Novel Regulator of DNA Mismatch Repair. Cells 2022; 11:cells11030521. [PMID: 35159331 PMCID: PMC8833972 DOI: 10.3390/cells11030521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
DNA mismatch repair (MMR) is a highly conserved pathway that corrects both base–base mispairs and insertion-deletion loops (IDLs) generated during DNA replication. Defects in MMR have been linked to carcinogenesis and drug resistance. However, the regulation of MMR is poorly understood. Interestingly, CNOT6 is one of four deadenylase subunits in the conserved CCR4-NOT complex and it targets poly(A) tails of mRNAs for degradation. CNOT6 is overexpressed in acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML) and androgen-independent prostate cancer cells, which suggests that an altered expression of CNOT6 may play a role in tumorigenesis. Here, we report that a depletion of CNOT6 sensitizes human U2OS cells to N-methyl-N′nitro-N-nitrosoguanidine (MNNG) and leads to enhanced apoptosis. We also demonstrate that the depletion of CNOT6 upregulates MMR and decreases the mutation frequency in MMR-proficient cells. Furthermore, the depletion of CNOT6 increases the stability of mRNA transcripts from MMR genes, leading to the increased expression of MMR proteins. Our work provides insight into a novel CNOT6-dependent mechanism for regulating MMR.
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18
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Barroso-González J, García-Expósito L, Galaviz P, Lynskey ML, Allen JAM, Hoang S, Watkins SC, Pickett HA, O'Sullivan RJ. Anti-recombination function of MutSα restricts telomere extension by ALT-associated homology-directed repair. Cell Rep 2021; 37:110088. [PMID: 34879271 PMCID: PMC8724847 DOI: 10.1016/j.celrep.2021.110088] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/13/2021] [Accepted: 11/10/2021] [Indexed: 01/02/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomere-elongation mechanism observed in ~15% of cancer subtypes. Current models indicate that ALT is mediated by homology-directed repair mechanisms. By disrupting MSH6 gene expression, we show that the deficiency of MutSα (MSH2/MSH6) DNA mismatch repair complex causes striking telomere hyperextension. Mechanistically, we show MutSα is specifically recruited to telomeres in ALT cells by associating with the proliferating-cell nuclear antigen (PCNA) subunit of the ALT telomere replisome. We also provide evidence that MutSα counteracts Bloom (BLM) helicase, which adopts a crucial role in stabilizing hyper-extended telomeres and maintaining the survival of MutSα-deficient ALT cancer cells. Lastly, we propose a model in which MutSα deficiency impairs heteroduplex rejection, leading to premature initiation of telomere DNA synthesis that coincides with an accumulation of telomere variant repeats (TVRs). These findings provide evidence that the MutSα DNA mismatch repair complex acts to restrain unwarranted ALT. Barroso-Gonzalez et al. show that the mismatch repair complex MutSα restricts the alternative lengthening of telomeres (ALT) pathway in cancer cells. MutSα has an anti-recombination function and limits recombination between heteroduplex sequences at telomeres, in part by counteracting the Bloom helicase (BLM).
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Affiliation(s)
- Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Pablo Galaviz
- Bioinformatics Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Michelle Lee Lynskey
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - SongMy Hoang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Simon C Watkins
- Department of Cell Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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19
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Chen PJ, Hussmann JA, Yan J, Knipping F, Ravisankar P, Chen PF, Chen C, Nelson JW, Newby GA, Sahin M, Osborn MJ, Weissman JS, Adamson B, Liu DR. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 2021; 184:5635-5652.e29. [PMID: 34653350 PMCID: PMC8584034 DOI: 10.1016/j.cell.2021.09.018] [Citation(s) in RCA: 301] [Impact Index Per Article: 100.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/09/2021] [Accepted: 09/09/2021] [Indexed: 12/26/2022]
Abstract
While prime editing enables precise sequence changes in DNA, cellular determinants of prime editing remain poorly understood. Using pooled CRISPRi screens, we discovered that DNA mismatch repair (MMR) impedes prime editing and promotes undesired indel byproducts. We developed PE4 and PE5 prime editing systems in which transient expression of an engineered MMR-inhibiting protein enhances the efficiency of substitution, small insertion, and small deletion prime edits by an average 7.7-fold and 2.0-fold compared to PE2 and PE3 systems, respectively, while improving edit/indel ratios by 3.4-fold in MMR-proficient cell types. Strategic installation of silent mutations near the intended edit can enhance prime editing outcomes by evading MMR. Prime editor protein optimization resulted in a PEmax architecture that enhances editing efficacy by 2.8-fold on average in HeLa cells. These findings enrich our understanding of prime editing and establish prime editing systems that show substantial improvement across 191 edits in seven mammalian cell types.
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Affiliation(s)
- Peter J Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jun Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Friederike Knipping
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55108, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Purnima Ravisankar
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Pin-Fang Chen
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Cidi Chen
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - James W Nelson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Mustafa Sahin
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Mark J Osborn
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55108, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Britt Adamson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
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20
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Gallagher DN, Haber JE. Single-strand template repair: key insights to increase the efficiency of gene editing. Curr Genet 2021; 67:747-753. [PMID: 33881574 DOI: 10.1007/s00294-021-01186-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/27/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
DNA double-strand breaks (DSBs) pose a serious hazard for the stability of the genome. CRISPR-Cas9-mediated gene editing intentionally creates a site-specific DSB to modify the genomic sequence, typically from an introduced single-stranded DNA donor. However, unlike typical forms of homologous recombination, single-strand template repair (SSTR) is Rad51-independent. Moreover, this pathway is distinct from other previously characterized Rad51-independent processes. Here, we briefly review the work characterizing this pathway, and how these findings can be used to guide and improve current gene editing strategies.
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Affiliation(s)
- Danielle N Gallagher
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, 02154, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, 02154, USA.
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21
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Al-Zain AM, Symington LS. The dark side of homology-directed repair. DNA Repair (Amst) 2021; 106:103181. [PMID: 34311272 DOI: 10.1016/j.dnarep.2021.103181] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 10/20/2022]
Abstract
DNA double strand breaks (DSB) are cytotoxic lesions that can lead to genome rearrangements and genomic instability, which are hallmarks of cancer. The two main DSB repair pathways are non-homologous end joining and homologous recombination (HR). While HR is generally highly accurate, it has the potential for rearrangements that occur directly or through intermediates generated during the repair process. Whole genome sequencing of cancers has revealed numerous types of structural rearrangement signatures that are often indicative of repair mediated by sequence homology. However, it can be challenging to delineate repair mechanisms from sequence analysis of rearrangement end products from cancer genomes, or even model systems, because the same rearrangements can be generated by different pathways. Here, we review homology-directed repair pathways and their consequences. Exploring those pathways can lead to a greater understanding of rearrangements that occur in cancer cells.
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Affiliation(s)
- Amr M Al-Zain
- Program in Biological Sciences, Columbia University, New York, NY, 10027, United States; Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, United States
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, United States; Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, 10032, United States.
