101
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Belmonte-Reche E, Martínez-García M, Guédin A, Zuffo M, Arévalo-Ruiz M, Doria F, Campos-Salinas J, Maynadier M, López-Rubio JJ, Freccero M, Mergny JL, Pérez-Victoria JM, Morales JC. G-Quadruplex Identification in the Genome of Protozoan Parasites Points to Naphthalene Diimide Ligands as New Antiparasitic Agents. J Med Chem 2018; 61:1231-1240. [PMID: 29323491 PMCID: PMC6148440 DOI: 10.1021/acs.jmedchem.7b01672] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
G-quadruplexes
(G4) are DNA secondary structures that take part
in the regulation of gene expression. Putative G4 forming sequences
(PQS) have been reported in mammals, yeast, bacteria, and viruses.
Here, we present PQS searches on the genomes of T. brucei,
L. major, and P. falciparum. We found telomeric
sequences and new PQS motifs. Biophysical experiments showed that
EBR1, a 29 nucleotide long highly repeated PQS in T. brucei, forms a stable G4 structure. G4 ligands based on carbohydrate conjugated
naphthalene diimides (carb-NDIs) that bind G4’s including hTel
could bind EBR1 with selectivity versus dsDNA. These ligands showed
important antiparasitic activity. IC50 values were in the
nanomolar range against T. brucei with high selectivity
against MRC-5 human cells. Confocal microscopy confirmed these ligands
localize in the nucleus and kinetoplast of T. brucei suggesting they can reach their potential G4 targets. Cytotoxicity
and zebrafish toxicity studies revealed sugar conjugation reduces
intrinsic toxicity of NDIs.
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Affiliation(s)
- Efres Belmonte-Reche
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Marta Martínez-García
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Aurore Guédin
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), 2 Rue Robert Escarpit, 33607 Pessac, France
| | - Michela Zuffo
- Department of Chemistry, University of Pavia , Via Taramelli 10, 27100 Pavia, Italy
| | - Matilde Arévalo-Ruiz
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Filippo Doria
- Department of Chemistry, University of Pavia , Via Taramelli 10, 27100 Pavia, Italy
| | - Jenny Campos-Salinas
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Marjorie Maynadier
- Dynamique des Interactions Membranaires Normales et Pathologiques, CNRS UMR 5235, Université de Montpellier, 34095 Montpellier, France
| | - José Juan López-Rubio
- CNRS, 5290, IRD 224, University of Montpellier (UMR "MiVEGEC"), INSERM, 34394 Montpellier, France
| | - Mauro Freccero
- Department of Chemistry, University of Pavia , Via Taramelli 10, 27100 Pavia, Italy
| | - Jean-Louis Mergny
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), 2 Rue Robert Escarpit, 33607 Pessac, France.,Institute of Biophysics , AS CR, v.v.i. Kralovopolska 135, 612 65 Brno, Czech Republic
| | - José María Pérez-Victoria
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
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102
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Bewg WP, Ci D, Tsai CJ. Genome Editing in Trees: From Multiple Repair Pathways to Long-Term Stability. FRONTIERS IN PLANT SCIENCE 2018; 9:1732. [PMID: 30532764 PMCID: PMC6265510 DOI: 10.3389/fpls.2018.01732] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/07/2018] [Indexed: 05/19/2023]
Abstract
The CRISPR technology continues to diversify with a broadening array of applications that touch all kingdoms of life. The simplicity, versatility and species-independent nature of the CRISPR system offers researchers a previously unattainable level of precision and control over genomic modifications. Successful applications in forest, fruit and nut trees have demonstrated the efficacy of CRISPR technology at generating null mutations in the first generation. This eliminates the lengthy process of multigenerational crosses to obtain homozygous knockouts (KO). The high degree of genome heterozygosity in outcrossing trees is both a challenge and an opportunity for genome editing: a challenge because sequence polymorphisms at the target site can render CRISPR editing ineffective; yet an opportunity because the power and specificity of CRISPR can be harnessed for allele-specific editing. Examination of CRISPR/Cas9-induced mutational profiles from published tree studies reveals the potential involvement of multiple DNA repair pathways, suggesting that the influence of sequence context at or near the target sites can define mutagenesis outcomes. For commercial production of elite trees that rely on vegetative propagation, available data suggest an excellent outlook for stable CRISPR-induced mutations and associated phenotypes over multiple clonal generations.
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Affiliation(s)
- William Patrick Bewg
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Dong Ci
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA, United States
- Department of Bioscience and Biotechnology, Beijing Forestry University, Beijing, China
| | - Chung-Jui Tsai
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA, United States
- *Correspondence: Chung-Jui Tsai,
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103
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Schimmel J, Kool H, van Schendel R, Tijsterman M. Mutational signatures of non-homologous and polymerase theta-mediated end-joining in embryonic stem cells. EMBO J 2017; 36:3634-3649. [PMID: 29079701 PMCID: PMC5730883 DOI: 10.15252/embj.201796948] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 09/05/2017] [Accepted: 09/29/2017] [Indexed: 12/11/2022] Open
Abstract
Cells employ potentially mutagenic DNA repair mechanisms to avoid the detrimental effects of chromosome breaks on cell survival. While classical non-homologous end-joining (cNHEJ) is largely error-free, alternative end-joining pathways have been described that are intrinsically mutagenic. Which end-joining mechanisms operate in germ and embryonic cells and thus contribute to heritable mutations found in congenital diseases is, however, still largely elusive. Here, we determined the genetic requirements for the repair of CRISPR/Cas9-induced chromosomal breaks of different configurations, and establish the mutational consequences. We find that cNHEJ and polymerase theta-mediated end-joining (TMEJ) act both parallel and redundant in mouse embryonic stem cells and account for virtually all end-joining activity. Surprisingly, mutagenic repair by polymerase theta (Pol θ, encoded by the Polq gene) is most prevalent for blunt double-strand breaks (DSBs), while cNHEJ dictates mutagenic repair of DSBs with protruding ends, in which the cNHEJ polymerases lambda and mu play minor roles. We conclude that cNHEJ-dependent repair of DSBs with protruding ends can explain de novo formation of tandem duplications in mammalian genomes.
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Affiliation(s)
- Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hanneke Kool
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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104
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Mateos-Gomez PA, Kent T, Deng SK, McDevitt S, Kashkina E, Hoang TM, Pomerantz RT, Sfeir A. The helicase domain of Polθ counteracts RPA to promote alt-NHEJ. Nat Struct Mol Biol 2017; 24:1116-1123. [PMID: 29058711 PMCID: PMC6047744 DOI: 10.1038/nsmb.3494] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/22/2017] [Indexed: 12/15/2022]
Abstract
Mammalian polymerase theta (Polθ) is a multifunctional enzyme that promotes error-prone DNA repair by alternative nonhomologous end joining (alt-NHEJ). Here we present structure-function analyses that reveal that, in addition to the polymerase domain, Polθ-helicase activity plays a central role during double-strand break (DSB) repair. Our results show that the helicase domain promotes chromosomal translocations by alt-NHEJ in mouse embryonic stem cells and also suppresses CRISPR-Cas9- mediated gene targeting by homologous recombination (HR). In vitro assays demonstrate that Polθ-helicase activity facilitates the removal of RPA from resected DSBs to allow their annealing and subsequent joining by alt-NHEJ. Consistent with an antagonistic role for RPA during alt-NHEJ, inhibition of RPA1 enhances end joining and suppresses recombination. Taken together, our results reveal that the balance between HR and alt-NHEJ is controlled by opposing activities of Polθ and RPA, providing further insight into the regulation of repair-pathway choice in mammalian cells.
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Affiliation(s)
- Pedro A. Mateos-Gomez
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, USA
- Department of Cell Biology, New York University School of Medicine, New York, USA
| | - Tatiana Kent
- Temple University Lewis Katz School of Medicine, Philadelphia, USA
| | - Sarah K. Deng
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, USA
- Department of Cell Biology, New York University School of Medicine, New York, USA
| | - Shane McDevitt
- Temple University Lewis Katz School of Medicine, Philadelphia, USA
| | | | - Trung M. Hoang
- Temple University Lewis Katz School of Medicine, Philadelphia, USA
| | | | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, USA
- Department of Cell Biology, New York University School of Medicine, New York, USA
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105
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DNA damage responses and p53 in the aging process. Blood 2017; 131:488-495. [PMID: 29141944 DOI: 10.1182/blood-2017-07-746396] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/01/2017] [Indexed: 12/18/2022] Open
Abstract
The genome is constantly attacked by genotoxic insults. DNA damage has long been established as a cause of cancer development through its mutagenic consequences. Conversely, radiation therapy and chemotherapy induce DNA damage to drive cells into apoptosis or senescence as outcomes of the DNA damage response (DDR). More recently, DNA damage has been recognized as a causal factor for the aging process. The role of DNA damage in aging and age-related diseases is illustrated by numerous congenital progeroid syndromes that are caused by mutations in genome maintenance pathways. During the past 2 decades, understanding how DDR drives cancer development and contributes to the aging process has progressed rapidly. It turns out that the DDR factor p53 takes center stage during tumor development and also plays an important role in the aging process. Studies in metazoan models ranging from Caenorhabditis elegans to mammals have revealed cell-autonomous and systemic DDR mechanisms that orchestrate adaptive responses that augment maintenance of the aging organism amid gradually accumulating DNA damage.
