1
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Ito M, Fujita Y, Shinohara A. Positive and negative regulators of RAD51/DMC1 in homologous recombination and DNA replication. DNA Repair (Amst) 2024; 134:103613. [PMID: 38142595 DOI: 10.1016/j.dnarep.2023.103613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/10/2023] [Accepted: 12/10/2023] [Indexed: 12/26/2023]
Abstract
RAD51 recombinase plays a central role in homologous recombination (HR) by forming a nucleoprotein filament on single-stranded DNA (ssDNA) to catalyze homology search and strand exchange between the ssDNA and a homologous double-stranded DNA (dsDNA). The catalytic activity of RAD51 assembled on ssDNA is critical for the DNA-homology-mediated repair of DNA double-strand breaks in somatic and meiotic cells and restarting stalled replication forks during DNA replication. The RAD51-ssDNA complex also plays a structural role in protecting the regressed/reversed replication fork. Two types of regulators control RAD51 filament formation, stability, and dynamics, namely positive regulators, including mediators, and negative regulators, so-called remodelers. The appropriate balance of action by the two regulators assures genome stability. This review describes the roles of positive and negative RAD51 regulators in HR and DNA replication and its meiosis-specific homolog DMC1 in meiotic recombination. We also provide future study directions for a comprehensive understanding of RAD51/DMC1-mediated regulation in maintaining and inheriting genome integrity.
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Affiliation(s)
- Masaru Ito
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
| | - Yurika Fujita
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
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2
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Jia BB, Jussila A, Kern C, Zhu Q, Ren B. A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nat Biotechnol 2023; 41:1004-1017. [PMID: 36593410 PMCID: PMC10344783 DOI: 10.1038/s41587-022-01568-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 10/13/2022] [Indexed: 01/03/2023]
Abstract
Multiplexed fluorescence in situ hybridization (FISH) is a widely used approach for analyzing three-dimensional genome organization, but it is challenging to derive chromosomal conformations from noisy fluorescence signals, and tracing chromatin is not straightforward. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. Using genomic distances separating imaged loci, our aligner estimates spatial distances expected to separate loci on a polymer in three-dimensional space. Our aligner then evaluates the physical probability observed signals belonging to these loci are connected, thereby tracing chromatin structures. We demonstrate that this spatial genome aligner can efficiently model chromosome architectures from DNA FISH data across multiple scales and be used to predict chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method indicates the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells and provides evidence for extranumerary chromosomes that remain tightly paired in postmitotic neurons of the adult mouse cortex.
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Affiliation(s)
- Bojing Blair Jia
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
- Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
| | - Adam Jussila
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Colin Kern
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Quan Zhu
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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3
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Boßelmann CM, Leu C, Lal D. Technological and computational approaches to detect somatic mosaicism in epilepsy. Neurobiol Dis 2023:106208. [PMID: 37343892 DOI: 10.1016/j.nbd.2023.106208] [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: 03/05/2023] [Revised: 06/03/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023] Open
Abstract
Lesional epilepsy is a common and severe disease commonly associated with malformations of cortical development, including focal cortical dysplasia and hemimegalencephaly. Recent advances in sequencing and variant calling technologies have identified several genetic causes, including both short/single nucleotide and structural somatic variation. In this review, we aim to provide a comprehensive overview of the methodological advancements in this field while highlighting the unresolved technological and computational challenges that persist, including ultra-low variant allele fractions in bulk tissue, low availability of paired control samples, spatial variability of mutational burden within the lesion, and the issue of false-positive calls and validation procedures. Information from genetic testing in focal epilepsy may be integrated into clinical care to inform histopathological diagnosis, postoperative prognosis, and candidate precision therapies.
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Affiliation(s)
- Christian M Boßelmann
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, London, UK.
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T., Cambridge, MA, USA; Cologne Center for Genomics (CCG), University of Cologne, Cologne, DE, USA
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4
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Elbakry A, Löbrich M. Homologous Recombination Subpathways: A Tangle to Resolve. Front Genet 2021; 12:723847. [PMID: 34408777 PMCID: PMC8365153 DOI: 10.3389/fgene.2021.723847] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/12/2021] [Indexed: 11/26/2022] Open
Abstract
Homologous recombination (HR) is an essential pathway for DNA double-strand break (DSB) repair, which can proceed through various subpathways that have distinct elements and genetic outcomes. In this mini-review, we highlight the main features known about HR subpathways operating at DSBs in human cells and the factors regulating subpathway choice. We examine new developments that provide alternative models of subpathway usage in different cell types revise the nature of HR intermediates involved and reassess the frequency of repair outcomes. We discuss the impact of expanding our understanding of HR subpathways and how it can be clinically exploited.
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Affiliation(s)
- Amira Elbakry
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Markus Löbrich
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
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5
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Prakash R, Sandoval T, Morati F, Zagelbaum JA, Lim PX, White T, Taylor B, Wang R, Desclos ECB, Sullivan MR, Rein HL, Bernstein KA, Krawczyk PM, Gautier J, Modesti M, Vanoli F, Jasin M. Distinct pathways of homologous recombination controlled by the SWS1-SWSAP1-SPIDR complex. Nat Commun 2021; 12:4255. [PMID: 34253720 PMCID: PMC8275761 DOI: 10.1038/s41467-021-24205-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Homology-directed repair (HDR), a critical DNA repair pathway in mammalian cells, is complex, leading to multiple outcomes with different impacts on genomic integrity. However, the factors that control these different outcomes are often not well understood. Here we show that SWS1-SWSAP1-SPIDR controls distinct types of HDR. Despite their requirement for stable assembly of RAD51 recombinase at DNA damage sites, these proteins are not essential for intra-chromosomal HDR, providing insight into why patients and mice with mutations are viable. However, SWS1-SWSAP1-SPIDR is critical for inter-homolog HDR, the first mitotic factor identified specifically for this function. Furthermore, SWS1-SWSAP1-SPIDR drives the high level of sister-chromatid exchange, promotes long-range loss of heterozygosity often involved with cancer initiation, and impels the poor growth of BLM helicase-deficient cells. The relevance of these genetic interactions is evident as SWSAP1 loss prolongs Blm-mutant embryo survival, suggesting a possible druggable target for the treatment of Bloom syndrome.
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Affiliation(s)
- Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Thomas Sandoval
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Florian Morati
- Cancer Research Center of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Jennifer A Zagelbaum
- Department of Genetics and Development and Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Pei-Xin Lim
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Travis White
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brett Taylor
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raymond Wang
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emilie C B Desclos
- Department of Medical Biology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Meghan R Sullivan
- Department of Microbiology and Molecular Genetics, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Hayley L Rein
- Department of Microbiology and Molecular Genetics, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kara A Bernstein
- Department of Microbiology and Molecular Genetics, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Przemek M Krawczyk
- Department of Medical Biology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Jean Gautier
- Department of Genetics and Development and Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Fabio Vanoli
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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6
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Wilde JJ, Aida T, Del Rosario RCH, Kaiser T, Qi P, Wienisch M, Zhang Q, Colvin S, Feng G. Efficient embryonic homozygous gene conversion via RAD51-enhanced interhomolog repair. Cell 2021; 184:3267-3280.e18. [PMID: 34043941 PMCID: PMC8240950 DOI: 10.1016/j.cell.2021.04.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 03/03/2021] [Accepted: 04/19/2021] [Indexed: 12/20/2022]
Abstract
Searching for factors to improve knockin efficiency for therapeutic applications, biotechnology, and generation of non-human primate models of disease, we found that the strand exchange protein RAD51 can significantly increase Cas9-mediated homozygous knockin in mouse embryos through an interhomolog repair (IHR) mechanism. IHR is a hallmark of meiosis but only occurs at low frequencies in somatic cells, and its occurrence in zygotes is controversial. Using multiple approaches, we provide evidence for an endogenous IHR mechanism in the early embryo that can be enhanced by RAD51. This process can be harnessed to generate homozygotes from wild-type zygotes using exogenous donors and to convert heterozygous alleles into homozygous alleles without exogenous templates. Furthermore, we identify additional IHR-promoting factors and describe features of IHR events. Together, our findings show conclusive evidence for IHR in mouse embryos and describe an efficient method for enhanced gene conversion.