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22
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Learning Yeast Genetics from Miro Radman. Cells 2021; 10:cells10040945. [PMID: 33923882 PMCID: PMC8072546 DOI: 10.3390/cells10040945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 11/17/2022] Open
Abstract
Miroslav Radman's far-sighted ideas have penetrated many aspects of our study of the repair of broken eukaryotic chromosomes. For over 35 years my lab has studied different aspects of the repair of chromosomal breaks in the budding yeast, Saccharomyces cerevisiae. From the start, we have made what we thought were novel observations that turned out to have been predicted by Miro's extraordinary work in the bacterium Escherichia coli and then later in the radiation-resistant Dienococcus radiodurans. In some cases, we have been able to extend some of his ideas a bit further.
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23
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Effects of the loss of mismatch repair genes on single-strand annealing between divergent sequences in Saccharomyces cerevisiae. J Microbiol 2021; 59:401-409. [PMID: 33779953 DOI: 10.1007/s12275-021-1076-x] [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: 02/04/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 10/21/2022]
Abstract
Eukaryotic genomes contain many duplicated genes closely located with each other, such as the hexose transporter (HXT) genes in Saccharomyces cerevisiae. They can potentially recombine via single-strand annealing (SSA) pathway. SSA between highly divergent sequences generates heteroduplex DNA intermediates with many mismatches, which can be corrected by mismatch repair (MMR), resulting in recombinant sequences with a single junction point. In this report, we demonstrate that SSA between HXT1 and HXT4 genes in MMR-deficient yeast cells produces recombinant genes with multiple-junctions resulting from alternating HXT1 and HXT4 tracts. The mutations in MMR genes had differential effects on SSA frequencies; msh6Δ mutation significantly stimulated SSA events, whereas msh2Δ and msh3Δ slightly suppressed it. We set up an assay that can identify a pair of recombinant genes derived from a single heteroduplex DNA. As a result, the recombinant genes with multiple-junctions were found to accompany genes with single-junctions. Based on the results presented here, a model was proposed to generate multiple-junctions in SSA pathway involving an alternative short-patch repair system.
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24
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Sanford EJ, Comstock WJ, Faça VM, Vega SC, Gnügge R, Symington LS, Smolka MB. Phosphoproteomics reveals a distinctive Mec1/ATR signaling response upon DNA end hyper-resection. EMBO J 2021; 40:e104566. [PMID: 33764556 DOI: 10.15252/embj.2020104566] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/16/2021] [Accepted: 02/22/2021] [Indexed: 01/27/2023] Open
Abstract
The Mec1/ATR kinase is crucial for genome maintenance in response to a range of genotoxic insults, but it remains unclear how it promotes context-dependent signaling and DNA repair. Using phosphoproteomic analyses, we uncovered a distinctive Mec1/ATR signaling response triggered by extensive nucleolytic processing (resection) of DNA ends. Budding yeast cells lacking Rad9, a checkpoint adaptor and an inhibitor of resection, exhibit a selective increase in Mec1-dependent phosphorylation of proteins associated with single-strand DNA (ssDNA) transactions, including the ssDNA-binding protein Rfa2, the translocase/ubiquitin ligase Uls1, and the Sgs1-Top3-Rmi1 (STR) complex that regulates homologous recombination (HR). Extensive Mec1-dependent phosphorylation of the STR complex, mostly on the Sgs1 helicase subunit, promotes an interaction between STR and the DNA repair scaffolding protein Dpb11. Fusion of Sgs1 to phosphopeptide-binding domains of Dpb11 strongly impairs HR-mediated repair, supporting a model whereby Mec1 signaling regulates STR upon hyper-resection to influence recombination outcomes. Overall, the identification of a distinct Mec1 signaling response triggered by hyper-resection highlights the multi-faceted action of this kinase in the coordination of checkpoint signaling and HR-mediated DNA repair.
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Affiliation(s)
- Ethan J Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - William J Comstock
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Vitor M Faça
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.,Department of Biochemistry and Immunology and Cell-Based Therapy Center, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Stephanie C Vega
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Robert Gnügge
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lorraine S Symington
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 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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25
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Morales ME, Kaul T, Walker J, Everett C, White T, Deininger P. Altered DNA repair creates novel Alu/Alu repeat-mediated deletions. Hum Mutat 2021; 42:600-613. [PMID: 33675284 PMCID: PMC8068675 DOI: 10.1002/humu.24193] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/25/2021] [Accepted: 02/24/2021] [Indexed: 12/21/2022]
Abstract
Alu elements are the most abundant source of nonallelic homology that influences genetic instability in the human genome. When there is a DNA double-stranded break, the Alu element's high copy number, moderate length and distance and mismatch between elements uniquely influence recombination processes. We utilize a reporter-gene assay to show the complex influence of Alu mismatches on Alu-related repeat-mediated deletions (RMDs). The Alu/Alu heteroduplex intermediate can result in a nonallelic homologous recombination (HR). Alternatively, the heteroduplex can result in various DNA breaks around the Alu elements caused by competing nucleases. These breaks can undergo Alt-nonhomologous end joining to cause deletions focused around the Alu elements. Formation of these heteroduplex intermediates is largely RAD52 dependent. Cells with low ERCC1 levels utilize more of these alternatives resolutions, while cells with MSH2 defects tend to have more RMDs with a specific increase in the HR events. Therefore, Alu elements are expected to create different forms of deletions in various cancers depending on a number of these DNA repair defects.
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Affiliation(s)
- Maria E Morales
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, USA
| | - Tiffany Kaul
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, USA
| | - JaNiece Walker
- Department of Biology, Xavier University, New Orleans, Louisiana, USA
| | - Chelsea Everett
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, USA
| | - Travis White
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, USA.,Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Prescott Deininger
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, USA.,Department of Epidemiology, Tulane University, New Orleans, Louisiana, USA
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26
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Mendez-Dorantes C, Tsai LJ, Jahanshir E, Lopezcolorado FW, Stark JM. BLM has Contrary Effects on Repeat-Mediated Deletions, based on the Distance of DNA DSBs to a Repeat and Repeat Divergence. Cell Rep 2021; 30:1342-1357.e4. [PMID: 32023454 PMCID: PMC7085117 DOI: 10.1016/j.celrep.2020.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/08/2019] [Accepted: 12/31/2019] [Indexed: 12/30/2022] Open
Abstract
Repeat-mediated deletions (RMDs) often involve repetitive elements (e.g., short interspersed elements) with sequence divergence that is separated by several kilobase pairs (kbps). We have examined RMDs induced by DNA double-strand breaks (DSBs) under varying conditions of repeat sequence divergence (identical versus 1% and 3% divergent) and DSB/repeat distance (16 bp–28.4 kbp). We find that the BLM helicase promotes RMDs with long DSB/repeat distances (e.g., 28.4 kbp), which is consistent with a role in extensive DSB end resection, because the resection nucleases EXO1 and DNA2 affect RMDs similarly to BLM. In contrast, BLM suppresses RMDs with sequence divergence and intermediate (e.g., 3.3 kbp) DSB/repeat distances, which supports a role in heteroduplex rejection. The role of BLM in heteroduplex rejection is not epistatic with MSH2 and is independent of the annealing factor RAD52. Accordingly, the role of BLM on RMDs is substantially affected by DSB/repeat distance and repeat sequence divergence. Mendez-Dorantes et al. identify the BLM helicase as a key regulator of repeat-mediated deletions (RMDs). BLM, EXO1, and DNA2 mediate RMDs with remarkably long DNA break/repeat distances. BLM suppresses RMDs with sequence divergence that is optimal with a long non-homologous tail and is independent of MSH2 and RAD52.