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106
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Han J, Ruan C, Huen MSY, Wang J, Xie A, Fu C, Liu T, Huang J. BRCA2 antagonizes classical and alternative nonhomologous end-joining to prevent gross genomic instability. Nat Commun 2017; 8:1470. [PMID: 29133916 PMCID: PMC5684403 DOI: 10.1038/s41467-017-01759-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/13/2017] [Indexed: 12/27/2022] Open
Abstract
BRCA2-deficient cells exhibit gross genomic instability, but the underlying mechanisms are not fully understood. Here we report that inactivation of BRCA2 but not RAD51 destabilizes RPA-coated single-stranded DNA (ssDNA) structures at resected DNA double-strand breaks (DSBs) and greatly enhances the frequency of nuclear fragmentation following cell exposure to DNA damage. Importantly, these BRCA2-associated deficits are fueled by the aberrant activation of classical (c)- and alternative (alt)- nonhomologous end-joining (NHEJ), and rely on the well-defined DNA damage signaling pathway involving the pro-c-NHEJ factor 53BP1 and its downstream effector RIF1. We further show that the 53BP1–RIF1 axis promotes toxic end-joining events via the retention of Artemis at DNA damage sites. Accordingly, loss of 53BP1, RIF1, or Artemis prolongs the stability of RPA-coated DSB intermediates in BRCA2-deficient cells and restores nuclear integrity. We propose that BRCA2 antagonizes 53BP1, RIF1, and Artemis-dependent c-NHEJ and alt-NHEJ to prevent gross genomic instability in a RAD51-independent manner. The genomic instability phenotype characteristic of BRCA2-deficient cells is not fully mechanistically understood. Here the authors show BRCA2 inactivation destabilizes RPA-coated single-stranded DNA and leads to toxic non homologous end-joining events.
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Affiliation(s)
- Jinhua Han
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Chunyan Ruan
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Michael S Y Huen
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Jiadong Wang
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Anyong Xie
- Institute of Translational Medicine, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Chun Fu
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Ting Liu
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Jun Huang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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107
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FAN1 interaction with ubiquitylated PCNA alleviates replication stress and preserves genomic integrity independently of BRCA2. Nat Commun 2017; 8:1073. [PMID: 29051491 PMCID: PMC5648898 DOI: 10.1038/s41467-017-01074-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 08/16/2017] [Indexed: 11/08/2022] Open
Abstract
Interstrand cross-link (ICL) hypersensitivity is a characteristic trait of Fanconi anemia (FA). Although FANCD2-associated nuclease 1 (FAN1) contributes to ICL repair, FAN1 mutations predispose to karyomegalic interstitial nephritis (KIN) and cancer rather than to FA. Thus, the biological role of FAN1 remains unclear. Because fork stalling in FAN1-deficient cells causes chromosomal instability, we reasoned that the key function of FAN1 might lie in the processing of halted replication forks. Here, we show that FAN1 contains a previously-uncharacterized PCNA interacting peptide (PIP) motif that, together with its ubiquitin-binding zinc finger (UBZ) domain, helps recruit FAN1 to ubiquitylated PCNA accumulated at stalled forks. This prevents replication fork collapse and controls their progression. Furthermore, we show that FAN1 preserves replication fork integrity by a mechanism that is distinct from BRCA2-dependent homologous recombination. Thus, targeting FAN1 activities and its interaction with ubiquitylated PCNA may offer therapeutic opportunities for treatment of BRCA-deficient tumors.
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108
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Vu GTH, Cao HX, Fauser F, Reiss B, Puchta H, Schubert I. Endogenous sequence patterns predispose the repair modes of CRISPR/Cas9-induced DNA double-stranded breaks in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:57-67. [PMID: 28696528 DOI: 10.1111/tpj.13634] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/03/2017] [Accepted: 07/07/2017] [Indexed: 05/20/2023]
Abstract
The possibility to predict the outcome of targeted DNA double-stranded break (DSB) repair would be desirable for genome editing. Furthermore the consequences of mis-repair of potentially cell-lethal DSBs and the underlying pathways are not yet fully understood. Here we study the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-induced mutation spectra at three selected endogenous loci in Arabidopsis thaliana by deep sequencing of long amplicon libraries. Notably, we found sequence-dependent genomic features that affected the DNA repair outcome. Deletions of 1-bp to <1000-bp size and/or very short insertions, deletions >1 kbp (all due to NHEJ) and deletions combined with insertions between 5-bp to >100 bp [caused by a synthesis-dependent strand annealing (SDSA)-like mechanism] occurred most frequently at all three loci. The appearance of single-stranded annealing events depends on the presence and distance between repeats flanking the DSB. The frequency and size of insertions is increased if a sequence with high similarity to the target site was available in cis. Most deletions were linked to pre-existing microhomology. Deletion and/or insertion mutations were blunt-end ligated or via de novo generated microhomology. While most mutation types and, to some degree, their predictability are comparable with animal systems, the broad range of deletion mutations seems to be a peculiar feature of the plant A. thaliana.
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Affiliation(s)
- Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D 06466, Gatersleben, Stadt Seeland, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D 06466, Gatersleben, Stadt Seeland, Germany
| | - Friedrich Fauser
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, Karlsruhe, 76049, Germany
| | - Bernd Reiss
- Max Planck Institute for Plant Breeding Research, 50829, Köln, Germany
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, Karlsruhe, 76049, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D 06466, Gatersleben, Stadt Seeland, Germany
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109
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Zafar MK, Eoff RL. Translesion DNA Synthesis in Cancer: Molecular Mechanisms and Therapeutic Opportunities. Chem Res Toxicol 2017; 30:1942-1955. [PMID: 28841374 DOI: 10.1021/acs.chemrestox.7b00157] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The genomic landscape of cancer is one marred by instability, but the mechanisms that underlie these alterations are multifaceted and remain a topic of intense research. Cellular responses to DNA damage and/or replication stress can affect genome stability in tumors and influence the response of patients to therapy. In addition to direct repair, DNA damage tolerance (DDT) is an element of genomic maintenance programs that contributes to the etiology of several types of cancer. DDT mechanisms primarily act to resolve replication stress, and this can influence the effectiveness of genotoxic drugs. Translesion DNA synthesis (TLS) is an important component of DDT that facilitates direct bypass of DNA adducts and other barriers to replication. The central role of TLS in the bypass of drug-induced DNA lesions, the promotion of tumor heterogeneity, and the involvement of these enzymes in the maintenance of the cancer stem cell niche presents an opportunity to leverage inhibition of TLS as a way of improving existing therapies. In the review that follows, we summarize mechanisms of DDT, misregulation of TLS in cancer, and discuss the potential for targeting these pathways as a means of improving cancer therapies.
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Affiliation(s)
- Maroof K Zafar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Robert L Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
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110
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Bournique E, Dall'Osto M, Hoffmann JS, Bergoglio V. Role of specialized DNA polymerases in the limitation of replicative stress and DNA damage transmission. Mutat Res 2017; 808:62-73. [PMID: 28843435 DOI: 10.1016/j.mrfmmm.2017.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 01/31/2023]
Abstract
Replication stress is a strong and early driving force for genomic instability and tumor development. Beside replicative DNA polymerases, an emerging group of specialized DNA polymerases is involved in the technical assistance of the replication machinery in order to prevent replicative stress and its deleterious consequences. During S-phase, altered progression of the replication fork by endogenous or exogenous impediments induces replicative stress, causing cells to reach mitosis with genomic regions not fully duplicated. Recently, specific mechanisms to resolve replication intermediates during mitosis with the aim of limiting DNA damage transmission to daughter cells have been identified. In this review, we detail the two major actions of specialized DNA polymerases that limit DNA damage transmission: the prevention of replicative stress by non-B DNA replication and the recovery of stalled replication forks.
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Affiliation(s)
- Elodie Bournique
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France
| | - Marina Dall'Osto
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France
| | - Jean-Sébastien Hoffmann
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France
| | - Valérie Bergoglio
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France.
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111
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González-Huici V, Wang B, Gartner A. A Role for the Nonsense-Mediated mRNA Decay Pathway in Maintaining Genome Stability in Caenorhabditis elegans. Genetics 2017; 206:1853-1864. [PMID: 28634159 PMCID: PMC5560793 DOI: 10.1534/genetics.117.203414] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/05/2017] [Indexed: 12/31/2022] Open
Abstract
Ionizing radiation (IR) is commonly used in cancer therapy and is a main source of DNA double-strand breaks (DSBs), one of the most toxic forms of DNA damage. We have used Caenorhabditis elegans as an invertebrate model to identify novel factors required for repair of DNA damage inflicted by IR. We have performed an unbiased genetic screen, finding that smg-1 mutations confer strong hyper-sensitivity to IR. SMG-1 is a phosphoinositide-3 kinase (PI3K) involved in mediating nonsense-mediated mRNA decay (NMD) of transcripts containing premature stop codons and related to the ATM and ATR kinases which are at the apex of DNA damage signaling pathways. Hyper-sensitivity to IR also occurs when other genes mediating NMD are mutated. The hyper-sensitivity to bleomycin, a drug known to induce DSBs, further supports that NMD pathway mutants are defective in DSB repair. Hyper-sensitivity was not observed upon treatment with alkylating agents or UV irradiation. We show that SMG-1 mainly acts in mitotically dividing germ cells, and during late embryonic and larval development. Based on epistasis experiments, SMG-1 does not appear to act in any of the three major pathways known to mend DNA DSBs, namely homologous recombination (HR), nonhomologous end-joining (NHEJ), and microhomology-mediated end-joining (MMEJ). We speculate that SMG-1 kinase activity could be activated following DNA damage to phosphorylate specific DNA repair proteins and/or that NMD inactivation may lead to aberrant mRNAs leading to synthesis of malfunctioning DNA repair proteins.
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Affiliation(s)
- Víctor González-Huici
- School of Life Sciences, Centre for Gene Regulation and Expression, University of Dundee, DD1 5EH, UK
| | - Bin Wang
- School of Life Sciences, Centre for Gene Regulation and Expression, University of Dundee, DD1 5EH, UK
| | - Anton Gartner
- School of Life Sciences, Centre for Gene Regulation and Expression, University of Dundee, DD1 5EH, UK
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112
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Saito S, Maeda R, Adachi N. Dual loss of human POLQ and LIG4 abolishes random integration. Nat Commun 2017; 8:16112. [PMID: 28695890 PMCID: PMC5508229 DOI: 10.1038/ncomms16112] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/30/2017] [Indexed: 12/16/2022] Open
Abstract
Homologous recombination-mediated gene targeting has greatly contributed to genetic analysis in a wide range of species, but is highly inefficient in human cells because of overwhelmingly frequent random integration events, whose molecular mechanism remains elusive. Here we show that DNA polymerase θ, despite its minor role in chromosomal DNA repair, substantially contributes to random integration, and that cells lacking both DNA polymerase θ and DNA ligase IV, which is essential for non-homologous end joining (NHEJ), exhibit 100% efficiency of spontaneous gene targeting by virtue of undetectable levels of random integration. Thus, DNA polymerase θ-mediated end joining is the sole homology-independent repair route in the absence of NHEJ and, intriguingly, their combined absence reveals rare Alu-Alu recombination events utilizing a stretch of homology. Our findings provide new insights into the mechanics of foreign DNA integration and the role of DNA polymerase θ in human genome maintenance.