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Affiliation(s)
- Jonathan J Wilde
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
| | - Tomomi Aida
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Ricardo C H Del Rosario
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tobias Kaiser
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Peimin Qi
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Martin Wienisch
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Qiangge Zhang
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Steven Colvin
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Guoping Feng
- Department of Brain & Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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7
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Chromothripsis as an on-target consequence of CRISPR-Cas9 genome editing. Nat Genet 2021; 53:895-905. [PMID: 33846636 PMCID: PMC8192433 DOI: 10.1038/s41588-021-00838-7] [Citation(s) in RCA: 266] [Impact Index Per Article: 88.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 03/08/2021] [Indexed: 12/16/2022]
Abstract
Genome editing has therapeutic potential for treating genetic diseases and cancer. However, the currently most practicable approaches rely on the generation of DNA double-strand breaks (DSBs), which can give rise to a poorly characterized spectrum of chromosome structural abnormalities. Here, using model cells and single-cell whole-genome sequencing, as well as by editing at a clinically relevant locus in clinically relevant cells, we show that CRISPR-Cas9 editing generates structural defects of the nucleus, micronuclei and chromosome bridges, which initiate a mutational process called chromothripsis. Chromothripsis is extensive chromosome rearrangement restricted to one or a few chromosomes that can cause human congenital disease and cancer. These results demonstrate that chromothripsis is a previously unappreciated on-target consequence of CRISPR-Cas9-generated DSBs. As genome editing is implemented in the clinic, the potential for extensive chromosomal rearrangements should be considered and monitored.
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8
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Abstract
Homologous recombination is a critical mechanism for the repair of DNA double-strand breaks (DSBs). It occurs predominantly between identical sister chromatids and at lower frequency can also occur between homologs. Interhomolog homologous recombination (IH-HR) has the potential lead to substantial loss of genetic information, i.e., loss of heterozygosity (LOH), when it is accompanied by crossing over. In this chapter, we describe a system to study IH-HR induced by a defined DSB in mouse embryonic stem cells derived from F1 hybrid mice. This system is based on the placement of mutant selectable marker genes, one of which contains an I-SceI endonuclease cleavage site, on the two homologs such that repair of the I-SceI-generated DSB from the homolog leads to drug resistance. Loss of heterozygosity arising during IH-HR is analyzed using a PCR-based approach. Finally, we present a strategy to analyze the role of BLM helicase in this system.
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9
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Davis L, Khoo KJ, Zhang Y, Maizels N. POLQ suppresses interhomolog recombination and loss of heterozygosity at targeted DNA breaks. Proc Natl Acad Sci U S A 2020; 117:22900-22909. [PMID: 32873648 PMCID: PMC7502765 DOI: 10.1073/pnas.2008073117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interhomolog recombination (IHR) occurs spontaneously in somatic human cells at frequencies that are low but sufficient to ameliorate some genetic diseases caused by heterozygous mutations or autosomal dominant mutations. Here we demonstrate that DNA nicks or double-strand breaks (DSBs) targeted by CRISPR-Cas9 to both homologs can stimulate IHR and associated copy-neutral loss of heterozygosity (cnLOH) in human cells. The frequency of IHR is 10-fold lower at nicks than at DSBs, but cnLOH is evident in a greater fraction of recombinants. IHR at DSBs occurs predominantly via reciprocal end joining. At DSBs, depletion of POLQ caused a dramatic increase in IHR and in the fraction of recombinants exhibiting cnLOH, suggesting that POLQ promotes end joining in cis, which limits breaks available for recombination in trans These results define conditions that may produce cnLOH as a mutagenic signature in cancer and may, conversely, promote therapeutic correction of both compound heterozygous and dominant negative mutations associated with genetic disease.
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Affiliation(s)
- Luther Davis
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195
| | - Kevin J Khoo
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195
| | - Yinbo Zhang
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195
| | - Nancy Maizels
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195;
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195
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10
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Gómez-Herreros F. DNA Double Strand Breaks and Chromosomal Translocations Induced by DNA Topoisomerase II. Front Mol Biosci 2019; 6:141. [PMID: 31921889 PMCID: PMC6915882 DOI: 10.3389/fmolb.2019.00141] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/19/2019] [Indexed: 01/03/2023] Open
Abstract
DNA double strand breaks (DSBs) are the most cytotoxic lesions of those occurring in the DNA and can lead to cell death or result in genome mutagenesis and chromosomal translocations. Although most of these rearrangements have detrimental effects for cellular survival, single events can provide clonal advantage and result in abnormal cellular proliferation and cancer. The origin and the environment of the DNA break or the repair pathway are key factors that influence the frequency at which these events appear. However, the molecular mechanisms that underlie the formation of chromosomal translocations remain unclear. DNA topoisomerases are essential enzymes present in all cellular organisms with critical roles in DNA metabolism and that have been linked to the formation of deleterious DSBs for a long time. DSBs induced by the abortive activity of DNA topoisomerase II (TOP2) are “trending topic” because of their possible role in genome instability and oncogenesis. Furthermore, transcription associated TOP2 activity appears to be one of the most determining causes behind the formation of chromosomal translocations. In this review, the origin of recombinogenic TOP2 breaks and the determinants behind their tendency to translocate will be summarized.
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Affiliation(s)
- Fernando Gómez-Herreros
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
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11
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Roychowdhury T, Abyzov A. Chromatin organization modulates the origin of heritable structural variations in human genome. Nucleic Acids Res 2019; 47:2766-2777. [PMID: 30773596 PMCID: PMC6451188 DOI: 10.1093/nar/gkz103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/06/2019] [Accepted: 02/14/2019] [Indexed: 12/11/2022] Open
Abstract
Structural variations (SVs) in the human genome originate from different mechanisms related to DNA repair, replication errors, and retrotransposition. Our analyses of 26 927 SVs from the 1000 Genomes Project revealed differential distributions and consequences of SVs of different origin, e.g. deletions from non-allelic homologous recombination (NAHR) are more prone to disrupt chromatin organization while processed pseudogenes can create accessible chromatin. Spontaneous double stranded breaks (DSBs) are the best predictor of enrichment of NAHR deletions in open chromatin. This evidence, along with strong physical interaction of NAHR breakpoints belonging to the same deletion suggests that majority of NAHR deletions are non-meiotic i.e. originate from errors during homology directed repair (HDR) of spontaneous DSBs. In turn, the origin of the spontaneous DSBs is associated with transcription factor binding in accessible chromatin revealing the vulnerability of functional, open chromatin. The chromatin itself is enriched with repeats, particularly fixed Alu elements that provide the homology required to maintain stability via HDR. Through co-localization of fixed Alus and NAHR deletions in open chromatin we hypothesize that old Alu expansion had a stabilizing role on the human genome.
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Affiliation(s)
- Tanmoy Roychowdhury
- Mayo Clinic, Department of Health Sciences Research, Center for Individualized Medicine, Rochester, MN 55905, USA
| | - Alexej Abyzov
- Mayo Clinic, Department of Health Sciences Research, Center for Individualized Medicine, Rochester, MN 55905, USA
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12
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Bouberhan S, Pujade-Lauraine E, Cannistra SA. Advances in the Management of Platinum-Sensitive Relapsed Ovarian Cancer. J Clin Oncol 2019; 37:2424-2436. [PMID: 31403861 DOI: 10.1200/jco.19.00314] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Sara Bouberhan
- Beth Israel Medical Center and Harvard Medical School, Boston, MA
| | - Eric Pujade-Lauraine
- Association of Research on Cancers Including Gynecological-Group of National Investigators for the Study of Ovarian Cancer and Breast, Paris, France
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13
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Yamato T, Handa A, Arazoe T, Kuroki M, Nozaka A, Kamakura T, Ohsato S, Arie T, Kuwata S. Single crossover-mediated targeted nucleotide substitution and knock-in strategies with CRISPR/Cas9 system in the rice blast fungus. Sci Rep 2019; 9:7427. [PMID: 31092866 PMCID: PMC6520371 DOI: 10.1038/s41598-019-43913-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/01/2019] [Indexed: 01/10/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated genome editing has become a promising approach for efficient and versatile genetic engineering in various organisms; however, simple and precise nucleotide modification methods in filamentous fungi have been restricted to double crossover type homologous recombination (HR). In this study, we developed a novel genome editing strategy via single crossover-mediated HR in the model filamentous fungus Pyricularia (Magnaporthe) oryzae. This method includes the CRISPR/Cas9 system and a donor vector harboring a single homology arm with point mutations at the CRISPR/Cas9 cleavage site. Using this strategy, we demonstrated highly efficient and freely programmable base substitutions within the desired genomic locus, and target gene disrupted mutants were also obtained via a shortened (100-1000 bp) single homology arm. We further demonstrated that this method allowed a one-step GFP gene knock-in at the C-terminus of the targeted gene. Since the genomic recombination does not require an intact protospacer-adjacent motif within the donor construct and any additional modifications of host components, this method can be used in various filamentous fungi for CRISPR/Cas9-based basic and applied biological analyses.