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Affiliation(s)
- Carlos Mendez-Dorantes
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - L Jillianne Tsai
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Eva Jahanshir
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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27
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The Amazing Acrobat: Yeast's Histone H3K56 Juggles Several Important Roles While Maintaining Perfect Balance. Genes (Basel) 2021; 12:genes12030342. [PMID: 33668997 PMCID: PMC7996553 DOI: 10.3390/genes12030342] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 01/16/2023] Open
Abstract
Acetylation on lysine 56 of histone H3 of the yeast Saccharomyces cerevisiae has been implicated in many cellular processes that affect genome stability. Despite being the object of much research, the complete scope of the roles played by K56 acetylation is not fully understood even today. The acetylation is put in place at the S-phase of the cell cycle, in order to flag newly synthesized histones that are incorporated during DNA replication. The signal is removed by two redundant deacetylases, Hst3 and Hst4, at the entry to G2/M phase. Its crucial location, at the entry and exit points of the DNA into and out of the nucleosome, makes this a central modification, and dictates that if acetylation and deacetylation are not well concerted and executed in a timely fashion, severe genomic instability arises. In this review, we explore the wealth of information available on the many roles played by H3K56 acetylation and the deacetylases Hst3 and Hst4 in DNA replication and repair.
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28
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Single-Strand Annealing in Cancer. Int J Mol Sci 2021; 22:ijms22042167. [PMID: 33671579 PMCID: PMC7926775 DOI: 10.3390/ijms22042167] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/23/2022] Open
Abstract
DNA double-strand breaks (DSBs) are among the most serious forms of DNA damage. In humans, DSBs are repaired mainly by non-homologous end joining (NHEJ) and homologous recombination repair (HRR). Single-strand annealing (SSA), another DSB repair system, uses homologous repeats flanking a DSB to join DNA ends and is error-prone, as it removes DNA fragments between repeats along with one repeat. Many DNA deletions observed in cancer cells display homology at breakpoint junctions, suggesting the involvement of SSA. When multiple DSBs occur in different chromosomes, SSA may result in chromosomal translocations, essential in the pathogenesis of many cancers. Inhibition of RAD52 (RAD52 Homolog, DNA Repair Protein), the master regulator of SSA, results in decreased proliferation of BRCA1/2 (BRCA1/2 DNA Repair Associated)-deficient cells, occurring in many hereditary breast and ovarian cancer cases. Therefore, RAD52 may be targeted in synthetic lethality in cancer. SSA may modulate the response to platinum-based anticancer drugs and radiation. SSA may increase the efficacy of the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 (CRISPR associated 9) genome editing and reduce its off-target effect. Several basic problems associated with SSA, including its evolutionary role, interplay with HRR and NHEJ and should be addressed to better understand its role in cancer pathogenesis and therapy.
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29
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Mackenroth B, Alani E. Collaborations between chromatin and nuclear architecture to optimize DNA repair fidelity. DNA Repair (Amst) 2021; 97:103018. [PMID: 33285474 PMCID: PMC8486310 DOI: 10.1016/j.dnarep.2020.103018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/18/2020] [Accepted: 11/05/2020] [Indexed: 01/22/2023]
Abstract
Homologous recombination (HR), considered the highest fidelity DNA double-strand break (DSB) repair pathway that a cell possesses, is capable of repairing multiple DSBs without altering genetic information. However, in "last resort" scenarios, HR can be directed to low fidelity subpathways which often use non-allelic donor templates. Such repair mechanisms are often highly mutagenic and can also yield chromosomal rearrangements and/or deletions. While the choice between HR and its less precise counterpart, non-homologous end joining (NHEJ), has received much attention, less is known about how cells manage and prioritize HR subpathways. In this review, we describe work focused on how chromatin and nuclear architecture orchestrate subpathway choice and repair template usage to maintain genome integrity without sacrificing cell survival. Understanding the relationships between nuclear architecture and recombination mechanics will be critical to understand these cellular repair decisions.
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Affiliation(s)
- Beata Mackenroth
- Department of Molecular Biology and Genetics, Cornell University, 459 Biotechnology Building, Ithaca, NY, 14853-2703, United States
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, 459 Biotechnology Building, Ithaca, NY, 14853-2703, United States.
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30
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Choi JH, Lim YS, Kim MK, Bae SH. Analyses of DNA double-strand break repair pathways in tandem arrays of HXT genes of Saccharomyces cerevisiae. J Microbiol 2020; 58:957-966. [PMID: 33125670 DOI: 10.1007/s12275-020-0461-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 01/02/2023]
Abstract
Eukaryotic genomes contain numerous homologous repeat sequences including redundant genes with divergent homology that can be potential recombination targets. Recombination between divergent sequences is rare but poses a substantial threat to genome stability. The hexose transporter (HXT) gene family shares high sequence similarities at both protein and DNA levels, and some members are placed close together in tandem arrays. In this study, we show that spontaneous interstitial deletions occur at significantly high rates in HXT gene clusters, resulting in chimeric HXT sequences that contain a single junction point. We also observed that DNA double-strand breaks created between HXT genes produce primarily interstitial deletions, whereas internal cleavage of the HXT gene resulted in gene conversions as well as deletion products. Interestingly, interstitial deletions were less constrained by sequence divergence than gene conversion. Moreover, recombination-defective mutations differentially affected the survival frequency. Mutations that impair single-strand annealing (SSA) pathway greatly reduced the survival frequency by 10-1,000-fold, whereas disruption of Rad51-dependent homologous recombination exhibited only modest reduction. Our results indicate that recombination in the tandemly repeated HXT genes occurs primarily via SSA pathway.
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Affiliation(s)
- Ju-Hee Choi
- Department of Biological Sciences, College of Natural Science, Inha University, Incheon, 22212, Republic of Korea
| | - Ye-Seul Lim
- Department of Biological Sciences, College of Natural Science, Inha University, Incheon, 22212, Republic of Korea
| | - Min-Ku Kim
- Department of Biological Sciences, College of Natural Science, Inha University, Incheon, 22212, Republic of Korea
| | - Sung-Ho Bae
- Department of Biological Sciences, College of Natural Science, Inha University, Incheon, 22212, Republic of Korea.
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31
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Datta A, Dhar S, Awate S, Brosh RM. Synthetic Lethal Interactions of RECQ Helicases. Trends Cancer 2020; 7:146-161. [PMID: 33041245 DOI: 10.1016/j.trecan.2020.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/20/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023]
Abstract
DNA helicases have risen to the forefront as genome caretakers. Their prominent roles in chromosomal stability are demonstrated by the linkage of mutations in helicase genes to hereditary disorders with defects in DNA repair, the replication stress response, and/or transcriptional activation. Conversely, accumulating evidence suggests that DNA helicases in cancer cells have a network of pathway interactions such that codeficiency of some helicases and their genetically interacting proteins results in synthetic lethality (SL). Such genetic interactions may potentially be exploited for cancer therapies. We discuss the roles of RECQ DNA helicases in cancer, emphasizing some of the more recent developments in SL.