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Affiliation(s)
- Shinta Saito
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama 236-0027, Japan
| | - Ryo Maeda
- Department of Biology, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| | - Noritaka Adachi
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama 236-0027, Japan
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
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113
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Zelensky AN, Schimmel J, Kool H, Kanaar R, Tijsterman M. Inactivation of Pol θ and C-NHEJ eliminates off-target integration of exogenous DNA. Nat Commun 2017; 8:66. [PMID: 28687761 PMCID: PMC5501794 DOI: 10.1038/s41467-017-00124-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 06/01/2017] [Indexed: 11/09/2022] Open
Abstract
Off-target or random integration of exogenous DNA hampers precise genomic engineering and presents a safety risk in clinical gene therapy strategies. Genetic definition of random integration has been lacking for decades. Here, we show that the A-family DNA polymerase θ (Pol θ) promotes random integration, while canonical non-homologous DNA end joining plays a secondary role; cells double deficient for polymerase θ and canonical non-homologous DNA end joining are devoid of any integration events, demonstrating that these two mechanisms define random integration. In contrast, homologous recombination is not reduced in these cells and gene targeting is improved to 100% efficiency. Such complete reversal of integration outcome, from predominately random integration to exclusively gene targeting, provides a rational way forward to improve the efficacy and safety of DNA delivery and gene correction approaches.Random off-target integration events can impair precise gene targeting and poses a safety risk for gene therapy. Here the authors show that repression of polymerase θ and classical non-homologous recombination eliminates random integration.
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Affiliation(s)
- Alex N Zelensky
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Centre, Rotterdam,, 3000 CA, The Netherlands
| | - Joost Schimmel
- Department of Human Genetics, Leiden University Medical Centre, PO Box 9600, Leiden,, 2300 RC, The Netherlands
| | - Hanneke Kool
- Department of Human Genetics, Leiden University Medical Centre, PO Box 9600, Leiden,, 2300 RC, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Centre, Rotterdam,, 3000 CA, The Netherlands.
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Centre, PO Box 9600, Leiden,, 2300 RC, The Netherlands.
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114
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Moore JM, Correa R, Rosenberg SM, Hastings PJ. Persistent damaged bases in DNA allow mutagenic break repair in Escherichia coli. PLoS Genet 2017; 13:e1006733. [PMID: 28727736 PMCID: PMC5542668 DOI: 10.1371/journal.pgen.1006733] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 08/03/2017] [Accepted: 04/03/2017] [Indexed: 12/31/2022] Open
Abstract
Bacteria, yeast and human cancer cells possess mechanisms of mutagenesis upregulated by stress responses. Stress-inducible mutagenesis potentially accelerates adaptation, and may provide important models for mutagenesis that drives cancers, host pathogen interactions, antibiotic resistance and possibly much of evolution generally. In Escherichia coli repair of double-strand breaks (DSBs) becomes mutagenic, using low-fidelity DNA polymerases under the control of the SOS DNA-damage response and RpoS general stress response, which upregulate and allow the action of error-prone DNA polymerases IV (DinB), II and V to make mutations during repair. Pol IV is implied to compete with and replace high-fidelity DNA polymerases at the DSB-repair replisome, causing mutagenesis. We report that up-regulated Pol IV is not sufficient for mutagenic break repair (MBR); damaged bases in the DNA are also required, and that in starvation-stressed cells, these are caused by reactive-oxygen species (ROS). First, MBR is reduced by either ROS-scavenging agents or constitutive activation of oxidative-damage responses, both of which reduce cellular ROS levels. The ROS promote MBR other than by causing DSBs, saturating mismatch repair, oxidizing proteins, or inducing the SOS response or the general stress response. We find that ROS drive MBR through oxidized guanines (8-oxo-dG) in DNA, in that overproduction of a glycosylase that removes 8-oxo-dG from DNA prevents MBR. Further, other damaged DNA bases can substitute for 8-oxo-dG because ROS-scavenged cells resume MBR if either DNA pyrimidine dimers or alkylated bases are induced. We hypothesize that damaged bases in DNA pause the replisome and allow the critical switch from high fidelity to error-prone DNA polymerases in the DSB-repair replisome, thus allowing MBR. The data imply that in addition to the indirect stress-response controlled switch to MBR, a direct cis-acting switch to MBR occurs independently of DNA breakage, caused by ROS oxidation of DNA potentially regulated by ROS regulators.
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Affiliation(s)
- Jessica M. Moore
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Raul Correa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Susan M. Rosenberg
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - P. J. Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
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115
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Beagan K, Armstrong RL, Witsell A, Roy U, Renedo N, Baker AE, Schärer OD, McVey M. Drosophila DNA polymerase theta utilizes both helicase-like and polymerase domains during microhomology-mediated end joining and interstrand crosslink repair. PLoS Genet 2017; 13:e1006813. [PMID: 28542210 PMCID: PMC5466332 DOI: 10.1371/journal.pgen.1006813] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 06/09/2017] [Accepted: 05/12/2017] [Indexed: 11/20/2022] Open
Abstract
Double strand breaks (DSBs) and interstrand crosslinks (ICLs) are toxic DNA lesions that can be repaired through multiple pathways, some of which involve shared proteins. One of these proteins, DNA Polymerase θ (Pol θ), coordinates a mutagenic DSB repair pathway named microhomology-mediated end joining (MMEJ) and is also a critical component for bypass or repair of ICLs in several organisms. Pol θ contains both polymerase and helicase-like domains that are tethered by an unstructured central region. While the role of the polymerase domain in promoting MMEJ has been studied extensively both in vitro and in vivo, a function for the helicase-like domain, which possesses DNA-dependent ATPase activity, remains unclear. Here, we utilize genetic and biochemical analyses to examine the roles of the helicase-like and polymerase domains of Drosophila Pol θ. We demonstrate an absolute requirement for both polymerase and ATPase activities during ICL repair in vivo. However, similar to mammalian systems, polymerase activity, but not ATPase activity, is required for ionizing radiation-induced DSB repair. Using a site-specific break repair assay, we show that overall end-joining efficiency is not affected in ATPase-dead mutants, but there is a significant decrease in templated insertion events. In vitro, Pol θ can efficiently bypass a model unhooked nitrogen mustard crosslink and promote DNA synthesis following microhomology annealing, although ATPase activity is not required for these functions. Together, our data illustrate the functional importance of the helicase-like domain of Pol θ and suggest that its tethering to the polymerase domain is important for its multiple functions in DNA repair and damage tolerance. Error-prone DNA Polymerase θ (Pol θ) plays a conserved role in a mutagenic DNA double-strand break repair mechanism called microhomology-mediated end joining (MMEJ). In many organisms, it also participates in a process crucial to the removal/repair of DNA interstrand crosslinks. The exact mechanism by which Pol θ promotes these processes is unclear, but a clue may lie in its dual-domain structure. While the role of its polymerase domain has been well-studied, the function of its helicase-like domain remains an open question. Here we report an absolute requirement for ATPase activity of the helicase-like domain during interstrand crosslink repair in Drosophila melanogaster. We also find that although end joining frequency does not decrease in ATPase-dead mutants, ATPase activity is critical for generating templated insertions. Using purified Pol θ protein, we show that it can bypass synthetic substrates mimicking interstrand crosslink intermediates and can promote MMEJ-like reactions with partial double-stranded and single-stranded DNA. Together, these data demonstrate a novel function for the helicase-like domain of Pol θ in both interstrand crosslink repair and MMEJ and provide insight into why the dual-domain structure has been conserved throughout evolution.
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Affiliation(s)
- Kelly Beagan
- Department of Biology, Tufts University, Medford, Massachusetts
| | | | - Alice Witsell
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Upasana Roy
- Department of Chemistry and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Nikolai Renedo
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Amy E. Baker
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Orlando D. Schärer
- Department of Chemistry and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, United States of America
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea and Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Mitch McVey
- Department of Biology, Tufts University, Medford, Massachusetts
- * E-mail:
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116
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Malaby AW, Martin SK, Wood RD, Doublié S. Expression and Structural Analyses of Human DNA Polymerase θ (POLQ). Methods Enzymol 2017; 592:103-121. [PMID: 28668117 PMCID: PMC5624038 DOI: 10.1016/bs.mie.2017.03.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DNA polymerase theta (pol θ) is an evolutionarily conserved protein encoded by the POLQ gene in mammalian genomes. Pol θ is the defining enzyme for a pathway of DSB repair termed "alternative end-joining" (altEJ) or "theta-mediated end-joining." This pathway contributes significantly to the radiation resistance of mammalian cells. It also modulates accuracy in repair of breaks that occur at stalled DNA replication forks, during diversification steps of the mammalian immune system, during repair of CRISPR-Cas9, and in many DNA integration events. Pol θ is a potentially important clinical target, particularly for cancers deficient in other break repair strategies. The enzyme is uniquely able to mediate joining of single-stranded 3' ends. Because of these unusual biochemical properties and its therapeutic importance, it is essential to study structures of pol θ bound to DNA. However, challenges for expression and purification are presented by the large size of pol θ (2590 residues in humans) and unusual juxtaposition of domains (a helicase-like domain and distinct DNA polymerase, separated by a region predicted to be largely disordered). Here we summarize work on the expression and purification of the full-length protein, and then focus on the design, expression, and purification of an active C-terminal polymerase fragment. The generation of this active construct was nontrivial and time consuming. Almost all published biochemical work to date has been performed with this domain fragment. Strategies to obtain and improve crystals of a ternary pol θ complex (enzyme:DNA:nucleotide) are also presented, along with key elements of the structure.