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Affiliation(s)
- Tohru Yamato
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Ai Handa
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Takayuki Arazoe
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
| | - Misa Kuroki
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Akihito Nozaka
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Takashi Kamakura
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Shuichi Ohsato
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Tsutomu Arie
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-0509, Japan
| | - Shigeru Kuwata
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
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14
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Abstract
Homologous Recombination (HR) is a high-fidelity process with a range of biologic functions from generation of genetic diversity to repair of DNA double-strand breaks (DSBs). In mammalian cells, BRCA2 facilitates the polymerization of RAD51 onto ssDNA to form a presynaptic nucleoprotein filament. This filament can then strand invade a homologous dsDNA to form the displacement loop (D-loop) structure leading to the eventual DSB repair. Here, we have found that RAD51 in stoichiometric excess over ssDNA can cause D-loop disassembly in vitro; furthermore, we show that this RAD51 activity is countered by BRCA2. These results demonstrate that BRCA2 may have a previously unexpected activity: regulation of HR at a post-synaptic stage by modulating RAD51-mediated D-loop dissociation. Our in vitro results suggest a mechanistic underpinning of homeostasis between RAD51 and BRCA2, which is an important factor of HR in mammalian cells.
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15
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Egli D, Zuccaro MV, Kosicki M, Church GM, Bradley A, Jasin M. Inter-homologue repair in fertilized human eggs? Nature 2018; 560:E5-E7. [PMID: 30089924 DOI: 10.1038/s41586-018-0379-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 04/05/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Dieter Egli
- Department of Obstetrics and Gynecology and Department of Pediatrics, Columbia University, New York, NY, USA.
| | - Michael V Zuccaro
- Graduate Program, Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | | | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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16
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Homologous recombination occurs frequently at innate GT microsatellites in normal somatic and germ cells in vivo. BMC Genomics 2018; 19:359. [PMID: 29751739 PMCID: PMC5948810 DOI: 10.1186/s12864-018-4758-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/03/2018] [Indexed: 12/30/2022] Open
Abstract
Background In somatic cells, homologous recombination (HR) is a rare event caused by eventual DNA double-strand breaks (DSBs). In contrast, germ cells show high frequency of HR caused by programmed DSBs. Microsatellites are prone to DSBs during genome replication and, thereby, capable of promoting HR. It remains unclear whether HR occurs frequently at microsatellites both in normal somatic cells and germ cells in a similar manner. Results By examining the linkage pattern of multiple paternal and maternal markers flanking innate GT microsatellites, we measured HR at the GT microsatellites in various somatic cells and germ cells in a goldfish intraspecific heterozygote. During embryogenesis, the HR products accumulate gradually with the increase of the number of cell divisions. The frequency of HR at the GT microsatellites in advanced embryos, adult tissues and germ cells is surprisingly high. The type of exchanges between the homologous chromosomes is similar in normal advanced embryos and germ cells. Furthermore, a long GT microsatellite is more active than a short one in promoting HR in both somatic and germ cells. Conclusions HR occurs frequently at innate GT microsatellites in normal somatic cells and germ cells in a similar manner. Electronic supplementary material The online version of this article (10.1186/s12864-018-4758-y) contains supplementary material, which is available to authorized users.
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Andriuskevicius T, Kotenko O, Makovets S. Putting together and taking apart: assembly and disassembly of the Rad51 nucleoprotein filament in DNA repair and genome stability. Cell Stress 2018; 2:96-112. [PMID: 31225474 PMCID: PMC6551702 DOI: 10.15698/cst2018.05.134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Homologous recombination is a key mechanism providing both genome stability and genetic diversity in all living organisms. Recombinases play a central role in this pathway: multiple protein subunits of Rad51 or its orthologues bind single-stranded DNA to form a nucleoprotein filament which is essential for initiating recombination events. Multiple factors are involved in the regulation of this step, both positively and negatively. In this review, we discuss Rad51 nucleoprotein assembly and disassembly, how it is regulated and what functional significance it has in genome maintenance.
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Affiliation(s)
| | - Oleksii Kotenko
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh
| | - Svetlana Makovets
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh
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Brunet E, Jasin M. Induction of Chromosomal Translocations with CRISPR-Cas9 and Other Nucleases: Understanding the Repair Mechanisms That Give Rise to Translocations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:15-25. [PMID: 29956288 DOI: 10.1007/978-981-13-0593-1_2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Chromosomal translocations are associated with several tumor types, including hematopoietic malignancies, sarcomas, and solid tumors of epithelial origin, due to their activation of a proto-oncogene or generation of a novel fusion protein with oncogenic potential. In many cases, the availability of suitable human models has been lacking because of the difficulty in recapitulating precise expression of the fusion protein or other reasons. Further, understanding how translocations form mechanistically has been a goal, as it may suggest ways to prevent their occurrence. Chromosomal translocations arise when DNA ends from double-strand breaks (DSBs) on two heterologous chromosomes are improperly joined. This review provides a summary of DSB repair mechanisms and their contribution to translocation formation, the various programmable nuclease platforms that have been used to generate translocations, and the successes that have been achieved in this area.
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Affiliation(s)
- Erika Brunet
- Genome Dynamics in the Immune System Laboratory, Institut Imagine, INSERM UMR 1163, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Claussin C, Porubský D, Spierings DCJ, Halsema N, Rentas S, Guryev V, Lansdorp PM, Chang M. Genome-wide mapping of sister chromatid exchange events in single yeast cells using Strand-seq. eLife 2017; 6:e30560. [PMID: 29231811 PMCID: PMC5734873 DOI: 10.7554/elife.30560] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/08/2017] [Indexed: 01/09/2023] Open
Abstract
Homologous recombination involving sister chromatids is the most accurate, and thus most frequently used, form of recombination-mediated DNA repair. Despite its importance, sister chromatid recombination is not easily studied because it does not result in a change in DNA sequence, making recombination between sister chromatids difficult to detect. We have previously developed a novel DNA template strand sequencing technique, called Strand-seq, that can be used to map sister chromatid exchange (SCE) events genome-wide in single cells. An increase in the rate of SCE is an indicator of elevated recombination activity and of genome instability, which is a hallmark of cancer. In this study, we have adapted Strand-seq to detect SCE in the yeast Saccharomyces cerevisiae. We provide the first quantifiable evidence that most spontaneous SCE events in wild-type cells are not due to the repair of DNA double-strand breaks.
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Affiliation(s)
- Clémence Claussin
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
| | - David Porubský
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
| | - Diana CJ Spierings
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
| | - Nancy Halsema
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
| | | | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
- Terry Fox LaboratoryBC Cancer AgencyVancouverCanada
- Department of Medical GeneticsUniversity of British ColumbiaVancouverCanada
| | - Michael Chang
- European Research Institute for the Biology of Ageing, University Medical Center GroningenUniversity of GroningenGroningenNetherlands
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Onyango DO, Howard SM, Neherin K, Yanez DA, Stark JM. Tetratricopeptide repeat factor XAB2 mediates the end resection step of homologous recombination. Nucleic Acids Res 2016; 44:5702-16. [PMID: 27084940 PMCID: PMC4937314 DOI: 10.1093/nar/gkw275] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 04/05/2016] [Indexed: 12/15/2022] Open
Abstract
We examined the influence of the tetratricopeptide repeat factor XAB2 on chromosomal break repair, and found that XAB2 promotes end resection that generates the 3′ ssDNA intermediate for homologous recombination (HR). Namely, XAB2 is important for chromosomal double-strand break (DSB) repair via two pathways of HR that require end resection as an intermediate step, end resection of camptothecin (Cpt)-induced DNA damage, and RAD51 recruitment to ionizing radiation induced foci (IRIF), which requires end resection. Furthermore, XAB2 mediates specific aspects of the DNA damage response associated with end resection proficiency: CtIP hyperphosphorylation induced by Cpt and BRCA1 IRIF. XAB2 also promotes histone acetylation events linked to HR proficiency. From truncation mutation analysis, the capacity for XAB2 to promote HR correlates with its ability to form a complex with ISY1 and PRP19, which show a similar influence as XAB2 on HR. This XAB2 complex localizes to punctate structures consistent with interchromatin granules that show a striking adjacent-localization to the DSB marker γH2AX. In summary, we suggest that the XAB2 complex mediates DNA damage response events important for the end resection step of HR, and speculate that its adjacent-localization relative to DSBs marked by γH2AX is important for this function.