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Affiliation(s)
- Arindam Datta
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Srijita Dhar
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Sanket Awate
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Robert M Brosh
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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32
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Gallagher DN, Pham N, Tsai AM, Janto NV, Choi J, Ira G, Haber JE. A Rad51-independent pathway promotes single-strand template repair in gene editing. PLoS Genet 2020; 16:e1008689. [PMID: 33057349 PMCID: PMC7591047 DOI: 10.1371/journal.pgen.1008689] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 10/27/2020] [Accepted: 08/03/2020] [Indexed: 01/26/2023] Open
Abstract
The Rad51/RecA family of recombinases perform a critical function in typical repair of double-strand breaks (DSBs): strand invasion of a resected DSB end into a homologous double-stranded DNA (dsDNA) template sequence to initiate repair. However, repair of a DSB using single stranded DNA (ssDNA) as a template, a common method of CRISPR/Cas9-mediated gene editing, is Rad51-independent. We have analyzed the genetic requirements for these Rad51-independent events in Saccharomyces cerevisiae by creating a DSB with the site-specific HO endonuclease and repairing the DSB with 80-nt single-stranded oligonucleotides (ssODNs), and confirmed these results by Cas9-mediated DSBs in combination with a bacterial retron system that produces ssDNA templates in vivo. We show that single strand template repair (SSTR), is dependent on Rad52, Rad59, Srs2 and the Mre11-Rad50-Xrs2 (MRX) complex, but unlike other Rad51-independent recombination events, independent of Rdh54. We show that Rad59 acts to alleviate the inhibition of Rad51 on Rad52's strand annealing activity both in SSTR and in single strand annealing (SSA). Gene editing is Rad51-dependent when double-stranded oligonucleotides of the same size and sequence are introduced as templates. The assimilation of mismatches during gene editing is dependent on the activity of Msh2, which acts very differently on the 3' side of the ssODN which can anneal directly to the resected DSB end compared to the 5' end. In addition DNA polymerase Polδ's 3' to 5' proofreading activity frequently excises a mismatch very close to the 3' end of the template. We further report that SSTR is accompanied by as much as a 600-fold increase in mutations in regions adjacent to the sequences directly undergoing repair. These DNA polymerase ζ-dependent mutations may compromise the accuracy of gene editing.
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Affiliation(s)
- Danielle N. Gallagher
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, United States of America
| | - Nhung Pham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Annie M. Tsai
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, United States of America
| | - Nicolas V. Janto
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, United States of America
| | - Jihyun Choi
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, United States of America
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - James E. Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, United States of America
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33
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Young TZ, Liu P, Urbonaite G, Acar M. Quantitative Insights into Age-Associated DNA-Repair Inefficiency in Single Cells. Cell Rep 2020; 28:2220-2230.e7. [PMID: 31433994 PMCID: PMC6744837 DOI: 10.1016/j.celrep.2019.07.082] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/02/2019] [Accepted: 07/23/2019] [Indexed: 01/03/2023] Open
Abstract
Although double-strand break (DSB) repair is essential for a cell's survival, little is known about how DSB repair mechanisms are affected by age. Here we characterize the impact of cellular aging on the efficiency of single-strand annealing (SSA), a DSB repair mechanism. We measure SSA repair efficiency in young and old yeast cells and report a 23.4% decline in repair efficiency. This decline is not due to increased use of non-homologous end joining. Instead, we identify increased G1 phase duration in old cells as a factor responsible for the decreased SSA repair efficiency. Expression of 3xCLN2 leads to higher SSA repair efficiency in old cells compared with expression of 1xCLN2, confirming the involvement of cell-cycle regulation in age-associated repair inefficiency. Examining how SSA repair efficiency is affected by sequence heterology, we find that heteroduplex rejection remains high in old cells. Our work provides insights into the links between single-cell aging and DSB repair efficiency.
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Affiliation(s)
- Thomas Z Young
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Ping Liu
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Guste Urbonaite
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Murat Acar
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06511, USA; Department of Physics, Yale University, 217 Prospect Street, New Haven, CT 06511, USA.
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A Genome-Wide Screen for Genes Affecting Spontaneous Direct-Repeat Recombination in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2020; 10:1853-1867. [PMID: 32265288 PMCID: PMC7263696 DOI: 10.1534/g3.120.401137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Homologous recombination is an important mechanism for genome integrity maintenance, and several homologous recombination genes are mutated in various cancers and cancer-prone syndromes. However, since in some cases homologous recombination can lead to mutagenic outcomes, this pathway must be tightly regulated, and mitotic hyper-recombination is a hallmark of genomic instability. We performed two screens in Saccharomyces cerevisiae for genes that, when deleted, cause hyper-recombination between direct repeats. One was performed with the classical patch and replica-plating method. The other was performed with a high-throughput replica-pinning technique that was designed to detect low-frequency events. This approach allowed us to validate the high-throughput replica-pinning methodology independently of the replicative aging context in which it was developed. Furthermore, by combining the two approaches, we were able to identify and validate 35 genes whose deletion causes elevated spontaneous direct-repeat recombination. Among these are mismatch repair genes, the Sgs1-Top3-Rmi1 complex, the RNase H2 complex, genes involved in the oxidative stress response, and a number of other DNA replication, repair and recombination genes. Since several of our hits are evolutionarily conserved, and repeated elements constitute a significant fraction of mammalian genomes, our work might be relevant for understanding genome integrity maintenance in humans.
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35
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Wang H, Cao Q, Zhao Q, Arfan M, Liu W. Mechanisms used by DNA MMR system to cope with Cadmium-induced DNA damage in plants. CHEMOSPHERE 2020; 246:125614. [PMID: 31883478 DOI: 10.1016/j.chemosphere.2019.125614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 05/27/2023]
Abstract
Cadmium (Cd) is found widely in soil and is severely toxic for plants, causing oxidative damage in plant cells because of its heavy metal characteristics. The DNA damage response (DDR) is triggered in plants to cope with the Cd stress. The DNA mismatch repair (MMR) system known for its mismatch repair function determines DDR, as mispairs are easily generated by a translesional synthesis under Cd-induced genomic instability. Cd-induced mismatches are recognized by three heterodimeric complexes including MutSα (MSH2/MSH6), MutSβ (MSH2/MSH3), and MutSγ (MSH2/MSH7). MutLα (MLH1/PMS1), PCNA/RFC, EXO1, DNA polymerase δ and DNA ligase participate in mismatch repair in turn. Meanwhile, ATR is preferentially activated by MSH2 to trigger DDR including the regulation of the cell cycle, endoreduplication, cell death, and recruitment of other DNA repair, which enhances plant tolerance to Cd. However, plants with deficient MutS will bypass MMR-mediated DDR and release the multiple-effect MLH1 from requisition of the MMR system, which leads to weak tolerance to Cd in plants. In this review, we systematically illustrate how the plant DNA MMR system works in a Cd-induced DDR, and how MMR genes regulate plant tolerance to Cd. Additionally, we also reviewed multiple epigenetic regulation systems acting on MMR genes under stress.
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Affiliation(s)
- Hetong Wang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Shenyang, 110044, PR China.
| | - Qijiang Cao
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Shenyang, 110044, PR China.
| | - Qiang Zhao
- Agricultural College, Shenyang Agricultural University, Shenyang, 110866, PR China.
| | - Muhammad Arfan
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China.
| | - Wan Liu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China.