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Affiliation(s)
| | - Sara K Martin
- The University of Texas MD Anderson Cancer Center, Smithville, TX, United States; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Richard D Wood
- The University of Texas MD Anderson Cancer Center, Smithville, TX, United States; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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117
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Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol 2017; 18:495-506. [PMID: 28512351 DOI: 10.1038/nrm.2017.48] [Citation(s) in RCA: 1019] [Impact Index Per Article: 145.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA double-strand breaks (DSBs) are the most dangerous type of DNA damage because they can result in the loss of large chromosomal regions. In all mammalian cells, DSBs that occur throughout the cell cycle are repaired predominantly by the non-homologous DNA end joining (NHEJ) pathway. Defects in NHEJ result in sensitivity to ionizing radiation and the ablation of lymphocytes. The NHEJ pathway utilizes proteins that recognize, resect, polymerize and ligate the DNA ends in a flexible manner. This flexibility permits NHEJ to function on a wide range of DNA-end configurations, with the resulting repaired DNA junctions often containing mutations. In this Review, we discuss the most recent findings regarding the relative involvement of the different NHEJ proteins in the repair of various DNA-end configurations. We also discuss the shunting of DNA-end repair to the auxiliary pathways of alternative end joining (a-EJ) or single-strand annealing (SSA) and the relevance of these different pathways to human disease.
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118
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van Bostelen I, Tijsterman M. Combined loss of three DNA damage response pathways renders C. elegans intolerant to light. DNA Repair (Amst) 2017; 54:55-62. [PMID: 28472716 DOI: 10.1016/j.dnarep.2017.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/17/2017] [Accepted: 04/10/2017] [Indexed: 12/20/2022]
Abstract
Infliction of DNA damage initiates a complex cellular reaction - the DNA damage response - that involves both signaling and DNA repair networks with many redundancies and parallel pathways. Here, we reveal the three strategies that the simple multicellular eukaryote, C. elegans, uses to deal with DNA damage induced by light. Separately inactivating repair or replicative bypass of photo-lesions results in cellular hypersensitivity towards UV-light, but impeding repair of replication associated DNA breaks does not. Yet, we observe an unprecedented synergistic relationship when these pathways are inactivated in combination. C. elegans mutants that lack nucleotide excision repair (NER), translesion synthesis (TLS) and alternative end joining (altEJ) grow undisturbed in the dark, but become sterile when grown in light. Even exposure to very low levels of normal daylight impedes animal growth. We show that NER and TLS operate to suppress the formation of lethal DNA breaks that require polymerase theta-mediated end joining (TMEJ) for their repair. Our data testifies to the enormous genotoxicity of light and to the demand of multiple layers of protection against an environmental threat that is so common.
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Affiliation(s)
- Ivo van Bostelen
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC, Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC, Leiden, The Netherlands.
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119
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Kolinjivadi AM, Sannino V, de Antoni A, Técher H, Baldi G, Costanzo V. Moonlighting at replication forks - a new life for homologous recombination proteins BRCA1, BRCA2 and RAD51. FEBS Lett 2017; 591:1083-1100. [PMID: 28079255 DOI: 10.1002/1873-3468.12556] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 12/27/2016] [Accepted: 01/09/2017] [Indexed: 12/30/2022]
Abstract
Coordination between DNA replication and DNA repair ensures maintenance of genome integrity, which is lost in cancer cells. Emerging evidence has linked homologous recombination (HR) proteins RAD51, BRCA1 and BRCA2 to the stability of nascent DNA. This function appears to be distinct from double-strand break (DSB) repair and is in part due to the prevention of MRE11-mediated degradation of nascent DNA at stalled forks. The role of RAD51 in fork protection resembles the activity described for its prokaryotic orthologue RecA, which prevents nuclease-mediated degradation of DNA and promotes replication fork restart in cells challenged by DNA-damaging agents. Here, we examine the mechanistic aspects of HR-mediated fork protection, addressing the crosstalk between HR and replication proteins.
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Affiliation(s)
| | - Vincenzo Sannino
- DNA metabolism laboratory, IFOM-The Firc Institute of Molecular Oncology, Milan, Italy
| | - Anna de Antoni
- DNA metabolism laboratory, IFOM-The Firc Institute of Molecular Oncology, Milan, Italy
| | - Hervé Técher
- DNA metabolism laboratory, IFOM-The Firc Institute of Molecular Oncology, Milan, Italy
| | - Giorgio Baldi
- DNA metabolism laboratory, IFOM-The Firc Institute of Molecular Oncology, Milan, Italy
| | - Vincenzo Costanzo
- DNA metabolism laboratory, IFOM-The Firc Institute of Molecular Oncology, Milan, Italy
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120
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Xu H, Di Antonio M, McKinney S, Mathew V, Ho B, O'Neil NJ, Santos ND, Silvester J, Wei V, Garcia J, Kabeer F, Lai D, Soriano P, Banáth J, Chiu DS, Yap D, Le DD, Ye FB, Zhang A, Thu K, Soong J, Lin SC, Tsai AHC, Osako T, Algara T, Saunders DN, Wong J, Xian J, Bally MB, Brenton JD, Brown GW, Shah SP, Cescon D, Mak TW, Caldas C, Stirling PC, Hieter P, Balasubramanian S, Aparicio S. CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours. Nat Commun 2017; 8:14432. [PMID: 28211448 PMCID: PMC5321743 DOI: 10.1038/ncomms14432] [Citation(s) in RCA: 346] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 12/28/2016] [Indexed: 12/29/2022] Open
Abstract
G-quadruplex DNAs form four-stranded helical structures and are proposed to play key roles in different cellular processes. Targeting G-quadruplex DNAs for cancer treatment is a very promising prospect. Here, we show that CX-5461 is a G-quadruplex stabilizer, with specific toxicity against BRCA deficiencies in cancer cells and polyclonal patient-derived xenograft models, including tumours resistant to PARP inhibition. Exposure to CX-5461, and its related drug CX-3543, blocks replication forks and induces ssDNA gaps or breaks. The BRCA and NHEJ pathways are required for the repair of CX-5461 and CX-3543-induced DNA damage and failure to do so leads to lethality. These data strengthen the concept of G4 targeting as a therapeutic approach, specifically for targeting HR and NHEJ deficient cancers and other tumours deficient for DNA damage repair. CX-5461 is now in advanced phase I clinical trial for patients with BRCA1/2 deficient tumours (Canadian trial, NCT02719977, opened May 2016).
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Affiliation(s)
- Hong Xu
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Marco Di Antonio
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Steven McKinney
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Veena Mathew
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Brandon Ho
- Department of Biochemistry and Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada M5S 3E1
| | - Nigel J. O'Neil
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Nancy Dos Santos
- Advanced Therapeutics, BC Cancer Agency and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Jennifer Silvester
- Campbell Family Institute for Breast Cancer Research, Princess Margret Cancer Centre, 610 University Avenue, Toronto, Canada M5G 2M9
| | - Vivien Wei
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Jessica Garcia
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Farhia Kabeer
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Daniel Lai
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Priscilla Soriano
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Judit Banáth
- Department of Integrative Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Derek S. Chiu
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Damian Yap
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Daniel D. Le
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Frank B. Ye
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Anni Zhang
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Kelsie Thu
- Campbell Family Institute for Breast Cancer Research, Princess Margret Cancer Centre, 610 University Avenue, Toronto, Canada M5G 2M9
| | - John Soong
- Senhwa Biosciences, Inc., 9 F, No.205-1, Section 3, Peihsin Road, Hsintien District, New Taipei City 23143, Taiwan R.O.C
| | - Shu-chuan Lin
- Senhwa Biosciences, Inc., 9 F, No.205-1, Section 3, Peihsin Road, Hsintien District, New Taipei City 23143, Taiwan R.O.C
| | - Angela Hsin Chin Tsai
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Tomo Osako
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Teresa Algara
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Darren N. Saunders
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Jason Wong
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Jian Xian
- Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Marcel B. Bally
- Advanced Therapeutics, BC Cancer Agency and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - James D. Brenton
- Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Grant W. Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada M5S 3E1
| | - Sohrab P. Shah
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - David Cescon
- Campbell Family Institute for Breast Cancer Research, Princess Margret Cancer Centre, 610 University Avenue, Toronto, Canada M5G 2M9
- Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto, Canada M5S 1A8
| | - Tak W. Mak
- Campbell Family Institute for Breast Cancer Research, Princess Margret Cancer Centre, 610 University Avenue, Toronto, Canada M5G 2M9
| | - Carlos Caldas
- Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Peter C. Stirling
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
| | - Phil Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, and Department of Pathology and Laboratory Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
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121
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Shen H, Strunks GD, Klemann BJPM, Hooykaas PJJ, de Pater S. CRISPR/Cas9-Induced Double-Strand Break Repair in Arabidopsis Nonhomologous End-Joining Mutants. G3 (BETHESDA, MD.) 2017; 7:193-202. [PMID: 27866150 PMCID: PMC5217109 DOI: 10.1534/g3.116.035204] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/03/2016] [Indexed: 01/31/2023]
Abstract
Double-strand breaks (DSBs) are one of the most harmful DNA lesions. Cells utilize two main pathways for DSB repair: homologous recombination (HR) and nonhomologous end-joining (NHEJ). NHEJ can be subdivided into the KU-dependent classical NHEJ (c-NHEJ) and the more error-prone KU-independent backup-NHEJ (b-NHEJ) pathways, involving the poly (ADP-ribose) polymerases (PARPs). However, in the absence of these factors, cells still seem able to adequately maintain genome integrity, suggesting the presence of other b-NHEJ repair factors or pathways independent from KU and PARPs. The outcome of DSB repair by NHEJ pathways can be investigated by using artificial sequence-specific nucleases such as CRISPR/Cas9 to induce DSBs at a target of interest. Here, we used CRISPR/Cas9 for DSB induction at the Arabidopsis cruciferin 3 (CRU3) and protoporphyrinogen oxidase (PPO) genes. DSB repair outcomes via NHEJ were analyzed using footprint analysis in wild-type plants and plants deficient in key factors of c-NHEJ (ku80), b-NHEJ (parp1 parp2), or both (ku80 parp1 parp2). We found that larger deletions of >20 bp predominated after DSB repair in ku80 and ku80 parp1 parp2 mutants, corroborating with a role of KU in preventing DSB end resection. Deletion lengths did not significantly differ between ku80 and ku80 parp1 parp2 mutants, suggesting that a KU- and PARP-independent b-NHEJ mechanism becomes active in these mutants. Furthermore, microhomologies and templated insertions were observed at the repair junctions in the wild type and all mutants. Since these characteristics are hallmarks of polymerase θ-mediated DSB repair, we suggest a possible role for this recently discovered polymerase in DSB repair in plants.