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Affiliation(s)
- David O Onyango
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA
| | - Sean M Howard
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010, USA
| | - Kashfia Neherin
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA Department of Biology, California State University, San Bernardino, CA 92407 USA; current address University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Diana A Yanez
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010, USA
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Corrigan-Curay J, O'Reilly M, Kohn DB, Cannon PM, Bao G, Bushman FD, Carroll D, Cathomen T, Joung JK, Roth D, Sadelain M, Scharenberg AM, von Kalle C, Zhang F, Jambou R, Rosenthal E, Hassani M, Singh A, Porteus MH. Genome editing technologies: defining a path to clinic. Mol Ther 2016; 23:796-806. [PMID: 25943494 DOI: 10.1038/mt.2015.54] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
| | | | - Donald B Kohn
- University of California, Los Angeles, Los Angeles, California, USA
| | - Paula M Cannon
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Gang Bao
- Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Frederic D Bushman
- University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, USA
| | - Dana Carroll
- University of Utah, School of Medicine, Salt Lake City, Utah, USA
| | - Toni Cathomen
- University Medical Center Freiberg, Freiberg, Germany
| | - J Keith Joung
- Massachusetts General Hospital, Charlestown, Massachusetts; Harvard Medical School, Boston, Massachusetts, USA
| | - David Roth
- University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, USA
| | - Michel Sadelain
- Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Andrew M Scharenberg
- Seattle Children's Research Institute and University of Washington, School of Medicine, Seattle, Washington, USA
| | - Christof von Kalle
- National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
| | - Feng Zhang
- Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Robert Jambou
- National Institutes of Health, Bethesda, Maryland, USA
| | | | - Morad Hassani
- National Institutes of Health, Bethesda, Maryland, USA
| | - Aparna Singh
- National Institutes of Health, Bethesda, Maryland, USA
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Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MCU, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt ANJ. Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers. Cancer Discov 2015; 5:488-505. [PMID: 25770156 PMCID: PMC4490184 DOI: 10.1158/2159-8290.cd-14-1092] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 03/10/2015] [Indexed: 11/16/2022]
Abstract
UNLABELLED Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE Previous studies have shown correlation between mutational "scars" and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such "scars" and expression of meiotic genes as predictive biomarkers.
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Affiliation(s)
- Johnathan Watkins
- Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom. Institute for Mathematical and Molecular Biomedicine, King's College London, London, United Kingdom. Department of Research Oncology, King's Health Partners AHSC, Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Daniel Weekes
- Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom. Department of Research Oncology, King's Health Partners AHSC, Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Vandna Shah
- Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom. Department of Research Oncology, King's Health Partners AHSC, Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Patrycja Gazinska
- Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom. Department of Research Oncology, King's Health Partners AHSC, Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Shalaka Joshi
- Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom. Department of Research Oncology, King's Health Partners AHSC, Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Bhavna Sidhu
- Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom. Department of Research Oncology, King's Health Partners AHSC, Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Cheryl Gillett
- Department of Research Oncology, King's Health Partners AHSC, Life Sciences and Medicine, King's College London, London, United Kingdom. King's Health Partners Cancer Biobank, King's College London, London, United Kingdom
| | - Sarah Pinder
- Department of Research Oncology, King's Health Partners AHSC, Life Sciences and Medicine, King's College London, London, United Kingdom. King's Health Partners Cancer Biobank, King's College London, London, United Kingdom
| | - Fabio Vanoli
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Markus Mayrhofer
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Anders Isaksson
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Maggie C U Cheang
- Clinical Trials and Statistics Unit (ICR-CTSU), The Institute of Cancer Research, Surrey, United Kingdom
| | - Hasan Mirza
- Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom. Department of Research Oncology, King's Health Partners AHSC, Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Jessica Frankum
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Christopher J Lord
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Alan Ashworth
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Shaveta Vinayak
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - James M Ford
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Melinda L Telli
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Anita Grigoriadis
- Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom. Department of Research Oncology, King's Health Partners AHSC, Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Andrew N J Tutt
- Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom. Department of Research Oncology, King's Health Partners AHSC, Life Sciences and Medicine, King's College London, London, United Kingdom. The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
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Aciole EHP, Guimarães NN, Silva AS, Amorim EM, Nunomura SM, Garcia ACL, Cunha KS, Rohde C. Genetic toxicity of dillapiol and spinosad larvicides in somatic cells of Drosophila melanogaster. PEST MANAGEMENT SCIENCE 2014; 70:559-565. [PMID: 23650150 DOI: 10.1002/ps.3573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 04/24/2013] [Accepted: 05/06/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Higher rates of diseases transmitted from insects to humans led to the increased use of organophosphate insecticides, proven to be harmful to human health and the environment. New, more effective chemical formulations with minimum genetic toxicity effects have become the object of intense research. These formulations include larvicides derived from plant extracts such as dillapiol, a phenylpropanoid extracted from Piper aduncum, and from microorganisms such as spinosad, formed by spinosyns A and D derived from the Saccharopolyspora spinosa fermentation process. This study investigated the genotoxicity of dillapiol and spinosad, characterising and quantifying mutation events and chromosomal and/or mitotic recombination using the somatic mutation and recombination test (SMART) in wings of Drosophila melanogaster. RESULTS Standard cross larvae (72 days old) were treated with different dillapiol and spinosad concentrations. Both compounds presented positive genetic toxicity, mainly as mitotic recombination events. Distilled water and doxorubicin were used as negative and positive controls respectively. CONCLUSION Spinosad was 14 times more genotoxic than dillapiol, and the effect was found to be purely recombinogenic. However, more studies on the potential risks of insecticides such as spinosad and dillapiol are necessary, based on other experimental models and methodologies, to ensure safe use.
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Affiliation(s)
- Eliezer H Pires Aciole
- Programa de Pós-Graduação em Saúde Humana e Meio Ambiente (PPGSHMA), Universidade Federal de Pernambuco (UFPE), Centro Acadêmico de Vitória, Rua do Alto do Reservatório s/n, Bairro Bela Vista, CEP 55608-680, Vitória de Santo Antão, PE, Brasil
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White RR, Sung P, Vestal CG, Benedetto G, Cornelio N, Richardson C. Double-strand break repair by interchromosomal recombination: an in vivo repair mechanism utilized by multiple somatic tissues in mammals. PLoS One 2013; 8:e84379. [PMID: 24349572 PMCID: PMC3862804 DOI: 10.1371/journal.pone.0084379] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 11/22/2013] [Indexed: 01/22/2023] Open
Abstract
Homologous recombination (HR) is essential for accurate genome duplication and maintenance of genome stability. In eukaryotes, chromosomal double strand breaks (DSBs) are central to HR during specialized developmental programs of meiosis and antigen receptor gene rearrangements, and form at unusual DNA structures and stalled replication forks. DSBs also result from exposure to ionizing radiation, reactive oxygen species, some anti-cancer agents, or inhibitors of topoisomerase II. Literature predicts that repair of such breaks normally will occur by non-homologous end-joining (in G1), intrachromosomal HR (all phases), or sister chromatid HR (in S/G2). However, no in vivo model is in place to directly determine the potential for DSB repair in somatic cells of mammals to occur by HR between repeated sequences on heterologs (i.e., interchromosomal HR). To test this, we developed a mouse model with three transgenes—two nonfunctional green fluorescent protein (GFP) transgenes each containing a recognition site for the I-SceI endonuclease, and a tetracycline-inducible I-SceI endonuclease transgene. If interchromosomal HR can be utilized for DSB repair in somatic cells, then I-SceI expression and induction of DSBs within the GFP reporters may result in a functional GFP+ gene. Strikingly, GFP+ recombinant cells were observed in multiple organs with highest numbers in thymus, kidney, and lung. Additionally, bone marrow cultures demonstrated interchromosomal HR within multiple hematopoietic subpopulations including multi-lineage colony forming unit–granulocyte-erythrocyte-monocyte-megakaryocte (CFU-GEMM) colonies. This is a direct demonstration that somatic cells in vivo search genome-wide for homologous sequences suitable for DSB repair, and this type of repair can occur within early developmental populations capable of multi-lineage differentiation.
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Affiliation(s)
- Ryan R. White
- Department of Biology, University of North Carolina-Charlotte, Charlotte, North Carolina, United States of America
| | - Patricia Sung
- Developmental Biology, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - C. Greer Vestal
- Department of Biology, University of North Carolina-Charlotte, Charlotte, North Carolina, United States of America
| | - Gregory Benedetto
- Department of Biology, University of North Carolina-Charlotte, Charlotte, North Carolina, United States of America
| | - Noelle Cornelio
- Department of Biology, University of North Carolina-Charlotte, Charlotte, North Carolina, United States of America
| | - Christine Richardson
- Department of Biology, University of North Carolina-Charlotte, Charlotte, North Carolina, United States of America
- * E-mail:
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Pádua PFMR, Dihl RR, Lehmann M, de Abreu BRR, Richter MF, de Andrade HHR. Genotoxic, antigenotoxic and phytochemical assessment of Terminalia actinophylla ethanolic extract. Food Chem Toxicol 2013; 62:521-7. [PMID: 24071477 DOI: 10.1016/j.fct.2013.09.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 09/12/2013] [Accepted: 09/16/2013] [Indexed: 11/20/2022]
Abstract
Terminalia actinophylla has been used for anti-diarrheic and haemostatic purposes in Brazil. The fly spot data obtained after exposure of marker-heterozygous Drosophila melanogaster larvae to T. actinophylla ethanolic extract (TAE) in the standard (ST) and high bioactivation (HB) crosses revealed that TAE did not induce any statistically significant increment in any spot categories. Differences between the two crosses are related to cytochrome P450 (CYPs) levels. In this sense, our data pointed out the absence of TAE-direct and indirect mutagenic and recombinagenic action in the Somatic Mutation and Recombination Test (SMART). When the anti-genotoxicity of TAE was analyzed, neither mitomycin C (MMC) nor ethylmethanesulfonate (EMS) genotoxicity was modified by the post-exposure to TAE, which suggests that TAE has no effect on the mechanisms involved in the processing of the lesions induced by both genotoxins. In the mwh/flr(3) genotype, co-treatment with TAE may lead to a significant protection against the genotoxicity of MMC and a weak but significant effect in the toxic genetic action of EMS. The overall findings suggested that the favorable modulations by TAE could be, at least in part, due to its antioxidative potential.