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36
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Ho V, Chung L, Singh A, Lea V, Abubakar A, Lim SH, Chua W, Ng W, Lee M, Roberts TL, de Souza P, Lee CS. Aberrant Expression of RAD52, Its Prognostic Impact in Rectal Cancer and Association with Poor Survival of Patients. Int J Mol Sci 2020; 21:ijms21051768. [PMID: 32143539 PMCID: PMC7084626 DOI: 10.3390/ijms21051768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/29/2020] [Accepted: 03/01/2020] [Indexed: 12/18/2022] Open
Abstract
The DNA damage response enables cells to survive and maintain genome integrity. RAD52 is a DNA-binding protein involved in the homologous recombination in DNA repair, and is important for the maintenance of tumour genome integrity. We investigated possible correlations between RAD52 expression and cancer survival and response to preoperative radiotherapy. RAD52 expression was examined in tumour samples from 179 patients who underwent surgery for rectal cancer, including a sub-cohort of 40 patients who were treated with neoadjuvant therapy. A high score for RAD52 expression in the tumour centre was significantly associated with worse disease-free survival (DFS; p = 0.045). In contrast, reduced RAD52 expression in tumour centre samples from patients treated with neoadjuvant therapy (n = 40) significantly correlated with poor DFS (p = 0.025) and overall survival (OS; p = 0.048). Our results suggested that RAD52 may have clinical value as a prognostic marker of tumour response to neoadjuvant radiation and both disease-free status and overall survival in patients with rectal cancer.
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Affiliation(s)
- Vincent Ho
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (L.C.); (A.A.); (T.L.R.); (P.d.S.); (C.S.L.)
- Correspondence: ; Tel.: +61-2-4620-3845; Fax: +61-2-4520-3116
| | - Liping Chung
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (L.C.); (A.A.); (T.L.R.); (P.d.S.); (C.S.L.)
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.H.L.); (W.C.)
| | - Amandeep Singh
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia; (A.S.); (V.L.)
| | - Vivienne Lea
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia; (A.S.); (V.L.)
| | - Askar Abubakar
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (L.C.); (A.A.); (T.L.R.); (P.d.S.); (C.S.L.)
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.H.L.); (W.C.)
| | - Stephanie H. Lim
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.H.L.); (W.C.)
- Macarthur Cancer Therapy Centre, Campbelltown Hospital, NSW 2560, Australia
- Discipline of Medical Oncology, School of Medicine, Western Sydney University, Liverpool, NSW 2170, Australia
| | - Wei Chua
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.H.L.); (W.C.)
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
- South Western Sydney Clinical School, University of New South Wales, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Weng Ng
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
| | - Mark Lee
- Department of Radiation Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
| | - Tara L. Roberts
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (L.C.); (A.A.); (T.L.R.); (P.d.S.); (C.S.L.)
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.H.L.); (W.C.)
- South Western Sydney Clinical School, University of New South Wales, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Paul de Souza
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (L.C.); (A.A.); (T.L.R.); (P.d.S.); (C.S.L.)
- Discipline of Medical Oncology, School of Medicine, Western Sydney University, Liverpool, NSW 2170, Australia
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
| | - Cheok Soon Lee
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (L.C.); (A.A.); (T.L.R.); (P.d.S.); (C.S.L.)
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.H.L.); (W.C.)
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia; (A.S.); (V.L.)
- Department of Radiation Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
- Discipline of Pathology, School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
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37
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Gupta SV, Schmidt KH. Maintenance of Yeast Genome Integrity by RecQ Family DNA Helicases. Genes (Basel) 2020; 11:E205. [PMID: 32085395 PMCID: PMC7074392 DOI: 10.3390/genes11020205] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 12/28/2022] Open
Abstract
With roles in DNA repair, recombination, replication and transcription, members of the RecQ DNA helicase family maintain genome integrity from bacteria to mammals. Mutations in human RecQ helicases BLM, WRN and RecQL4 cause incurable disorders characterized by genome instability, increased cancer predisposition and premature adult-onset aging. Yeast cells lacking the RecQ helicase Sgs1 share many of the cellular defects of human cells lacking BLM, including hypersensitivity to DNA damaging agents and replication stress, shortened lifespan, genome instability and mitotic hyper-recombination, making them invaluable model systems for elucidating eukaryotic RecQ helicase function. Yeast and human RecQ helicases have common DNA substrates and domain structures and share similar physical interaction partners. Here, we review the major cellular functions of the yeast RecQ helicases Sgs1 of Saccharomyces cerevisiae and Rqh1 of Schizosaccharomyces pombe and provide an outlook on some of the outstanding questions in the field.
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Affiliation(s)
- Sonia Vidushi Gupta
- Department of Cell Biology, Microbiology and Molecular Biology, University of South, Florida, Tampa, FL 33620, USA;
| | - Kristina Hildegard Schmidt
- Department of Cell Biology, Microbiology and Molecular Biology, University of South, Florida, Tampa, FL 33620, USA;
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research, Institute, Tampa, FL 33612, USA
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38
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Gonzalez V, Spampinato CP. The mismatch repair protein MSH6 regulates somatic recombination in Arabidopsis thaliana. DNA Repair (Amst) 2020; 87:102789. [PMID: 31945543 DOI: 10.1016/j.dnarep.2020.102789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/29/2019] [Accepted: 01/08/2020] [Indexed: 11/28/2022]
Abstract
The mismatch repair (MMR) pathway promotes genome stability by controlling the fidelity of replication and recombination. The first step of the pathway involves recognition of the mismatch by heterodimers composed of MutS homologs (MSH). Although MSH6 has been well characterized in yeasts and humans, the role of the plant protein has not been extensively studied. We first analyzed gene expression in Arabidopsis thaliana. The use of transgenic plants expressing the β-glucuronidase (GUS) reporter gene under the control of approximately 1-kb region upstream of the start codon of the AtMSH6 gene demonstrated that MSH6 is preferentially expressed in undifferentiated cells with an intense cell division rate. We then examined protein function in meiotic and somatic recombination. Suppression of AtMSH6 did not affect the rate of meiotic recombination, but increased the frequency of recombination between two homeologous repeats of a marker gene by 3-fold relative to wild-type plants. Expression of the AtMSH6 gene under the control of its own promoter in msh6 homozygous mutant plants rescued the altered somatic recombination phenotype. We conclude that MSH6 shows a functional conservation across different biological kingdoms and a functional specificity in plants.
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Affiliation(s)
- Valentina Gonzalez
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Claudia P Spampinato
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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39
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Hum YF, Jinks-Robertson S. Mismatch recognition and subsequent processing have distinct effects on mitotic recombination intermediates and outcomes in yeast. Nucleic Acids Res 2019; 47:4554-4568. [PMID: 30809658 PMCID: PMC6511840 DOI: 10.1093/nar/gkz126] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/12/2019] [Accepted: 02/23/2019] [Indexed: 01/25/2023] Open
Abstract
The post-replicative mismatch repair (MMR) system has anti-recombination activity that limits interactions between diverged sequences by recognizing mismatches in strand-exchange intermediates. In contrast to their equivalent roles during replication-error repair, mismatch recognition is more important for anti-recombination than subsequent mismatch processing. To obtain insight into this difference, ectopic substrates with 2% sequence divergence were used to examine mitotic recombination outcome (crossover or noncrossover; CO and NCO, respectively) and to infer molecular intermediates formed during double-strand break repair in Saccharomyces cerevisiae. Experiments were performed in an MMR-proficient strain, a strain with compromised mismatch-recognition activity (msh6Δ) and a strain that retained mismatch-recognition activity but was unable to process mismatches (mlh1Δ). While the loss of either mismatch binding or processing elevated the NCO frequency to a similar extent, CO events increased only when mismatch binding was compromised. The molecular features of NCOs, however, were altered in fundamentally different ways depending on whether mismatch binding or processing was eliminated. These data suggest a model in which mismatch recognition reverses strand-exchange intermediates prior to the initiation of end extension, while subsequent mismatch processing that is linked to end extension specifically destroys NCO intermediates that contain conflicting strand-discrimination signals for mismatch removal.