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Affiliation(s)
- Hexi Shen
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, 2333 BE, The Netherlands
| | - Gary D Strunks
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, 2333 BE, The Netherlands
| | - Bart J P M Klemann
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, 2333 BE, The Netherlands
| | - Paul J J Hooykaas
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, 2333 BE, The Netherlands
| | - Sylvia de Pater
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, 2333 BE, The Netherlands
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122
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Hoang TM, Kent T, Pomerantz RT. Modification of 3' Terminal Ends of DNA and RNA Using DNA Polymerase θ Terminal Transferase Activity. Bio Protoc 2017; 7:e2330. [PMID: 28824932 DOI: 10.21769/bioprotoc.2330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
DNA polymerase θ (Polθ) is a promiscuous enzyme that is essential for the error-prone DNA double-strand break (DSB) repair pathway called alternative end-joining (alt-EJ). During this form of DSB repair, Polθ performs terminal transferase activity at the 3' termini of resected DSBs via templated and non-templated nucleotide addition cycles. Since human Polθ is able to modify the 3' terminal ends of both DNA and RNA with a wide array of large and diverse ribonucleotide and deoxyribonucleotide analogs, its terminal transferase activity is more useful for biotechnology applications than terminal deoxynucleotidyl transferase (TdT). Here, we present in detail simple methods by which purified human Polθ is utilized to modify the 3' terminal ends of RNA and DNA for various applications in biotechnology and biomedical research.
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Affiliation(s)
- Trung M Hoang
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Tatiana Kent
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Richard T Pomerantz
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
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123
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Boussaha M, Michot P, Letaief R, Hozé C, Fritz S, Grohs C, Esquerré D, Duchesne A, Philippe R, Blanquet V, Phocas F, Floriot S, Rocha D, Klopp C, Capitan A, Boichard D. Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences. Genet Sel Evol 2016; 48:87. [PMID: 27846802 PMCID: PMC5111192 DOI: 10.1186/s12711-016-0268-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 11/04/2016] [Indexed: 12/22/2022] Open
Abstract
Background In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability. Results In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data. Conclusions To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0268-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Pauline Michot
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Rabia Letaief
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Chris Hozé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Sébastien Fritz
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Diane Esquerré
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Amandine Duchesne
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Romain Philippe
- GMA, INRA, Université de Limoges, 87060, Limoges Cedex, France
| | | | - Florence Phocas
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Sandrine Floriot
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Aurélien Capitan
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Didier Boichard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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124
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Multiple mechanisms contribute to double-strand break repair at rereplication forks in Drosophila follicle cells. Proc Natl Acad Sci U S A 2016; 113:13809-13814. [PMID: 27849606 DOI: 10.1073/pnas.1617110113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rereplication generates double-strand breaks (DSBs) at sites of fork collisions and causes genomic damage, including repeat instability and chromosomal aberrations. However, the primary mechanism used to repair rereplication DSBs varies across different experimental systems. In Drosophila follicle cells, developmentally regulated rereplication is used to amplify six genomic regions, two of which contain genes encoding eggshell proteins. We have exploited this system to test the roles of several DSB repair pathways during rereplication, using fork progression as a readout for DSB repair efficiency. Here we show that a null mutation in the microhomology-mediated end-joining (MMEJ) component, polymerase θ/mutagen-sensitive 308 (mus308), exhibits a sporadic thin eggshell phenotype and reduced chorion gene expression. Unlike other thin eggshell mutants, mus308 displays normal origin firing but reduced fork progression at two regions of rereplication. We also find that MMEJ compensates for loss of nonhomologous end joining to repair rereplication DSBs in a site-specific manner. Conversely, we show that fork progression is enhanced in the absence of both Drosophila Rad51 homologs, spindle-A and spindle-B, revealing homologous recombination is active and actually impairs fork movement during follicle cell rereplication. These results demonstrate that several DSB repair pathways are used during rereplication in the follicle cells and their contribution to productive fork progression is influenced by genomic position and repair pathway competition. Furthermore, our findings illustrate that specific rereplication DSB repair pathways can have major effects on cellular physiology, dependent upon genomic context.
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125
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Stanton A, Harris LM, Graham G, Merrick CJ. Recombination events among virulence genes in malaria parasites are associated with G-quadruplex-forming DNA motifs. BMC Genomics 2016; 17:859. [PMID: 27809775 PMCID: PMC5093961 DOI: 10.1186/s12864-016-3183-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/21/2016] [Indexed: 11/10/2022] Open
Abstract
Background Malaria parasites of the genus Plasmodium possess large hyper-variable families of antigen-encoding genes. These are often variantly-expressed and are major virulence factors for immune evasion and the maintenance of chronic infections. Recombination and diversification of these gene families occurs readily, and may be promoted by G-quadruplex (G4) DNA motifs within and close to the variant genes. G4s have been shown to cause replication fork stalling, DNA breakage and recombination in model systems, but these motifs remain largely unstudied in Plasmodium. Results We examined the nature and distribution of putative G4-forming sequences in multiple Plasmodium genomes, finding that their co-distribution with variant gene families is conserved across different Plasmodium species that have different types of variant gene families. In P. falciparum, where a large set of recombination events that occurred over time in cultured parasites has been mapped, we found a strong spatial association between these recombination events and putative G4-forming sequences. Finally, we searched Plasmodium genomes for the three classes of helicase that can unwind G4s: Plasmodium spp. have no identifiable homologue of the highly efficient G4 helicase PIF1, but they do encode two putative RecQ helicases and one homologue of the RAD3-family helicase FANCJ. Conclusions Our analyses, conducted at the whole-genome level in multiple species of Plasmodium, support the concept that G4s are likely to be involved in recombination and diversification of antigen-encoding gene families in this important protozoan pathogen. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3183-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam Stanton
- School of Computing and Mathematics, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST55BG, UK
| | - Lynne M Harris
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST55BG, UK
| | - Gemma Graham
- School of Medicine, Keele University, Keele, Staffordshire, ST55BG, UK
| | - Catherine J Merrick
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST55BG, UK.
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126
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Valton AL, Prioleau MN. G-Quadruplexes in DNA Replication: A Problem or a Necessity? Trends Genet 2016; 32:697-706. [DOI: 10.1016/j.tig.2016.09.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/01/2016] [Indexed: 10/21/2022]
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127
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van Kregten M, de Pater S, Romeijn R, van Schendel R, Hooykaas PJJ, Tijsterman M. T-DNA integration in plants results from polymerase-θ-mediated DNA repair. NATURE PLANTS 2016; 2:16164. [PMID: 27797358 DOI: 10.1038/nplants.2016.164] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/27/2016] [Indexed: 05/22/2023]
Abstract
Agrobacterium tumefaciens is a pathogenic bacterium, which transforms plants by transferring a discrete segment of its DNA, the T-DNA, to plant cells. The T-DNA then integrates into the plant genome. T-DNA biotechnology is widely exploited in the genetic engineering of model plants and crops. However, the molecular mechanism underlying T-DNA integration remains unknown1. Here we demonstrate that in Arabidopsis thaliana T-DNA integration critically depends on polymerase theta (Pol θ). We find that TEBICHI/POLQ mutant plants (which have mutated Pol θ), although susceptible to Agrobacterium infection, are resistant to T-DNA integration. Characterization of >10,000 T-DNA-plant genome junctions reveals a distinct signature of Pol θ action and also indicates that 3' end capture at genomic breaks is the prevalent mechanism of T-DNA integration. The primer-template switching ability of Pol θ can explain the molecular patchwork known as filler DNA that is frequently observed at sites of integration. T-DNA integration signatures in other plant species closely resemble those of Arabidopsis, suggesting that Pol-θ-mediated integration is evolutionarily conserved. Thus, Pol θ provides the mechanism for T-DNA random integration into the plant genome, demonstrating a potential to disrupt random integration so as to improve the quality and biosafety of plant transgenesis.
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Affiliation(s)
- Maartje van Kregten
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Sylvia de Pater
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Ron Romeijn
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Paul J J Hooykaas
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
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128
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Dai CH, Chen P, Li J, Lan T, Chen YC, Qian H, Chen K, Li MY. Co-inhibition of pol θ and HR genes efficiently synergize with cisplatin to suppress cisplatin-resistant lung cancer cells survival. Oncotarget 2016; 7:65157-65170. [PMID: 27533083 PMCID: PMC5323145 DOI: 10.18632/oncotarget.11214] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 07/18/2016] [Indexed: 12/14/2022] Open
Abstract
Cisplatin exert its anticancer effect by creating intrastrand and interstrand DNA cross-links which block DNA replication and is a major drug used to treat lung cancer. However, the main obstacle of the efficacy of treatment is drug resistance. Here, we show that expression of translesion synthesis (TLS) polymerase Q (POLQ) was significantly elevated by exposure of lung cancer cells A549/DR (a cisplatin-resistant A549 cell line) to cisplatin. POLQ expression correlated inversely with homologous recombination (HR) activity. Co-depletion of BRCA2 and POLQ by siRNA markedly increased sensitivity of A549/DR cells to cisplatin, which was accompanied with impairment of double strand breaks (DSBs) repair reflected by prominent cell cycle checkpoint response, increased chromosomal aberrations and persistent colocalization of p-ATM and 53BP1 foci induced by cisplatin. Thus, co-knockdown of POLQ and HR can efficiently synergize with cisplatin to inhibit A549/DR cell survival by inhibiting DNA DSBs repair. Similar results were observed in A549/DR cells co-depleted of BRCA2 and POLQ following BMN673 (a PARP inhibitor) treatment. Importantly, the sensitization effects to cisplatin and BMN673 in A549/DR cells by co-depleting BRCA2 and POLQ was stronger than those by co-depleting BRCA2 and other TLS factors including POLH, REV3, or REV1. Our results indicate that there is a synthetic lethal relationship between pol θ-mediated DNA repair and HR pathways. Pol θ may be considered as a novel target for lung cancer therapy.