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Affiliation(s)
- P F M R Pádua
- Programa de Pós-Graduação em Genética e Toxicologia Aplicada (PPGGTA), Universidade Luterana do Brasil (ULBRA), Canoas, RS, Brazil
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26
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Comparative analysis of genetic toxicity of antiretroviral combinations in somatic cells of Drosophila melanogaster. Food Chem Toxicol 2013; 53:299-309. [DOI: 10.1016/j.fct.2012.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 11/19/2012] [Accepted: 12/04/2012] [Indexed: 12/11/2022]
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Srs2 mediates PCNA-SUMO-dependent inhibition of DNA repair synthesis. EMBO J 2013; 32:742-55. [PMID: 23395907 PMCID: PMC3594751 DOI: 10.1038/emboj.2013.9] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 01/10/2013] [Indexed: 12/11/2022] Open
Abstract
Completion of DNA replication needs to be ensured even when challenged with fork progression problems or DNA damage. PCNA and its modifications constitute a molecular switch to control distinct repair pathways. In yeast, SUMOylated PCNA (S-PCNA) recruits Srs2 to sites of replication where Srs2 can disrupt Rad51 filaments and prevent homologous recombination (HR). We report here an unexpected additional mechanism by which S-PCNA and Srs2 block the synthesis-dependent extension of a recombination intermediate, thus limiting its potentially hazardous resolution in association with a cross-over. This new Srs2 activity requires the SUMO interaction motif at its C-terminus, but neither its translocase activity nor its interaction with Rad51. Srs2 binding to S-PCNA dissociates Polδ and Polη from the repair synthesis machinery, thus revealing a novel regulatory mechanism controlling spontaneous genome rearrangements. Our results suggest that cycling cells use the Siz1-dependent SUMOylation of PCNA to limit the extension of repair synthesis during template switch or HR and attenuate reciprocal DNA strand exchanges to maintain genome stability. An unexpected non-catalytic function of the recombination-attenuating helicase Srs2 further expands the manifold roles of PCNA modifications in ensuring genome stability.
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I-SceI-based assays to examine distinct repair outcomes of mammalian chromosomal double strand breaks. Methods Mol Biol 2013; 920:379-91. [PMID: 22941618 DOI: 10.1007/978-1-61779-998-3_27] [Citation(s) in RCA: 247] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Chromosomal double strand breaks (DSBs) can be repaired by a number of mechanisms that result in diverse genetic outcomes. To examine distinct outcomes of chromosomal DSB repair, a panel of human cell lines has been developed that contain GFP-based reporters with recognition sites for the rare-cutting endonuclease I-SceI. One set of reporters is used to measure DSB repair events that require access to homology: homology-directed repair, homology-directed repair that requires the removal of a nonhomologous insertion, single strand annealing, and alternative end joining. An additional reporter (EJ5-GFP) is used to measure end joining (EJ) between distal DSB ends of two tandem I-SceI sites. These Distal-EJ events do not require access to homology, and thus are distinct from the repair events described above. Indeed, this assay provides a measure of DSB end protection during EJ, via physical analysis of Distal-EJ products to determine the frequency of I-SceI-restoration. The EJ5-GFP reporter can also be adapted to examine EJ of non-cohesive DSB ends, using co-expression of I-SceI with a non-processive 3' exonuclease (Trex2), which can cause partial degradation of the 4 nucleotide 3' cohesive overhangs generated by I-SceI. Such co-expression of I-SceI and Trex2 leads to measurable I-SceI-resistant EJ products that use proximal DSB ends (Proximal-EJ), as well as distal DSB ends (Distal-EJ). Therefore, this co-expression approach can be used to examine the relative frequency of Proximal-EJ versus Distal-EJ, and hence provide a measure of the fidelity of end utilization during repair of multiple DSBs. In this report, the repair outcomes examined by each reporter are described, along with methods for cell culture, transient expression of I-SceI and Trex2, and repair product analysis.
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Uniparental disomy analysis in trios using genome-wide SNP array and whole-genome sequencing data imply segmental uniparental isodisomy in general populations. Gene 2013; 512:267-74. [PMID: 23111162 DOI: 10.1016/j.gene.2012.10.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Revised: 10/04/2012] [Accepted: 10/19/2012] [Indexed: 11/24/2022]
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Abstract
Pancreatic β-cell dysfunction plays an important role in the pathogenesis of both type 1 and type 2 diabetes. Insulin, which is produced in β-cells, is a critical regulator of metabolism. Insulin is synthesized as preproinsulin and processed to proinsulin. Proinsulin is then converted to insulin and C-peptide and stored in secretary granules awaiting release on demand. Insulin synthesis is regulated at both the transcriptional and translational level. The cis-acting sequences within the 5' flanking region and trans-activators including paired box gene 6 (PAX6), pancreatic and duodenal homeobox- 1(PDX-1), MafA, and β-2/Neurogenic differentiation 1 (NeuroD1) regulate insulin transcription, while the stability of preproinsulin mRNA and its untranslated regions control protein translation. Insulin secretion involves a sequence of events in β-cells that lead to fusion of secretory granules with the plasma membrane. Insulin is secreted primarily in response to glucose, while other nutrients such as free fatty acids and amino acids can augment glucose-induced insulin secretion. In addition, various hormones, such as melatonin, estrogen, leptin, growth hormone, and glucagon like peptide-1 also regulate insulin secretion. Thus, the β-cell is a metabolic hub in the body, connecting nutrient metabolism and the endocrine system. Although an increase in intracellular [Ca2+] is the primary insulin secretary signal, cAMP signaling- dependent mechanisms are also critical in the regulation of insulin secretion. This article reviews current knowledge on how β-cells synthesize and secrete insulin. In addition, this review presents evidence that genetic and environmental factors can lead to hyperglycemia, dyslipidemia, inflammation, and autoimmunity, resulting in β-cell dysfunction, thereby triggering the pathogenesis of diabetes.
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Affiliation(s)
- Zhuo Fu
- Department of Human Nutrition, Foods and Exercise, Virginia Tech, Blacksburg, VA 24061, USA
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Fu Z, Gilbert ER, Liu D. Regulation of insulin synthesis and secretion and pancreatic Beta-cell dysfunction in diabetes. Curr Diabetes Rev 2013; 9:25-53. [PMID: 22974359 PMCID: PMC3934755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Revised: 09/11/2012] [Accepted: 09/11/2012] [Indexed: 11/11/2023]
Abstract
Pancreatic β-cell dysfunction plays an important role in the pathogenesis of both type 1 and type 2 diabetes. Insulin, which is produced in β-cells, is a critical regulator of metabolism. Insulin is synthesized as preproinsulin and processed to proinsulin. Proinsulin is then converted to insulin and C-peptide and stored in secretary granules awaiting release on demand. Insulin synthesis is regulated at both the transcriptional and translational level. The cis-acting sequences within the 5' flanking region and trans-activators including paired box gene 6 (PAX6), pancreatic and duodenal homeobox- 1(PDX-1), MafA, and β-2/Neurogenic differentiation 1 (NeuroD1) regulate insulin transcription, while the stability of preproinsulin mRNA and its untranslated regions control protein translation. Insulin secretion involves a sequence of events in β-cells that lead to fusion of secretory granules with the plasma membrane. Insulin is secreted primarily in response to glucose, while other nutrients such as free fatty acids and amino acids can augment glucose-induced insulin secretion. In addition, various hormones, such as melatonin, estrogen, leptin, growth hormone, and glucagon like peptide-1 also regulate insulin secretion. Thus, the β-cell is a metabolic hub in the body, connecting nutrient metabolism and the endocrine system. Although an increase in intracellular [Ca2+] is the primary insulin secretary signal, cAMP signaling- dependent mechanisms are also critical in the regulation of insulin secretion. This article reviews current knowledge on how β-cells synthesize and secrete insulin. In addition, this review presents evidence that genetic and environmental factors can lead to hyperglycemia, dyslipidemia, inflammation, and autoimmunity, resulting in β-cell dysfunction, thereby triggering the pathogenesis of diabetes.