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Affiliation(s)
- Yee Fang Hum
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
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40
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Hu Q, Lu H, Wang H, Li S, Truong L, Li J, Liu S, Xiang R, Wu X. Break-induced replication plays a prominent role in long-range repeat-mediated deletion. EMBO J 2019; 38:e101751. [PMID: 31571254 DOI: 10.15252/embj.2019101751] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 09/07/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022] Open
Abstract
Repetitive DNA sequences are often associated with chromosomal rearrangements in cancers. Conventionally, single-strand annealing (SSA) is thought to mediate homology-directed repair of double-strand breaks (DSBs) between two repeats, causing repeat-mediated deletion (RMD). In this report, we demonstrate that break-induced replication (BIR) is used predominantly over SSA in mammalian cells for mediating RMD, especially when repeats are far apart. We show that SSA becomes inefficient in mammalian cells when the distance between the DSBs and the repeats is increased to the 1-2 kb range, while BIR-mediated RMD (BIR/RMD) can act over a long distance (e.g., ~ 100-200 kb) when the DSB is close to one repeat. Importantly, oncogene expression potentiates BIR/RMD but not SSA, and BIR/RMD is used more frequently at single-ended DSBs formed at collapsed replication forks than at double-ended DSBs. In contrast to short-range SSA, H2AX is required for long-range BIR/RMD, and sequence divergence strongly suppresses BIR/RMD in a manner partially dependent on MSH2. Our finding that BIR/RMD has a more important role than SSA in mammalian cells has a significant impact on the understanding of repeat-mediated rearrangements associated with oncogenesis.
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Affiliation(s)
- Qing Hu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Hongyan Lu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,School of Medicine, Nankai University, Tianjin, China
| | - Hongjun Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Shibo Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Lan Truong
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jun Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,School of Medicine, Nankai University, Tianjin, China
| | - Shuo Liu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,School of Medicine, Nankai University, Tianjin, China
| | - Rong Xiang
- School of Medicine, Nankai University, Tianjin, China
| | - Xiaohua Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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41
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Li J, Sun H, Huang Y, Wang Y, Liu Y, Chen X. Pathways and assays for DNA double-strand break repair by homologous recombination. Acta Biochim Biophys Sin (Shanghai) 2019; 51:879-889. [PMID: 31294447 DOI: 10.1093/abbs/gmz076] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/17/2019] [Indexed: 12/11/2022] Open
Abstract
Double strand breaks (DSBs) are the most detrimental type of DNA damage that must be repaired to ensure genome integrity and cell survival. Unrepaired or improperly repaired DSBs can potentially cause tumorigenesis or cell death. DSBs are primarily repaired by non-homologous end joining or homologous recombination (HR). The HR pathway is initiated by processing of the 5'-end of DSBs to generate 3'-end single-strand DNA (ssDNA). Furthermore, the intermediate is channeled to one of the HR sub-pathways, including: (i) double Holliday junction (dHJ) pathway, (ii) synthesis-dependent strand annealing (SDSA), (iii) break-induced replication (BIR), and (iv) single-strand annealing (SSA). In the dHJ sub-pathway, the 3'-ssDNA coated with Rad51 recombinase performs homology search and strand invasion, forming a displacement loop (D-loop). Capture of the second end by the D-loop generates a dHJ intermediate that is subsequently dissolved by DNA helicase or resolved by nucleases, producing non-crossover or crossover products. In SDSA, the newly synthesized strand is displaced from the D-loop and anneals to the end on the other side of the DSBs, producing non-crossovers. In contrast, BIR repairs one-end DSBs by copying the sequence up to the end of the template chromosome, resulting in translocation or loss of heterozygosity. SSA takes place when resection reveals flanking homologous repeats that can anneal, leading to deletion of the intervening sequences. A variety of reporter assays have been developed to monitor distinct HR sub-pathways in both Saccharomyces cerevisiae and mammals. Here, we summarize the principles and representative assays for different HR sub-pathways with an emphasis on the studies in the budding yeast.
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Affiliation(s)
- Jinbao Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Huize Sun
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Yulin Huang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Yali Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Yuyan Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, China
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42
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Steinfeld JB, Beláň O, Kwon Y, Terakawa T, Al-Zain A, Smith MJ, Crickard JB, Qi Z, Zhao W, Rothstein R, Symington LS, Sung P, Boulton SJ, Greene EC. Defining the influence of Rad51 and Dmc1 lineage-specific amino acids on genetic recombination. Genes Dev 2019; 33:1191-1207. [PMID: 31371435 PMCID: PMC6719624 DOI: 10.1101/gad.328062.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023]
Abstract
The vast majority of eukaryotes possess two DNA recombinases: Rad51, which is ubiquitously expressed, and Dmc1, which is meiosis-specific. The evolutionary origins of this two-recombinase system remain poorly understood. Interestingly, Dmc1 can stabilize mismatch-containing base triplets, whereas Rad51 cannot. Here, we demonstrate that this difference can be attributed to three amino acids conserved only within the Dmc1 lineage of the Rad51/RecA family. Chimeric Rad51 mutants harboring Dmc1-specific amino acids gain the ability to stabilize heteroduplex DNA joints with mismatch-containing base triplets, whereas Dmc1 mutants with Rad51-specific amino acids lose this ability. Remarkably, RAD-51 from Caenorhabditis elegans, an organism without Dmc1, has acquired "Dmc1-like" amino acids. Chimeric C. elegans RAD-51 harboring "canonical" Rad51 amino acids gives rise to toxic recombination intermediates, which must be actively dismantled to permit normal meiotic progression. We propose that Dmc1 lineage-specific amino acids involved in the stabilization of heteroduplex DNA joints with mismatch-containing base triplets may contribute to normal meiotic recombination.