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Affiliation(s)
- Chun-Hua Dai
- Department of Radiation Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Ping Chen
- Department of Pulmonary Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Jian Li
- Department of Pulmonary Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Tin Lan
- Institute of Medical Science, Jiangsu University, Zhenjiang, China
| | - Yong-Chang Chen
- Institute of Medical Science, Jiangsu University, Zhenjiang, China
| | - Hai Qian
- Institute of Medical Science, Jiangsu University, Zhenjiang, China
| | - Kang Chen
- Department of Pulmonary Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Mei-Yu Li
- Department of Pulmonary Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
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129
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van Schendel R, van Heteren J, Welten R, Tijsterman M. Genomic Scars Generated by Polymerase Theta Reveal the Versatile Mechanism of Alternative End-Joining. PLoS Genet 2016; 12:e1006368. [PMID: 27755535 PMCID: PMC5068794 DOI: 10.1371/journal.pgen.1006368] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/16/2016] [Indexed: 12/22/2022] Open
Abstract
For more than half a century, genotoxic agents have been used to induce mutations in the genome of model organisms to establish genotype-phenotype relationships. While inaccurate replication across damaged bases can explain the formation of single nucleotide variants, it remained unknown how DNA damage induces more severe genomic alterations. Here, we demonstrate for two of the most widely used mutagens, i.e. ethyl methanesulfonate (EMS) and photo-activated trimethylpsoralen (UV/TMP), that deletion mutagenesis is the result of polymerase Theta (POLQ)-mediated end joining (TMEJ) of double strand breaks (DSBs). This discovery allowed us to survey many thousands of available C. elegans deletion alleles to address the biology of this alternative end-joining repair mechanism. Analysis of ~7,000 deletion breakpoints and their cognate junctions reveals a distinct order of events. We found that nascent strands blocked at sites of DNA damage can engage in one or more cycles of primer extension using a more downstream located break end as a template. Resolution is accomplished when 3' overhangs have matching ends. Our study provides a step-wise and versatile model for the in vivo mechanism of POLQ action, which explains the molecular nature of mutagen-induced deletion alleles.
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Affiliation(s)
- Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jane van Heteren
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Richard Welten
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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130
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Black SJ, Kashkina E, Kent T, Pomerantz RT. DNA Polymerase θ: A Unique Multifunctional End-Joining Machine. Genes (Basel) 2016; 7:E67. [PMID: 27657134 PMCID: PMC5042397 DOI: 10.3390/genes7090067] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/02/2016] [Accepted: 09/08/2016] [Indexed: 01/01/2023] Open
Abstract
The gene encoding DNA polymerase θ (Polθ) was discovered over ten years ago as having a role in suppressing genome instability in mammalian cells. Studies have now clearly documented an essential function for this unique A-family polymerase in the double-strand break (DSB) repair pathway alternative end-joining (alt-EJ), also known as microhomology-mediated end-joining (MMEJ), in metazoans. Biochemical and cellular studies show that Polθ exhibits a unique ability to perform alt-EJ and during this process the polymerase generates insertion mutations due to its robust terminal transferase activity which involves template-dependent and independent modes of DNA synthesis. Intriguingly, the POLQ gene also encodes for a conserved superfamily 2 Hel308-type ATP-dependent helicase domain which likely assists in alt-EJ and was reported to suppress homologous recombination (HR) via its anti-recombinase activity. Here, we review our current knowledge of Polθ-mediated end-joining, the specific activities of the polymerase and helicase domains, and put into perspective how this multifunctional enzyme promotes alt-EJ repair of DSBs formed during S and G2 cell cycle phases.
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Affiliation(s)
- Samuel J Black
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
| | - Ekaterina Kashkina
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
| | - Tatiana Kent
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
| | - Richard T Pomerantz
- Fels Institute for Cancer Research, Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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131
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Willis NA, Scully R. DNA Polymerase θ: Duct Tape and Zip Ties for a Fragile Genome. Mol Cell 2016; 63:542-544. [PMID: 27540853 DOI: 10.1016/j.molcel.2016.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Using a combination of genetics and cellular DNA rejoining assays, in this issue of Molecular Cell, Wyatt et al. (2016) demonstrate a critical role for mammalian DNA polymerase θ in the rejoining of DNA ends that are poor substrates for classical non-homologous end joining.
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Affiliation(s)
- Nicholas A Willis
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Ralph Scully
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA.
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132
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Abstract
DNA polymerase theta (pol θ) is encoded in the genomes of many eukaryotes, though not in fungi. Pol θ is encoded by the POLQ gene in mammalian cells. The C-terminal third of the protein is a family A DNA polymerase with additional insertion elements relative to prokaryotic homologs. The N-terminal third is a helicase-like domain with DNA-dependent ATPase activity. Pol θ is important in the repair of genomic double-strand breaks (DSBs) from many sources. These include breaks formed by ionizing radiation and topoisomerase inhibitors, breaks arising at stalled DNA replication forks, breaks introduced during diversification steps of the mammalian immune system, and DSB induced by CRISPR-Cas9. Pol θ participates in a route of DSB repair termed "alternative end-joining" (altEJ). AltEJ is independent of the DNA binding Ku protein complex and requires DNA end resection. Pol θ is able to mediate joining of two resected 3' ends harboring DNA sequence microhomology. "Signatures" of Pol θ action during altEJ are the frequent utilization of longer microhomologies, and the insertion of additional sequences at joining sites. The mechanism of end-joining employs the ability of Pol θ to tightly grasp a 3' terminus through unique contacts in the active site, allowing extension from minimally paired primers. Pol θ is involved in controlling the frequency of chromosome translocations and preserves genome integrity by limiting large deletions. It may also play a backup role in DNA base excision repair. POLQ is a member of a cluster of similarly upregulated genes that are strongly correlated with poor clinical outcome for breast cancer, ovarian cancer and other cancer types. Inhibition of pol θ is a compelling approach for combination therapy of radiosensitization.
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Affiliation(s)
- Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX 78957, USA; Graduate School of Biomedical Sciences at Houston, USA.
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405, USA.
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133
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Ahrabi S, Sarkar S, Pfister SX, Pirovano G, Higgins GS, Porter ACG, Humphrey TC. A role for human homologous recombination factors in suppressing microhomology-mediated end joining. Nucleic Acids Res 2016; 44:5743-57. [PMID: 27131361 PMCID: PMC4937322 DOI: 10.1093/nar/gkw326] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 04/13/2016] [Accepted: 04/14/2016] [Indexed: 12/22/2022] Open
Abstract
DNA double-strand breaks (DSBs) are toxic lesions, which if improperly repaired can result in cell death or genomic instability. DSB repair is usually facilitated by the classical non-homologous end joining (C-NHEJ), or homologous recombination (HR) pathways. However, a mutagenic alternative NHEJ pathway, microhomology-mediated end joining (MMEJ), can also be deployed. While MMEJ is suppressed by C-NHEJ, the relationship between HR and MMEJ is less clear. Here, we describe a role for HR genes in suppressing MMEJ in human cells. By monitoring DSB mis-repair using a sensitive HPRT assay, we found that depletion of HR proteins, including BRCA2, BRCA1 or RPA, resulted in a distinct mutational signature associated with significant increases in break-induced mutation frequencies, deletion lengths and the annealing of short regions of microhomology (2-6 bp) across the break-site. This signature was dependent on CtIP, MRE11, POLQ and PARP, and thus indicative of MMEJ. In contrast to CtIP or MRE11, depletion of BRCA1 resulted in increased partial resection and MMEJ, thus revealing a functional distinction between these early acting HR factors. Together these findings indicate that HR factors suppress mutagenic MMEJ following DSB resection.
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Affiliation(s)
- Sara Ahrabi
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sovan Sarkar
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sophia X Pfister
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Giacomo Pirovano
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Geoff S Higgins
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Andrew C G Porter
- Gene Targeting Group, Centre for Haematology, Imperial College Faculty of Medicine, London W12 0NN, UK
| | - Timothy C Humphrey
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
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134
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Getting Ready for the Dance: FANCJ Irons Out DNA Wrinkles. Genes (Basel) 2016; 7:genes7070031. [PMID: 27376332 PMCID: PMC4962001 DOI: 10.3390/genes7070031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/13/2016] [Accepted: 06/27/2016] [Indexed: 12/21/2022] Open
Abstract
Mounting evidence indicates that alternate DNA structures, which deviate from normal double helical DNA, form in vivo and influence cellular processes such as replication and transcription. However, our understanding of how the cellular machinery deals with unusual DNA structures such as G-quadruplexes (G4), triplexes, or hairpins is only beginning to emerge. New advances in the field implicate a direct role of the Fanconi Anemia Group J (FANCJ) helicase, which is linked to a hereditary chromosomal instability disorder and important for cancer suppression, in replication past unusual DNA obstacles. This work sets the stage for significant progress in dissecting the molecular mechanisms whereby replication perturbation by abnormal DNA structures leads to genomic instability. In this review, we focus on FANCJ and its role to enable efficient DNA replication when the fork encounters vastly abundant naturally occurring DNA obstacles, which may have implications for targeting rapidly dividing cancer cells.
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135
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Kent T, Mateos-Gomez PA, Sfeir A, Pomerantz RT. Polymerase θ is a robust terminal transferase that oscillates between three different mechanisms during end-joining. eLife 2016; 5:e13740. [PMID: 27311885 PMCID: PMC4912351 DOI: 10.7554/elife.13740] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/12/2016] [Indexed: 12/18/2022] Open
Abstract
DNA polymerase θ (Polθ) promotes insertion mutations during alternative end-joining (alt-EJ) by an unknown mechanism. Here, we discover that mammalian Polθ transfers nucleotides to the 3' terminus of DNA during alt-EJ in vitro and in vivo by oscillating between three different modes of terminal transferase activity: non-templated extension, templated extension in cis, and templated extension in trans. This switching mechanism requires manganese as a co-factor for Polθ template-independent activity and allows for random combinations of templated and non-templated nucleotide insertions. We further find that Polθ terminal transferase activity is most efficient on DNA containing 3' overhangs, is facilitated by an insertion loop and conserved residues that hold the 3' primer terminus, and is surprisingly more proficient than terminal deoxynucleotidyl transferase. In summary, this report identifies an unprecedented switching mechanism used by Polθ to generate genetic diversity during alt-EJ and characterizes Polθ as among the most proficient terminal transferases known.