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Affiliation(s)
- Zhuo Fu
- Department of Human Nutrition, Foods and Exercise, Virginia Tech, Blacksburg, VA 24061, USA
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Ho B, Baker PM, Singh S, Shih SJ, Vaughan AT. Localized DNA cleavage secondary to genotoxic exposure adjacent to an Alu inverted repeat. Genes Chromosomes Cancer 2012; 51:501-9. [PMID: 22334386 DOI: 10.1002/gcc.21938] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 01/05/2012] [Indexed: 01/12/2023] Open
Abstract
Radiation is a potent inducer of DNA damage leading to both random DNA loss and mutation. As part of a study focused on the mechanism whereby cells undergo loss of heterozygosity (LOH), a region of common LOH telomeric termination at 11q24 was observed in clones of H292 mucoepidermoid cells established after irradiation (IR). A 10-kbp region including the telomeric extent of LOH termination was analyzed after IR using six sets of ligation-mediated polymerase chain reaction (PCR) primers to detect the presence of DNA breaks. A cluster of DNA breaks was detected that closely mapped to the telomeric extent of LOH and which were observed up to 8 hr after IR. Repeating the experiment in the presence of the inhibitor of apoptosis, zVAD.fmk, did not change the location or amount of cleavage. A similar distribution of breaks was also seen in the MCF-10A breast cancer cell line after IR. Further inspection of the involved region showed that 22/32 and 7/7 DNA breaks found in H292 and MCF-10A cells, respectively, were located either in or immediately adjacent to an AluSx1 sequence, itself ≈ 1 kbp 5' to an AluSq2 that was in an inverted orientation to the AluSx1. The region between the inverted Alu repeats was notable for both DNAse hypersensitivity and an open chromatin conformation inferred from histone modification data. These factors may contribute to genomic instability at this location.
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Affiliation(s)
- Bay Ho
- Department of Radiation Oncology, University of California at Davis, Sacramento, CA 95817, USA
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Gunn A, Bennardo N, Cheng A, Stark JM. Correct end use during end joining of multiple chromosomal double strand breaks is influenced by repair protein RAD50, DNA-dependent protein kinase DNA-PKcs, and transcription context. J Biol Chem 2011; 286:42470-42482. [PMID: 22027841 PMCID: PMC3234933 DOI: 10.1074/jbc.m111.309252] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 10/19/2011] [Indexed: 12/27/2022] Open
Abstract
During repair of multiple chromosomal double strand breaks (DSBs), matching the correct DSB ends is essential to limit rearrangements. To investigate the maintenance of correct end use, we examined repair of two tandem noncohesive DSBs generated by endonuclease I-SceI and the 3' nonprocessive exonuclease Trex2, which can be expressed as an I-SceI-Trex2 fusion. We examined end joining (EJ) repair that maintains correct ends (proximal-EJ) versus using incorrect ends (distal-EJ), which provides a relative measure of incorrect end use (distal end use). Previous studies showed that ATM is important to limit distal end use. Here we show that DNA-PKcs kinase activity and RAD50 are also important to limit distal end use, but that H2AX is dispensable. In contrast, we find that ATM, DNA-PKcs, and RAD50 have distinct effects on repair events requiring end processing. Furthermore, we developed reporters to examine the effects of the transcription context on DSB repair, using an inducible promoter. We find that a DSB downstream from an active promoter shows a higher frequency of distal end use, and a greater reliance on ATM for limiting incorrect end use. Conversely, DSB transcription context does not affect end processing during EJ, the frequency of homology-directed repair, or the role of RAD50 and DNA-PKcs in limiting distal end use. We suggest that RAD50, DNA-PKcs kinase activity, and transcription context are each important to limit incorrect end use during EJ repair of multiple DSBs, but that these factors and conditions have distinct roles during repair events requiring end processing.
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Affiliation(s)
- Amanda Gunn
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Nicole Bennardo
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Anita Cheng
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Jeremy M Stark
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California 91010.
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Nagathihalli NS, Nagaraju G. RAD51 as a potential biomarker and therapeutic target for pancreatic cancer. Biochim Biophys Acta Rev Cancer 2011; 1816:209-18. [PMID: 21807066 DOI: 10.1016/j.bbcan.2011.07.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Revised: 07/14/2011] [Accepted: 07/16/2011] [Indexed: 11/30/2022]
Abstract
Chemotherapy is a very important therapeutic strategy for cancer treatment. The failure of conventional and molecularly targeted chemotherapeutic regimes for the treatment of pancreatic cancer highlights a desperate need for novel therapeutic interventions. Chemotherapy often fails to eliminate all tumor cells because of intrinsic or acquired drug resistance, which is the most common cause of tumor recurrence. Overexpression of RAD51 protein, a key player in DNA repair/recombination has been observed in many cancer cells and its hyperexpression is implicated in drug resistance. Recent studies suggest that RAD51 overexpression contributes to the development, progression and drug resistance of pancreatic cancer cells. Here we provide a brief overview of the available pieces of evidence in support of the role of RAD51 in pancreatic tumorigenesis and drug resistance, and hypothesize that RAD51 could serve as a potential biomarker for diagnosis of pancreatic cancer. We discuss the possible involvement of RAD51 in the drug resistance associated with epithelial to mesenchymal transition and with cancer stem cells. Finally, we speculate that targeting RAD51 in pancreatic cancer cells may be a novel approach for the treatment of pancreatic cancer.
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Affiliation(s)
- Nagaraj S Nagathihalli
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232-6860, USA.
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Genetic evidence that synaptonemal complex axial elements govern recombination pathway choice in mice. Genetics 2011; 189:71-82. [PMID: 21750255 DOI: 10.1534/genetics.111.130674] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chiasmata resulting from interhomolog recombination are critical for proper chromosome segregation at meiotic metaphase I, thus preventing aneuploidy and consequent deleterious effects. Recombination in meiosis is driven by programmed induction of double strand breaks (DSBs), and the repair of these breaks occurs primarily by recombination between homologous chromosomes, not sister chromatids. Almost nothing is known about the basis for recombination partner choice in mammals. We addressed this problem using a genetic approach. Since meiotic recombination is coupled with synaptonemal complex (SC) morphogenesis, we explored the role of axial elements--precursors to the lateral element in the mature SC--in recombination partner choice, DSB repair pathways, and checkpoint control. Female mice lacking the SC axial element protein SYCP3 produce viable, but often aneuploid, oocytes. We describe genetic studies indicating that while DSB-containing Sycp3-/- oocytes can be eliminated efficiently, those that survive have completed repair before the execution of an intact DNA damage checkpoint. We find that the requirement for DMC1 and TRIP13, proteins normally essential for recombination repair of meiotic DSBs, is substantially bypassed in Sycp3 and Sycp2 mutants. This bypass requires RAD54, a functionally conserved protein that promotes intersister recombination in yeast meiosis and mammalian mitotic cells. Immunocytological and genetic studies indicated that the bypass in Sycp3-/- Dmc1-/- oocytes was linked to increased DSB repair. These experiments lead us to hypothesize that axial elements mediate the activities of recombination proteins to favor interhomolog, rather than intersister recombinational repair of genetically programmed DSBs in mice. The elimination of this activity in SYCP3- or SYCP2-deficient oocytes may underlie the aneuploidy in derivative mouse embryos and spontaneous abortions in women.
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Interhomolog recombination and loss of heterozygosity in wild-type and Bloom syndrome helicase (BLM)-deficient mammalian cells. Proc Natl Acad Sci U S A 2011; 108:11971-6. [PMID: 21730139 DOI: 10.1073/pnas.1104421108] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic integrity often is compromised in tumor cells, as illustrated by genetic alterations leading to loss of heterozygosity (LOH). One mechanism of LOH is mitotic crossover recombination between homologous chromosomes, potentially initiated by a double-strand break (DSB). To examine LOH associated with DSB-induced interhomolog recombination, we analyzed recombination events using a reporter in mouse embryonic stem cells derived from F1 hybrid embryos. In this study, we were able to identify LOH events although they occur only rarely in wild-type cells (≤2.5%). The low frequency of LOH during interhomolog recombination suggests that crossing over is rare in wild-type cells. Candidate factors that may suppress crossovers include the RecQ helicase deficient in Bloom syndrome cells (BLM), which is part of a complex that dissolves recombination intermediates. We analyzed interhomolog recombination in BLM-deficient cells and found that, although interhomolog recombination is slightly decreased in the absence of BLM, LOH is increased by fivefold or more, implying significantly increased interhomolog crossing over. These events frequently are associated with a second homologous recombination event, which may be related to the mitotic bivalent structure and/or the cell-cycle stage at which the initiating DSB occurs.
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37
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Andersen SL, Sekelsky J. Meiotic versus mitotic recombination: two different routes for double-strand break repair: the different functions of meiotic versus mitotic DSB repair are reflected in different pathway usage and different outcomes. Bioessays 2010; 32:1058-66. [PMID: 20967781 PMCID: PMC3090628 DOI: 10.1002/bies.201000087] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Studies in the yeast Saccharomyces cerevisiae have validated the major features of the double-strand break repair (DSBR) model as an accurate representation of the pathway through which meiotic crossovers (COs) are produced. This success has led to this model being invoked to explain double-strand break (DSB) repair in other contexts. However, most non-crossover (NCO) recombinants generated during S. cerevisiae meiosis do not arise via a DSBR pathway. Furthermore, it is becoming increasingly clear that DSBR is a minor pathway for recombinational repair of DSBs that occur in mitotically-proliferating cells and that the synthesis-dependent strand annealing (SDSA) model appears to describe mitotic DSB repair more accurately. Fundamental dissimilarities between meiotic and mitotic recombination are not unexpected, since meiotic recombination serves a very different purpose (accurate chromosome segregation, which requires COs) than mitotic recombination (repair of DNA damage, which typically generates NCOs).