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Affiliation(s)
- Justin B Steinfeld
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Ondrej Beláň
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Tsuyoshi Terakawa
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Amr Al-Zain
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Michael J Smith
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - J Brooks Crickard
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Zhi Qi
- Center for Quantitative Biology, Peking University-Tsinghua University Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Lorraine S Symington
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
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43
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Eichmiller R, Medina-Rivera M, DeSanto R, Minca E, Kim C, Holland C, Seol JH, Schmit M, Oramus D, Smith J, Gallardo IF, Finkelstein IJ, Lee SE, Surtees JA. Coordination of Rad1-Rad10 interactions with Msh2-Msh3, Saw1 and RPA is essential for functional 3' non-homologous tail removal. Nucleic Acids Res 2019; 46:5075-5096. [PMID: 29660012 PMCID: PMC6007489 DOI: 10.1093/nar/gky254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 03/28/2018] [Indexed: 12/19/2022] Open
Abstract
Double strand DNA break repair (DSBR) comprises multiple pathways. A subset of DSBR pathways, including single strand annealing, involve intermediates with 3' non-homologous tails that must be removed to complete repair. In Saccharomyces cerevisiae, Rad1-Rad10 is the structure-specific endonuclease that cleaves the tails in 3' non-homologous tail removal (3' NHTR). Rad1-Rad10 is also an essential component of the nucleotide excision repair (NER) pathway. In both cases, Rad1-Rad10 requires protein partners for recruitment to the relevant DNA intermediate. Msh2-Msh3 and Saw1 recruit Rad1-Rad10 in 3' NHTR; Rad14 recruits Rad1-Rad10 in NER. We created two rad1 separation-of-function alleles, rad1R203A,K205A and rad1R218A; both are defective in 3' NHTR but functional in NER. In vitro, rad1R203A,K205A was impaired at multiple steps in 3' NHTR. The rad1R218A in vivo phenotype resembles that of msh2- or msh3-deleted cells; recruitment of rad1R218A-Rad10 to recombination intermediates is defective. Interactions among rad1R218A-Rad10 and Msh2-Msh3 and Saw1 are altered and rad1R218A-Rad10 interactions with RPA are compromised. We propose a model in which Rad1-Rad10 is recruited and positioned at the recombination intermediate through interactions, between Saw1 and DNA, Rad1-Rad10 and Msh2-Msh3, Saw1 and Msh2-Msh3 and Rad1-Rad10 and RPA. When any of these interactions is altered, 3' NHTR is impaired.
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Affiliation(s)
- Robin Eichmiller
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Melisa Medina-Rivera
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Rachel DeSanto
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Eugen Minca
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Christopher Kim
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | - Cory Holland
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | - Ja-Hwan Seol
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | - Megan Schmit
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Diane Oramus
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Jessica Smith
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Ignacio F Gallardo
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sang Eun Lee
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.,Department of Radiation Oncology, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | - Jennifer A Surtees
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA.,Genetics, Genomics and Bioinformatics Graduate Program, University at Buffalo (SUNY), Buffalo, NY 14214, USA
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Chakraborty U, Mackenroth B, Shalloway D, Alani E. Chromatin Modifiers Alter Recombination Between Divergent DNA Sequences. Genetics 2019; 212:1147-1162. [PMID: 31221666 PMCID: PMC6707472 DOI: 10.1534/genetics.119.302395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Recombination between divergent DNA sequences is actively prevented by heteroduplex rejection mechanisms. In baker's yeast, such antirecombination mechanisms can be initiated by the recognition of DNA mismatches in heteroduplex DNA by MSH proteins, followed by recruitment of the Sgs1-Top3-Rmi1 helicase-topoisomerase complex to unwind the recombination intermediate. We previously showed that the repair/rejection decision during single-strand annealing recombination is temporally regulated by MSH (MutShomolog) protein levels and by factors that excise nonhomologous single-stranded tails. These observations, coupled with recent studies indicating that mismatch repair (MMR) factors interact with components of the histone chaperone machinery, encouraged us to explore roles for epigenetic factors and chromatin conformation in regulating the decision to reject vs. repair recombination between divergent DNA substrates. This work involved the use of an inverted repeat recombination assay thought to measure sister chromatid repair during DNA replication. Our observations are consistent with the histone chaperones CAF-1 and Rtt106, and the histone deacetylase Sir2, acting to suppress heteroduplex rejection and the Rpd3, Hst3, and Hst4 deacetylases acting to promote heteroduplex rejection. These observations, and double-mutant analysis, have led to a model in which nucleosomes located at DNA lesions stabilize recombination intermediates and compete with MMR factors that mediate heteroduplex rejection.
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Affiliation(s)
- Ujani Chakraborty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Beata Mackenroth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - David Shalloway
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
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Lee K, Ji JH, Yoon K, Che J, Seol JH, Lee SE, Shim EY. Microhomology Selection for Microhomology Mediated End Joining in Saccharomyces cerevisiae. Genes (Basel) 2019; 10:genes10040284. [PMID: 30965655 PMCID: PMC6523938 DOI: 10.3390/genes10040284] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/03/2022] Open
Abstract
Microhomology-mediated end joining (MMEJ) anneals short, imperfect microhomologies flanking DNA breaks, producing repair products with deletions in a Ku- and RAD52-independent fashion. Puzzlingly, MMEJ preferentially selects certain microhomologies over others, even when multiple microhomologies are available. To define rules and parameters for microhomology selection, we altered the length, the position, and the level of mismatches to the microhomologies flanking homothallic switching (HO) endonuclease-induced breaks and assessed their effect on MMEJ frequency and the types of repair product formation. We found that microhomology of eight to 20 base pairs carrying no more than 20% mismatches efficiently induced MMEJ. Deletion of MSH6 did not impact MMEJ frequency. MMEJ preferentially chose a microhomology pair that was more proximal from the break. Interestingly, MMEJ events preferentially retained the centromere proximal side of the HO break, while the sequences proximal to the telomere were frequently deleted. The asymmetry in the deletional profile among MMEJ products was reduced when HO was induced on the circular chromosome. The results provide insight into how cells search and select microhomologies for MMEJ in budding yeast.
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Affiliation(s)
- Kihoon Lee
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
| | - Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine. 164, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea.
| | - Kihoon Yoon
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
| | - Jun Che
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
| | - Ja-Hwan Seol
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
| | - Sang Eun Lee
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
| | - Eun Yong Shim
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
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Griffin WC, Trakselis MA. The MCM8/9 complex: A recent recruit to the roster of helicases involved in genome maintenance. DNA Repair (Amst) 2019; 76:1-10. [PMID: 30743181 DOI: 10.1016/j.dnarep.2019.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/03/2019] [Indexed: 12/11/2022]
Abstract
There are several DNA helicases involved in seemingly overlapping aspects of homologous and homoeologous recombination. Mutations of many of these helicases are directly implicated in genetic diseases including cancer, rapid aging, and infertility. MCM8/9 are recent additions to the catalog of helicases involved in recombination, and so far, the evidence is sparse, making assignment of function difficult. Mutations in MCM8/9 correlate principally with primary ovarian failure/insufficiency (POF/POI) and infertility indicating a meiotic defect. However, they also act when replication forks collapse/break shuttling products into mitotic recombination and several mutations are found in various somatic cancers. This review puts MCM8/9 in context with other replication and recombination helicases to narrow down its genomic maintenance role. We discuss the known structure/function relationship, the mutational spectrum, and dissect the available cellular and organismal data to better define its role in recombination.
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Affiliation(s)
- Wezley C Griffin
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798, USA.