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Affiliation(s)
- Tatiana Kent
- Fels Institute for Cancer Research, Temple University Lewis Katz School of Medicine, Philadelphia, United States
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, United States
| | - Pedro A Mateos-Gomez
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States
- Department of Cell Biology, New York University School of Medicine, New York, United States
| | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States
- Department of Cell Biology, New York University School of Medicine, New York, United States
| | - Richard T Pomerantz
- Fels Institute for Cancer Research, Temple University Lewis Katz School of Medicine, Philadelphia, United States
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, United States
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136
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Stop pulling my strings - what telomeres taught us about the DNA damage response. Nat Rev Mol Cell Biol 2016; 17:364-78. [PMID: 27165790 DOI: 10.1038/nrm.2016.43] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mammalian cells have evolved specialized mechanisms to sense and repair double-strand breaks (DSBs) to maintain genomic stability. However, in certain cases, the activity of these pathways can lead to aberrant DNA repair, genomic instability and tumorigenesis. One such case is DNA repair at the natural ends of linear chromosomes, known as telomeres, which can lead to chromosome-end fusions. Here, we review data obtained over the past decade and discuss the mechanisms that protect mammalian chromosome ends from the DNA damage response. We also discuss how telomere research has helped to uncover key steps in DSB repair. Last, we summarize how dysfunctional telomeres and the ensuing genomic instability drive the progression of cancer.
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137
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The expanding biology of the C9orf72 nucleotide repeat expansion in neurodegenerative disease. Nat Rev Neurosci 2016; 17:383-95. [PMID: 27150398 DOI: 10.1038/nrn.2016.38] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A nucleotide repeat expansion (NRE) within the chromosome 9 open reading frame 72 (C9orf72) gene was the first of this type of mutation to be linked to multiple neurological conditions, including amyotrophic lateral sclerosis and frontotemporal dementia. The pathogenic mechanisms through which the C9orf72 NRE contributes to these disorders include loss of C9orf72 function and gain-of-function mechanisms of C9orf72 driven by toxic RNA and protein species encoded by the NRE. These mechanisms have been linked to several cellular defects - including nucleocytoplasmic trafficking deficits and nuclear stress - that have been observed in both patients and animal models.
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138
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Thyme SB, Schier AF. Polq-Mediated End Joining Is Essential for Surviving DNA Double-Strand Breaks during Early Zebrafish Development. Cell Rep 2016; 15:707-714. [PMID: 27149851 DOI: 10.1016/j.celrep.2016.03.072] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 02/02/2016] [Accepted: 03/18/2016] [Indexed: 01/12/2023] Open
Abstract
Error-prone repair of DNA double-strand breaks (DSBs) has been postulated to occur through classical non-homologous end joining (NHEJ) in systems ranging from nematode somatic tissues to zebrafish embryos. Contrary to this model, we show that zebrafish embryos mutant for DNA polymerase theta (Polq), a critical component of alternative end joining (alt-EJ), cannot repair DSBs induced by CRISPR/Cas9 or ionizing radiation. In the absence of DSBs, polq mutants are phenotypically normal, but they do not survive mutagenesis and display dramatic differences in the mutation profiles compared with the wild-type. These results show that alt-EJ repair is essential and dominant during the early development of a vertebrate.
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Affiliation(s)
- Summer B Thyme
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA; Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; FAS Center for Systems Biology, Harvard University, MA 02138, USA.
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139
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Kostyrko K, Mermod N. Assays for DNA double-strand break repair by microhomology-based end-joining repair mechanisms. Nucleic Acids Res 2016; 44:e56. [PMID: 26657630 PMCID: PMC4824085 DOI: 10.1093/nar/gkv1349] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 11/17/2015] [Accepted: 11/19/2015] [Indexed: 11/16/2022] Open
Abstract
DNA double stranded breaks (DSBs) are one of the most deleterious types of DNA lesions. The main pathways responsible for repairing these breaks in eukaryotic cells are homologous recombination (HR) and non-homologous end-joining (NHEJ). However, a third group of still poorly characterized DSB repair pathways, collectively termed microhomology-mediated end-joining (MMEJ), relies on short homologies for the end-joining process. Here, we constructed GFP reporter assays to characterize and distinguish MMEJ variant pathways, namely the simple MMEJ and the DNA synthesis-dependent (SD)-MMEJ mechanisms. Transfection of these assay vectors in Chinese hamster ovary (CHO) cells and characterization of the repaired DNA sequences indicated that while simple MMEJ is able to mediate relatively efficient DSB repair if longer microhomologies are present, the majority of DSBs were repaired using the highly error-prone SD-MMEJ pathway. To validate the involvement of DNA synthesis in the repair process, siRNA knock-down of different genes proposed to play a role in MMEJ were performed, revealing that the knock-down of DNA polymerase θ inhibited DNA end resection and repair through simple MMEJ, thus favoring the other repair pathway. Overall, we conclude that this approach provides a convenient assay to study MMEJ-related DNA repair pathways.
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Affiliation(s)
- Kaja Kostyrko
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
| | - Nicolas Mermod
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
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140
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Beagan K, McVey M. Linking DNA polymerase theta structure and function in health and disease. Cell Mol Life Sci 2016; 73:603-15. [PMID: 26514729 PMCID: PMC4715478 DOI: 10.1007/s00018-015-2078-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/10/2015] [Accepted: 10/19/2015] [Indexed: 10/22/2022]
Abstract
DNA polymerase theta (Pol θ) is an error-prone A-family polymerase that is highly conserved among multicellular eukaryotes and plays multiple roles in DNA repair and the regulation of genome integrity. Studies conducted in several model organisms have shown that Pol θ can be utilized during DNA interstrand crosslink repair and during alternative end-joining repair of double-strand breaks. Recent genetic and biochemical studies have begun to elucidate the unique structural features of Pol θ that promote alternative end-joining repair. Importantly, Pol θ-dependent end joining appears to be important for overall genome stability, as it affects chromosome translocation formation in murine and human cell lines. Pol θ has also been suggested to act as a modifier of replication timing in human cells, though the mechanism of action remains unknown. Pol θ is highly upregulated in a number of human cancer types, which could indicate that mutagenic Pol θ-dependent end joining is used during cancer cell proliferation. Here, we review the various roles of Pol θ across species and discuss how these roles may be relevant to cancer therapy.
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Affiliation(s)
- Kelly Beagan
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA, 02155, USA
| | - Mitch McVey
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA, 02155, USA.
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141
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Rodgers K, McVey M. Error-Prone Repair of DNA Double-Strand Breaks. J Cell Physiol 2016; 231:15-24. [PMID: 26033759 DOI: 10.1002/jcp.25053] [Citation(s) in RCA: 240] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 05/20/2015] [Indexed: 12/14/2022]
Abstract
Preserving the integrity of the DNA double helix is crucial for the maintenance of genomic stability. Therefore, DNA double-strand breaks represent a serious threat to cells. In this review, we describe the two major strategies used to repair double strand breaks: non-homologous end joining and homologous recombination, emphasizing the mutagenic aspects of each. We focus on emerging evidence that homologous recombination, long thought to be an error-free repair process, can in fact be highly mutagenic, particularly in contexts requiring large amounts of DNA synthesis. Recent investigations have begun to illuminate the molecular mechanisms by which error-prone double-strand break repair can create major genomic changes, such as translocations and complex chromosome rearrangements. We highlight these studies and discuss proposed models that may explain some of the more extreme genetic changes observed in human cancers and congenital disorders.
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Affiliation(s)
- Kasey Rodgers
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Mitch McVey
- Department of Biology, Tufts University, Medford, Massachusetts
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142
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Systematic discovery of complex insertions and deletions in human cancers. Nat Med 2015; 22:97-104. [PMID: 26657142 PMCID: PMC5003782 DOI: 10.1038/nm.4002] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 11/03/2015] [Indexed: 12/25/2022]
Abstract
Complex insertions and deletions (indels) are formed by simultaneously deleting and inserting DNA fragments of different sizes at a common genomic location. Here we present a systematic analysis of somatic complex indels in the coding sequences of samples from over 8,000 cancer cases using Pindel-C. We discovered 285 complex indels in cancer-associated genes (such as PIK3R1, TP53, ARID1A, GATA3 and KMT2D) in approximately 3.5% of cases analyzed; nearly all instances of complex indels were overlooked (81.1%) or misannotated (17.6%) in previous reports of 2,199 samples. In-frame complex indels are enriched in PIK3R1 and EGFR, whereas frameshifts are prevalent in VHL, GATA3, TP53, ARID1A, PTEN and ATRX. Furthermore, complex indels display strong tissue specificity (such as VHL in kidney cancer samples and GATA3 in breast cancer samples). Finally, structural analyses support findings of previously missed, but potentially druggable, mutations in the EGFR, MET and KIT oncogenes. This study indicates the critical importance of improving complex indel discovery and interpretation in medical research.
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143
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Abstract
Chromosome rearrangement plays a causal role in tumorigenesis by contributing to the inactivation of tumor suppressor genes, the dysregulated expression or amplification of oncogenes and the generation of novel gene fusions. Chromosome breaks are important intermediates in this process. How, when and where these breaks arise and the specific mechanisms engaged in their repair strongly influence the resulting patterns of chromosome rearrangement. Here, we review recent progress in understanding how certain distinctive features of the cancer genome, including clustered mutagenesis, tandem segmental duplications, complex breakpoints, chromothripsis, chromoplexy and chromoanasynthesis may arise.