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Affiliation(s)
- Sabrina L. Andersen
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel, Chapel Hill, NC 27599
| | - Jeff Sekelsky
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel, Chapel Hill, NC 27599
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38
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Rassool FV, Tomkinson AE. Targeting abnormal DNA double strand break repair in cancer. Cell Mol Life Sci 2010; 67:3699-710. [PMID: 20697770 PMCID: PMC3014093 DOI: 10.1007/s00018-010-0493-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 07/28/2010] [Indexed: 12/19/2022]
Abstract
A major challenge in cancer treatment is the development of therapies that target cancer cells with little or no toxicity to normal tissues and cells. Alterations in DNA double strand break (DSB) repair in cancer cells include both elevated and reduced levels of key repair proteins and changes in the relative contributions of the various DSB repair pathways. These differences can result in increased sensitivity to DSB-inducing agents and increased genomic instability. The development of agents that selectively inhibit the DSB repair pathways that cancer cells are more dependent upon will facilitate the design of therapeutic strategies that exploit the differences in DSB repair between normal and cancer cells. Here, we discuss the pathways of DSB repair, alterations in DSB repair in cancer, inhibitors of DSB repair and future directions for cancer therapies that target DSB repair.
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Affiliation(s)
- Feyruz V. Rassool
- Department of Radiation Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, 655 West Baltimore Street, BRB, Rm 7-025, Baltimore, MD 21201 USA
| | - Alan E. Tomkinson
- Department of Radiation Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, 655 West Baltimore Street, BRB, Rm 7-025, Baltimore, MD 21201 USA
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39
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Du N, Baker PM, Do TU, Bien C, Bier-Laning CM, Singh S, Shih SJ, Diaz MO, Vaughan AT. 11q21.1-11q23.3 Is a site of intrinsic genomic instability triggered by irradiation. Genes Chromosomes Cancer 2010; 49:831-43. [PMID: 20607707 DOI: 10.1002/gcc.20791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The chromosome location, 11q21-23, is linked to loss of heterozygosity (LOH) in multiple tumors including those of breast, lung, and head and neck. To examine the process of LOH induction, the H292 cell line (human muco-epidermoid carcinoma) was irradiated or treated with anti-CD95 antibody, and individual clones isolated through two rounds of cloning. Regions of LOH were determined by screening a suite of eight polymorphic microsatellite markers covering 11p15-11q24 using fluorescent primers and genetic analyzer peak discrimination. LOH induction was observed extending through 11q21.1-11q23.3 in 6/49 of clones surviving 4 Gy and 8/50 after 8 Gy. Analysis of selected clones by Affymetrix 6.0 single nucleotide polymorphism (SNP) arrays confirmed the initial assessment indicating a consistent 27.3-27.7 Mbp deletion in multiple clones. The telomeric border of LOH mapped to a 1 Mbp region of elevated recombination. Whole genome analysis of SNP data indicated that site-restricted LOH also occurred across multiple additional genomic locations. These data indicate that 11q21.1-11q23.3, and potentially other regions of this cell line are sites of intrinsic cell-specific instability leading to LOH after irradiation. Such deletions may subsequently be propagated by genetic selection and clonal expansion.
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Affiliation(s)
- Nga Du
- Department of Radiation Oncology, University of California at Davis, Sacramento, CA 95817, USA
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40
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Kass EM, Jasin M. Collaboration and competition between DNA double-strand break repair pathways. FEBS Lett 2010; 584:3703-8. [PMID: 20691183 DOI: 10.1016/j.febslet.2010.07.057] [Citation(s) in RCA: 251] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 07/28/2010] [Indexed: 12/12/2022]
Abstract
DNA double-strand breaks resulting from normal cellular processes including replication and exogenous sources such as ionizing radiation pose a serious risk to genome stability, and cells have evolved different mechanisms for their efficient repair. The two major pathways involved in the repair of double-strand breaks in eukaryotic cells are non-homologous end joining and homologous recombination. Numerous factors affect the decision to repair a double-strand break via these pathways, and accumulating evidence suggests these major repair pathways both cooperate and compete with each other at double-strand break sites to facilitate efficient repair and promote genomic integrity.
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Affiliation(s)
- Elizabeth M Kass
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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41
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Legerski RJ. Repair of DNA interstrand cross-links during S phase of the mammalian cell cycle. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:540-551. [PMID: 20658646 PMCID: PMC2911997 DOI: 10.1002/em.20566] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
DNA interstrand cross-linking (ICL) agents are widely used in anticancer chemotherapy regimens, yet our understanding of the DNA repair mechanisms by which these lesions are removed from the genome remains incomplete. This is at least in part due to the enormously complicated nature and variety of the biochemical pathways that operate on these complex lesions. In this review, we have focused specifically on the S-phase pathway of ICL repair in mammalian cells, which appears to be the major mechanism by which these lesions are removed in cycling cells. The various stages and components of this pathway are discussed, and a putative molecular model is presented. In addition, we propose an explanation as to how this pathway can lead to the observed high levels of sister chromatid exchanges known to be induced by ICLs.
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Affiliation(s)
- Randy J Legerski
- Department of Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA.
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42
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Shen X, Li L. Mutagenic repair of DNA interstrand crosslinks. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:493-9. [PMID: 20209624 PMCID: PMC2892553 DOI: 10.1002/em.20558] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Formation of DNA interstrand crosslinks (ICLs) in chromosomal DNA imposes acute obstruction of all essential DNA functions. For over 70 years bifunctional alkylators, also known as DNA crosslinkers, have been an important class of cancer chemotherapeutic regimens. The mechanisms of ICL repair remains largely elusive. Here, we review a eukaryotic mutagenic ICL repair pathway discovered by work from several laboratories. This repair pathway, alternatively termed recombination-independent ICL repair, involves the incision activities of the nucleotide excision repair (NER) mechanism and lesion bypass polymerase(s). Repair of the ICL is initiated by dual incisions flanking the ICL on one strand of the double helix; the resulting gap is filled in by lesion bypass polymerases. The remaining lesion is subsequently removed by a second round of NER reaction. The mutagenic repair of ICL likely interacts with other cellular mechanisms such as the Fanconi anemia pathway and recombinational repair of ICLs. These aspects will also be discussed.
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Affiliation(s)
- Xi Shen
- Department of Experimental Radiation Oncology, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030
| | - Lei Li
- Department of Experimental Radiation Oncology, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030
- Department of Genetics, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030
- Corresponding Author: Phone: (713) 792-2514, Fax: (713) 794-5369,
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Laulier C, Cheng A, Huang N, Stark JM. Mammalian Fbh1 is important to restore normal mitotic progression following decatenation stress. DNA Repair (Amst) 2010; 9:708-17. [PMID: 20457012 DOI: 10.1016/j.dnarep.2010.03.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/19/2010] [Accepted: 03/26/2010] [Indexed: 12/31/2022]
Abstract
We have addressed the role of the F-box helicase 1 (Fbh1) protein during genome maintenance in mammalian cells. For this, we generated two mouse embryonic stem cell lines deficient for Fbh1: one with a homozygous deletion of the N-terminal F-box domain (Fbh1(f/f)), and the other with a homozygous disruption (Fbh1(-/-)). Consistent with previous reports of Fbh1-deficiency in vertebrate cells, we found that Fbh1(-/-) cells show a moderate increase in Rad51 localization to DNA damage, but no clear defect in chromosome break repair. In contrast, we found that Fbh1(f/f) cells show a decrease in Rad51 localization to DNA damage and increased cytoplasmic localization of Rad51. However, these Fbh1(f/f) cells show no clear defects in chromosome break repair. Since some Rad51 partners and F-box-associated proteins (Skp1-Cul1) have been implicated in progression through mitosis, we considered whether Fbh1 might play a role in this process. To test this hypothesis, we disrupted mitosis using catalytic topoisomerase II inhibitors (bisdioxopiperazines), which inhibit chromosome decatenation. We found that both Fbh1(f/f) and Fbh1(-/-) cells show hypersensitivity to topoisomerase II catalytic inhibitors, even though the degree of decatenation stress was not affected. Furthermore, following topoisomerase II catalytic inhibition, both Fbh1-deficient cell lines show substantial defects in anaphase separation of chromosomes. These results indicate that Fbh1 is important for restoration of normal mitotic progression following decatenation stress.