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Minobe A, Fukui K, Yonezu H, Ohshita K, Mizobuchi S, Morisawa T, Hakumai Y, Yano T, Ashiuchi M, Wakamatsu T. Biochemical characterization of mismatch-binding protein MutS1 and nicking endonuclease MutL from a euryarchaeon Methanosaeta thermophila. DNA Repair (Amst) 2019; 75:29-38. [PMID: 30711824 DOI: 10.1016/j.dnarep.2019.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/20/2022]
Abstract
In eukaryotes and most bacteria, the MutS1/MutL-dependent mismatch repair system (MMR) corrects DNA mismatches that arise as replication errors. MutS1 recognizes mismatched DNA and stimulates the nicking endonuclease activity of MutL to incise mismatch-containing DNA. In archaea, there has been no experimental evidence to support the existence of the MutS1/MutL-dependent MMR. Instead, it was revealed that a large part of archaea possess mismatch-specific endonuclease EndoMS, indicating that the EndoMS-dependent MMR is widely adopted in archaea. However, some archaeal genomes encode MutS1 and MutL homologs, and their molecular functions have not been revealed. In this study, we purified and characterized recombinant MutS1 and the C-terminal endonuclease domain of MutL from a methanogenic archaeon Methanosaeta thermophila (mtMutS1 and the mtMutL CTD, respectively). mtMutS1 bound to mismatched DNAs with a higher affinity than to perfectly-matched and other structured DNAs, which resembles the DNA-binding specificities of eukaryotic and bacterial MutS1 homologs. The mtMutL CTD showed a Mn2+/Ni2+/Co2+-dependent nicking endonuclease activity that introduces single-strand breaks into a circular double-stranded DNA. The nicking endonuclease activity of the mtMutL CTD was impaired by mutagenizing the metal-binding motif that is identical to those of eukaryotic and bacterial MutL endonucleases. These results raise the possibility that not only the EndoMS-dependent MMR but also the traditional MutS1/MutL-dependent MMR exist in archaea.
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Affiliation(s)
- Ai Minobe
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Kenji Fukui
- Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686, Japan
| | - Hitomi Yonezu
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Koki Ohshita
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Saki Mizobuchi
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Takashi Morisawa
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Yuichi Hakumai
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Takato Yano
- Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686, Japan
| | - Makoto Ashiuchi
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Taisuke Wakamatsu
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan.
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Fukui K, Harada A, Wakamatsu T, Minobe A, Ohshita K, Ashiuchi M, Yano T. The GIY-YIG endonuclease domain of Arabidopsis MutS homolog 1 specifically binds to branched DNA structures. FEBS Lett 2018; 592:4066-4077. [PMID: 30372520 DOI: 10.1002/1873-3468.13279] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/16/2018] [Accepted: 10/24/2018] [Indexed: 01/18/2023]
Abstract
In plant organelle genomes, homeologous recombination between heteroallelic positions of repetitive sequences is increased by dysfunction of the gene encoding MutS homolog 1 (MSH1), a plant organelle-specific homolog of bacterial mismatch-binding protein MutS1. The C-terminal region of plant MSH1 contains the GIY-YIG endonuclease motif. The biochemical characteristics of plant MSH1 have not been investigated; accordingly, the molecular mechanism by which plant MSH1 suppresses homeologous recombination is unknown. Here, we characterized the recombinant GIY-YIG domain of Arabidopsis thaliana MSH1, showing that the domain possesses branched DNA-specific DNA-binding activity. Interestingly, the domain exhibited no endonuclease activity, suggesting that the mismatch-binding domain is required for DNA incision. Based on these results, we propose a possible mechanism for MSH1-dependent suppression of homeologous recombination.
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Affiliation(s)
- Kenji Fukui
- Department of Biochemistry, Osaka Medical College, Takatsuki, Japan
| | - Akiko Harada
- Department of Biology, Osaka Medical College, Takatsuki, Japan
| | - Taisuke Wakamatsu
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Ai Minobe
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Koki Ohshita
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Makoto Ashiuchi
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Takato Yano
- Department of Biochemistry, Osaka Medical College, Takatsuki, Japan
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Li S, Wehrenberg B, Waldman BC, Waldman AS. Mismatch tolerance during homologous recombination in mammalian cells. DNA Repair (Amst) 2018; 70:25-36. [PMID: 30103093 DOI: 10.1016/j.dnarep.2018.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/19/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022]
Abstract
We investigated the homology dependency of recombination in thymidine kinase (tk)-deficient mouse fibroblasts. Cells were transfected with DNA constructs harboring a herpes tk gene (the "recipient") rendered non-functional by an oligonucleotide containing the recognition site for endonuclease I-SceI. Constructs also contained a "donor" tk sequence that could restore function to the recipient gene through spontaneous gene conversion or via repair of a double-strand break (DSB) at the I-SceI site. Recombination events were recoverable by selection for tk-positive clones. Three different donors were used containing 16, 25, or 33 mismatches relative to the recipient. The mismatches were clustered, forming an interval of "homeology" relative to the recipient sequences. We show that when homeologous sequences were surrounded by high homology, mismatches were frequently included in gene conversion events. Notably, conversion tracts from spontaneous recombination included either all or none of the mismatches, suggesting that recombination must begin and end in high homology. This requirement was relaxed for events that occurred near an induced DSB, as a significant number of these latter conversion tracts had one end positioned within homeology. Knock-down of mismatch repair showed that incorporation of mismatches into gene conversion tracts can involve repair of mismatched heteroduplex intermediates, indicating that mismatch repair does not necessarily impede homeologous genetic exchange. Our results illustrate (1) genetic exchange between homeologous sequences in a mammalian genome is enabled by nearby homology, (2) proximity to a DSB impacts the homology requirements for where genetic exchange may begin and end, and (3) mismatch correction and previously documented anti-recombination activity are separable functions of the mismatch repair machinery in mammalian cells.
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Affiliation(s)
- Shen Li
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Bryan Wehrenberg
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Barbara C Waldman
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Alan S Waldman
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA.
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50
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Chakraborty U, Dinh TA, Alani E. Genomic Instability Promoted by Overexpression of Mismatch Repair Factors in Yeast: A Model for Understanding Cancer Progression. Genetics 2018; 209:439-456. [PMID: 29654124 PMCID: PMC5972419 DOI: 10.1534/genetics.118.300923] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/12/2018] [Indexed: 02/04/2023] Open
Abstract
Mismatch repair (MMR) proteins act in spellchecker roles to excise misincorporation errors that occur during DNA replication. Curiously, large-scale analyses of a variety of cancers showed that increased expression of MMR proteins often correlated with tumor aggressiveness, metastasis, and early recurrence. To better understand these observations, we used The Cancer Genome Atlas and Gene Expression across Normal and Tumor tissue databases to analyze MMR protein expression in cancers. We found that the MMR genes MSH2 and MSH6 are overexpressed more frequently than MSH3, and that MSH2 and MSH6 are often cooverexpressed as a result of copy number amplifications of these genes. These observations encouraged us to test the effects of upregulating MMR protein levels in baker's yeast, where we can sensitively monitor genome instability phenotypes associated with cancer initiation and progression. Msh6 overexpression (two- to fourfold) almost completely disrupted mechanisms that prevent recombination between divergent DNA sequences by interacting with the DNA polymerase processivity clamp PCNA and by sequestering the Sgs1 helicase. Importantly, cooverexpression of Msh2 and Msh6 (∼eightfold) conferred, in a PCNA interaction-dependent manner, several genome instability phenotypes including increased mutation rate, increased sensitivity to the DNA replication inhibitor HU and the DNA-damaging agents MMS and 4-nitroquinoline N-oxide, and elevated loss-of-heterozygosity. Msh2 and Msh6 cooverexpression also altered the cell cycle distribution of exponentially growing cells, resulting in an increased fraction of unbudded cells, consistent with a larger percentage of cells in G1. These novel observations suggested that overexpression of MSH factors affected the integrity of the DNA replication fork, causing genome instability phenotypes that could be important for promoting cancer progression.
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Affiliation(s)
- Ujani Chakraborty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Timothy A Dinh
- Curriculum in Genetics and Molecular Biology, Biological and Biomedical Sciences Program, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
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