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144
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Lemmens B, van Schendel R, Tijsterman M. Mutagenic consequences of a single G-quadruplex demonstrate mitotic inheritance of DNA replication fork barriers. Nat Commun 2015; 6:8909. [PMID: 26563448 PMCID: PMC4654259 DOI: 10.1038/ncomms9909] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 10/14/2015] [Indexed: 12/29/2022] Open
Abstract
Faithful DNA replication is vital to prevent disease-causing mutations, chromosomal aberrations and malignant transformation. However, accuracy conflicts with pace and flexibility and cells rely on specialized polymerases and helicases to ensure effective and timely replication of genomes that contain DNA lesions or secondary structures. If and how cells can tolerate a permanent barrier to replication is, however, unknown. Here we show that a single unresolved G-quadruplexed DNA structure can persist through multiple mitotic divisions without changing conformation. Failed replication across a G-quadruplex causes single-strand DNA gaps that give rise to DNA double-strand breaks in subsequent cell divisions, which are processed by polymerase theta (POLQ)-mediated alternative end joining. Lineage tracing experiments further reveal that persistent G-quadruplexes cause genetic heterogeneity during organ development. Our data demonstrate that a single lesion can cause multiple unique genomic rearrangements, and that alternative end joining enables cells to proliferate in the presence of mitotically inherited replication blocks.
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Affiliation(s)
- Bennie Lemmens
- Department of Human Genetics, Leiden University Medical Center, Postzone S-4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Postzone S-4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Postzone S-4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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145
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Microhomology-Mediated End Joining: A Back-up Survival Mechanism or Dedicated Pathway? Trends Biochem Sci 2015; 40:701-714. [PMID: 26439531 DOI: 10.1016/j.tibs.2015.08.006] [Citation(s) in RCA: 401] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/13/2015] [Accepted: 08/18/2015] [Indexed: 12/12/2022]
Abstract
DNA double-strand breaks (DSBs) disrupt the continuity of chromosomes and their repair by error-free mechanisms is essential to preserve genome integrity. Microhomology-mediated end joining (MMEJ) is an error-prone repair mechanism that involves alignment of microhomologous sequences internal to the broken ends before joining, and is associated with deletions and insertions that mark the original break site, as well as chromosome translocations. Whether MMEJ has a physiological role or is simply a back-up repair mechanism is a matter of debate. Here we review recent findings pertaining to the mechanism of MMEJ and discuss its role in normal and cancer cells.
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146
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Abstract
Recent research has established clear connections between G-quadruplexes and human disease. Features of quadruplex structures that promote genomic instability have been determined. Quadruplexes have been identified as transcriptional, translational and epigenetic regulatory targets of factors associated with human genetic disease. An expandable GGGGCC motif that can adopt a G4 structure, located in the previously obscure C9ORF72 locus, has been shown to contribute to two well-recognized neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). This review focuses on these advances, which further dispel the view that genomic biology is limited to the confines of the canonical B-form DNA duplex, and show how quadruplexes contribute spatial and temporal dimensionalities to linear sequence information. This recent progress also has clear practical ramifications, as prevention, diagnosis, and treatment of disease depend on understanding the underlying mechanisms.
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147
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van Schendel R, Roerink SF, Portegijs V, van den Heuvel S, Tijsterman M. Polymerase Θ is a key driver of genome evolution and of CRISPR/Cas9-mediated mutagenesis. Nat Commun 2015; 6:7394. [PMID: 26077599 PMCID: PMC4490562 DOI: 10.1038/ncomms8394] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/04/2015] [Indexed: 12/22/2022] Open
Abstract
Cells are protected from toxic DNA double-stranded breaks (DSBs) by a number of DNA repair mechanisms, including some that are intrinsically error prone, thus resulting in mutations. To what extent these mechanisms contribute to evolutionary diversification remains unknown. Here, we demonstrate that the A-family polymerase theta (POLQ) is a major driver of inheritable genomic alterations in Caenorhabditis elegans. Unlike somatic cells, which use non-homologous end joining (NHEJ) to repair DNA transposon-induced DSBs, germ cells use polymerase theta-mediated end joining, a conceptually simple repair mechanism requiring only one nucleotide as a template for repair. Also CRISPR/Cas9-induced genomic changes are exclusively generated through polymerase theta-mediated end joining, refuting a previously assumed requirement for NHEJ in their formation. Finally, through whole-genome sequencing of propagated populations, we show that only POLQ-proficient animals accumulate genomic scars that are abundantly present in genomes of wild C. elegans, pointing towards POLQ as a major driver of genome diversification.
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Affiliation(s)
- Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Sophie F. Roerink
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Vincent Portegijs
- Department of Biology, Division of Developmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sander van den Heuvel
- Department of Biology, Division of Developmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
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148
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Cea V, Cipolla L, Sabbioneda S. Replication of Structured DNA and its implication in epigenetic stability. Front Genet 2015; 6:209. [PMID: 26136769 PMCID: PMC4468945 DOI: 10.3389/fgene.2015.00209] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/29/2015] [Indexed: 11/23/2022] Open
Abstract
DNA replication is an extremely risky process that cells have to endure in order to correctly duplicate and segregate their genome. This task is particularly sensitive to DNA damage and multiple mechanisms have evolved to protect DNA replication as a block to the replication fork could lead to genomic instability and possibly cell death. The DNA in the genome folds, for the most part, into the canonical B-form but in some instances can form complex secondary structures such as G-quadruplexes (G4). These G rich regions are thermodynamically stable and can constitute an obstacle to DNA and RNA metabolism. The human genome contains more than 350,000 sequences potentially capable to form G-quadruplexes and these structures are involved in a variety of cellular processes such as initiation of DNA replication, telomere maintenance and control of gene expression. Only recently, we started to understand how G4 DNA poses a problem to DNA replication and how its successful bypass requires the coordinated activity of ssDNA binding proteins, helicases and specialized DNA polymerases. Their role in the resolution and replication of structured DNA crucially prevents both genetic and epigenetic instability across the genome.
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Affiliation(s)
- Valentina Cea
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche , Pavia, Italy
| | - Lina Cipolla
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche , Pavia, Italy
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche , Pavia, Italy
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149
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Lim KW, Jenjaroenpun P, Low ZJ, Khong ZJ, Ng YS, Kuznetsov VA, Phan AT. Duplex stem-loop-containing quadruplex motifs in the human genome: a combined genomic and structural study. Nucleic Acids Res 2015; 43:5630-46. [PMID: 25958397 PMCID: PMC4477648 DOI: 10.1093/nar/gkv355] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/02/2015] [Indexed: 12/12/2022] Open
Abstract
Duplex stem-loops and four-stranded G-quadruplexes have been implicated in (patho)biological processes. Overlap of stem-loop- and quadruplex-forming sequences could give rise to quadruplex-duplex hybrids (QDH), which combine features of both structural forms and could exhibit unique properties. Here, we present a combined genomic and structural study of stem-loop-containing quadruplex sequences (SLQS) in the human genome. Based on a maximum loop length of 20 nt, our survey identified 80 307 SLQS, embedded within 60 172 unique clusters. Our analysis suggested that these should cover close to half of total SLQS in the entire genome. Among these, 48 508 SLQS were strand-specifically located in genic/promoter regions, with the majority of genes displaying a low number of SLQS. Notably, genes containing abundant SLQS clusters were strongly associated with brain tissues. Enrichment analysis of SLQS-positive genes and mapping of SLQS onto transcriptional/mutagenesis hotspots and cancer-associated genes, provided a statistical framework supporting the biological involvements of SLQS. In vitro formation of diverse QDH by selective SLQS hits were successfully verified by nuclear magnetic resonance spectroscopy. Folding topologies of two SLQS were elucidated in detail. We also demonstrated that sequence changes at mutation/single-nucleotide polymorphism loci could affect the structural conformations adopted by SLQS. Thus, our predicted SLQS offer novel insights into the potential involvement of QDH in diverse (patho)biological processes and could represent novel regulatory signals.
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Affiliation(s)
- Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Piroon Jenjaroenpun
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, 138671, Singapore
| | - Zhen Jie Low
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Zi Jian Khong
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Yi Siang Ng
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | | | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
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150
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Piazza A, Adrian M, Samazan F, Heddi B, Hamon F, Serero A, Lopes J, Teulade-Fichou MP, Phan AT, Nicolas A. Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites. EMBO J 2015; 34:1718-34. [PMID: 25956747 DOI: 10.15252/embj.201490702] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/31/2015] [Indexed: 11/09/2022] Open
Abstract
G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids, with various biological roles. However, structural features dictating their formation and/or function in vivo are unknown. In S. cerevisiae, the pathological persistency of G4 within the CEB1 minisatellite induces its rearrangement during leading-strand replication. We now show that several other G4-forming sequences remain stable. Extensive mutagenesis of the CEB25 minisatellite motif reveals that only variants with very short (≤ 4 nt) G4 loops preferentially containing pyrimidine bases trigger genomic instability. Parallel biophysical analyses demonstrate that shortening loop length does not change the monomorphic G4 structure of CEB25 variants but drastically increases its thermal stability, in correlation with the in vivo instability. Finally, bioinformatics analyses reveal that the threat for genomic stability posed by G4 bearing short pyrimidine loops is conserved in C. elegans and humans. This work provides a framework explanation for the heterogeneous instability behavior of G4-forming sequences in vivo, highlights the importance of structure thermal stability, and questions the prevailing assumption that G4 structures with short or longer loops are as likely to form in vivo.
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Affiliation(s)
- Aurèle Piazza
- Institut Curie, Centre de Recherche, UMR3244 CNRS Université Pierre et Marie Curie, Paris Cedex 05, France
| | - Michael Adrian
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Frédéric Samazan
- Institut Curie, Centre de Recherche, UMR3244 CNRS Université Pierre et Marie Curie, Paris Cedex 05, France
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Florian Hamon
- Institut Curie, Centre de Recherche, UMR 176 CNRS Université Paris-Sud, Orsay, France
| | - Alexandre Serero
- Institut Curie, Centre de Recherche, UMR3244 CNRS Université Pierre et Marie Curie, Paris Cedex 05, France
| | - Judith Lopes
- Institut Curie, Centre de Recherche, UMR3244 CNRS Université Pierre et Marie Curie, Paris Cedex 05, France
| | | | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alain Nicolas
- Institut Curie, Centre de Recherche, UMR3244 CNRS Université Pierre et Marie Curie, Paris Cedex 05, France
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