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Affiliation(s)
- Corentin Laulier
- Department of Cancer Biology, Division of Radiation Biology, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010, USA
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44
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Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis. Nat Rev Mol Cell Biol 2010; 11:196-207. [PMID: 20177395 DOI: 10.1038/nrm2851] [Citation(s) in RCA: 670] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mitotic homologous recombination promotes genome stability through the precise repair of DNA double-strand breaks and other lesions that are encountered during normal cellular metabolism and from exogenous insults. As a result, homologous recombination repair is essential during proliferative stages in development and during somatic cell renewal in adults to protect against cell death and mutagenic outcomes from DNA damage. Mutations in mammalian genes encoding homologous recombination proteins, including BRCA1, BRCA2 and PALB2, are associated with developmental abnormalities and tumorigenesis. Recent advances have provided a clearer understanding of the connections between these proteins and of the key steps of homologous recombination and DNA strand exchange.
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45
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Maréchal A, Brisson N. Recombination and the maintenance of plant organelle genome stability. THE NEW PHYTOLOGIST 2010; 186:299-317. [PMID: 20180912 DOI: 10.1111/j.1469-8137.2010.03195.x] [Citation(s) in RCA: 290] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Like their nuclear counterpart, the plastid and mitochondrial genomes of plants have to be faithfully replicated and repaired to ensure the normal functioning of the plant. Inability to maintain organelle genome stability results in plastid and/or mitochondrial defects, which can lead to potentially detrimental phenotypes. Fortunately, plant organelles have developed multiple strategies to maintain the integrity of their genetic material. Of particular importance among these processes is the extensive use of DNA recombination. In fact, recombination has been implicated in both the replication and the repair of organelle genomes. Revealingly, deregulation of recombination in organelles results in genomic instability, often accompanied by adverse consequences for plant fitness. The recent identification of four families of proteins that prevent aberrant recombination of organelle DNA sheds much needed mechanistic light on this important process. What comes out of these investigations is a partial portrait of the recombination surveillance machinery in which plants have co-opted some proteins of prokaryotic origin but have also evolved whole new factors to keep their organelle genomes intact. These new features presumably optimized the protection of plastid and mitochondrial genomes against the particular genotoxic stresses they face.
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Affiliation(s)
- Alexandre Maréchal
- Department of Biochemistry, Université de Montréal, PO Box 6128, Station Centre-ville, Montréal, QC H3C 3J7, Canada
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46
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Abstract
Homologous recombination (HR) performs crucial functions including DNA repair, segregation of homologous chromosomes, propagation of genetic diversity, and maintenance of telomeres. HR is responsible for the repair of DNA double-strand breaks and DNA interstrand cross-links. The process of HR is initiated at the site of DNA breaks and gaps and involves a search for homologous sequences promoted by Rad51 and auxiliary proteins followed by the subsequent invasion of broken DNA ends into the homologous duplex DNA that then serves as a template for repair. The invasion produces a cross-stranded structure, known as the Holliday junction. Here, we describe the properties of Rad54, an important and versatile HR protein that is evolutionarily conserved in eukaryotes. Rad54 is a motor protein that translocates along dsDNA and performs several important functions in HR. The current review focuses on the recently identified Rad54 activities which contribute to the late phase of HR, especially the branch migration of Holliday junctions.
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Affiliation(s)
- Alexander V Mazin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
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Mechanisms of recombination between diverged sequences in wild-type and BLM-deficient mouse and human cells. Mol Cell Biol 2010; 30:1887-97. [PMID: 20154148 DOI: 10.1128/mcb.01553-09] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Double-strand breaks (DSBs) are particularly deleterious DNA lesions for which cells have developed multiple mechanisms of repair. One major mechanism of DSB repair in mammalian cells is homologous recombination (HR), whereby a homologous donor sequence is used as a template for repair. For this reason, HR repair of DSBs is also being exploited for gene modification in possible therapeutic approaches. HR is sensitive to sequence divergence, such that the cell has developed ways to suppress recombination between diverged ("homeologous") sequences. In this report, we have examined several aspects of HR between homeologous sequences in mouse and human cells. We found that gene conversion tracts are similar for mouse and human cells and are generally < or =100 bp, even in Msh2(-)(/)(-) cells which fail to suppress homeologous recombination. Gene conversion tracts are mostly unidirectional, with no observed mutations. Additionally, no alterations were observed in the donor sequences. While both mouse and human cells suppress homeologous recombination, the suppression is substantially less in the transformed human cells, despite similarities in the gene conversion tracts. BLM-deficient mouse and human cells suppress homeologous recombination to a similar extent as wild-type cells, unlike Sgs1-deficient Saccharomyces cerevisiae.
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Bennardo N, Gunn A, Cheng A, Hasty P, Stark JM. Limiting the persistence of a chromosome break diminishes its mutagenic potential. PLoS Genet 2009; 5:e1000683. [PMID: 19834534 PMCID: PMC2752804 DOI: 10.1371/journal.pgen.1000683] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 09/15/2009] [Indexed: 01/05/2023] Open
Abstract
To characterize the repair pathways of chromosome double-strand breaks (DSBs), one approach involves monitoring the repair of site-specific DSBs generated by rare-cutting endonucleases, such as I-SceI. Using this method, we first describe the roles of Ercc1, Msh2, Nbs1, Xrcc4, and Brca1 in a set of distinct repair events. Subsequently, we considered that the outcome of such assays could be influenced by the persistent nature of I-SceI-induced DSBs, in that end-joining (EJ) products that restore the I-SceI site are prone to repeated cutting. To address this aspect of repair, we modified I-SceI-induced DSBs by co-expressing I-SceI with a non-processive 3′ exonuclease, Trex2, which we predicted would cause partial degradation of I-SceI 3′ overhangs. We find that Trex2 expression facilitates the formation of I-SceI-resistant EJ products, which reduces the potential for repeated cutting by I-SceI and, hence, limits the persistence of I-SceI-induced DSBs. Using this approach, we find that Trex2 expression causes a significant reduction in the frequency of repair pathways that result in substantial deletion mutations: EJ between distal ends of two tandem DSBs, single-strand annealing, and alternative-NHEJ. In contrast, Trex2 expression does not inhibit homology-directed repair. These results indicate that limiting the persistence of a DSB causes a reduction in the frequency of repair pathways that lead to significant genetic loss. Furthermore, we find that individual genetic factors play distinct roles during repair of non-cohesive DSB ends that are generated via co-expression of I-SceI with Trex2. A deleterious lesion in DNA is a break of both strands, or a chromosome double-strand break (DSB). DSBs can arise during normal cellular metabolism, but are also a consequence of many forms of cancer therapy. If DSBs are not repaired prior to cell division, entire segments of a chromosome can be lost. Several pathways ensure that DSBs are repaired, though some pathways are prone to causing mutations and/or chromosomal rearrangements, each of which can contribute to cancer development. In the first part of this study, we describe the roles of individual genetic factors in distinct repair pathways of DSBs generated by the I-SceI endonuclease. From these studies, we find that some factors can function in multiple repair pathways. In the second part of this study, we present a method for partially degrading the cohesive DSB overhangs that are generated by I-SceI, which we find facilitates repair products that are not prone to being re-cut by the endonuclease. As a consequence, we have limited the persistence of such breaks, which we find causes a reduction in repair pathways that lead to significant genetic loss. As well, we use this method to characterize the role of individual genetic factors during the repair of non-cohesive DSB ends.
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Affiliation(s)
- Nicole Bennardo
- Department of Cancer Biology, Division of Radiation Biology, Beckman Research Institute of the City of Hope, Duarte, California, USA
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Abstract
DNA chromosomal DSBs (double-strand breaks) are potentially hazardous DNA lesions, and their accurate repair is essential for the successful maintenance and propagation of genetic information. Two major pathways have evolved to repair DSBs: HR (homologous recombination) and NHEJ (non-homologous end-joining). Depending on the context in which the break is encountered, HR and NHEJ may either compete or co-operate to fix DSBs in eukaryotic cells. Defects in either pathway are strongly associated with human disease, including immunodeficiency and cancer predisposition. Here we review the current knowledge of how NHEJ and HR are controlled in somatic mammalian cells, and discuss the role of the chromatin context in regulating each pathway. We also review evidence for both co-operation and competition between the two pathways.
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Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet 2009. [PMID: 19597530 DOI: 10.1038/nrg2593.mechanisms] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Deletions and duplications of chromosomal segments (copy number variants, CNVs) are a major source of variation between individual humans and are an underlying factor in human evolution and in many diseases, including mental illness, developmental disorders and cancer. CNVs form at a faster rate than other types of mutation, and seem to do so by similar mechanisms in bacteria, yeast and humans. Here we review current models of the mechanisms that cause copy number variation. Non-homologous end-joining mechanisms are well known, but recent models focus on perturbation of DNA replication and replication of non-contiguous DNA segments. For example, cellular stress might induce repair of broken replication forks to switch from high-fidelity homologous recombination to non-homologous repair, thus promoting copy number change.
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Affiliation(s)
- P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
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