1
|
Rastokina A, Cebrián J, Mozafari N, Mandel NH, Smith CI, Lopes M, Zain R, Mirkin S. Large-scale expansions of Friedreich's ataxia GAA•TTC repeats in an experimental human system: role of DNA replication and prevention by LNA-DNA oligonucleotides and PNA oligomers. Nucleic Acids Res 2023; 51:8532-8549. [PMID: 37216608 PMCID: PMC10484681 DOI: 10.1093/nar/gkad441] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/02/2023] [Accepted: 05/20/2023] [Indexed: 05/24/2023] Open
Abstract
Friedreich's ataxia (FRDA) is caused by expansions of GAA•TTC repeats in the first intron of the human FXN gene that occur during both intergenerational transmissions and in somatic cells. Here we describe an experimental system to analyze large-scale repeat expansions in cultured human cells. It employs a shuttle plasmid that can replicate from the SV40 origin in human cells or be stably maintained in S. cerevisiae utilizing ARS4-CEN6. It also contains a selectable cassette allowing us to detect repeat expansions that accumulated in human cells upon plasmid transformation into yeast. We indeed observed massive expansions of GAA•TTC repeats, making it the first genetically tractable experimental system to study large-scale repeat expansions in human cells. Further, GAA•TTC repeats stall replication fork progression, while the frequency of repeat expansions appears to depend on proteins implicated in replication fork stalling, reversal, and restart. Locked nucleic acid (LNA)-DNA mixmer oligonucleotides and peptide nucleic acid (PNA) oligomers, which interfere with triplex formation at GAA•TTC repeats in vitro, prevented the expansion of these repeats in human cells. We hypothesize, therefore, that triplex formation by GAA•TTC repeats stall replication fork progression, ultimately leading to repeat expansions during replication fork restart.
Collapse
Affiliation(s)
| | - Jorge Cebrián
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Negin Mozafari
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | | | - C I Edvard Smith
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Rula Zain
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
- Center for Rare Diseases, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
| |
Collapse
|
2
|
Mellor C, Perez C, Sale JE. Creation and resolution of non-B-DNA structural impediments during replication. Crit Rev Biochem Mol Biol 2022; 57:412-442. [PMID: 36170051 PMCID: PMC7613824 DOI: 10.1080/10409238.2022.2121803] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 01/27/2023]
Abstract
During replication, folding of the DNA template into non-B-form secondary structures provides one of the most abundant impediments to the smooth progression of the replisome. The core replisome collaborates with multiple accessory factors to ensure timely and accurate duplication of the genome and epigenome. Here, we discuss the forces that drive non-B structure formation and the evidence that secondary structures are a significant and frequent source of replication stress that must be actively countered. Taking advantage of recent advances in the molecular and structural biology of the yeast and human replisomes, we examine how structures form and how they may be sensed and resolved during replication.
Collapse
Affiliation(s)
- Christopher Mellor
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Consuelo Perez
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| |
Collapse
|
3
|
Dusek CO, Dash RC, McPherson KS, Calhoun JT, Bezsonova I, Korzhnev DM, Hadden MK. DNA Sequence Specificity Reveals a Role of the HLTF HIRAN Domain in the Recognition of Trinucleotide Repeats. Biochemistry 2022; 61:10.1021/acs.biochem.2c00027. [PMID: 35608245 PMCID: PMC9684356 DOI: 10.1021/acs.biochem.2c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA damage tolerance (DDT) pathways enable cells to cope with a variety of replication blocks that threaten their ability to complete DNA replication. Helicase-like transcription factor (HLTF) plays a central role in the error-free DDT pathway, template switching (TS), by serving as a ubiquitin ligase to polyubiquitinate the DNA sliding clamp PCNA, which promotes TS initiation. HLTF also serves as an ATP-dependent DNA translocase facilitating replication fork remodeling. The HIP116, Rad5p N-terminal (HIRAN) domain of HLTF specifically recognizes the unmodified 3'-end of single-stranded DNA (ssDNA) at stalled replication forks to promote fork regression. Several crystal structures of the HIRAN domain in complex with ssDNA have been reported; however, optimal ssDNA sequences for high-affinity binding with the domain have not been described. Here we elucidated DNA sequence preferences of HLTF HIRAN through systematic studies of its binding to ssDNA substrates using fluorescence polarization assays and a computational analysis of the ssDNA:HIRAN interaction. These studies reveal that the HLTF HIRAN domain preferentially recognizes a (T/C)TG sequence at the 3'-hydroxyl ssDNA end, which occurs in the CTG trinucleotide repeat (TNR) regions that are susceptible to expansion and deletion mutations identified in neuromuscular and neurodegenerative disorders. These findings support a role for HLTF in maintaining the stability of difficult to replicate TNR microsatellite regions.
Collapse
Affiliation(s)
- Christopher O Dusek
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269-3092, United States
| | - Radha Charan Dash
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269-3092, United States
| | - Kerry S McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Jackson T Calhoun
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269-3092, United States
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269-3092, United States
| |
Collapse
|
4
|
Abstract
At fifteen different genomic locations, the expansion of a CAG/CTG repeat causes a neurodegenerative or neuromuscular disease, the most common being Huntington's disease and myotonic dystrophy type 1. These disorders are characterized by germline and somatic instability of the causative CAG/CTG repeat mutations. Repeat lengthening, or expansion, in the germline leads to an earlier age of onset or more severe symptoms in the next generation. In somatic cells, repeat expansion is thought to precipitate the rate of disease. The mechanisms underlying repeat instability are not well understood. Here we review the mammalian model systems that have been used to study CAG/CTG repeat instability, and the modifiers identified in these systems. Mouse models have demonstrated prominent roles for proteins in the mismatch repair pathway as critical drivers of CAG/CTG instability, which is also suggested by recent genome-wide association studies in humans. We draw attention to a network of connections between modifiers identified across several systems that might indicate pathway crosstalk in the context of repeat instability, and which could provide hypotheses for further validation or discovery. Overall, the data indicate that repeat dynamics might be modulated by altering the levels of DNA metabolic proteins, their regulation, their interaction with chromatin, or by direct perturbation of the repeat tract. Applying novel methodologies and technologies to this exciting area of research will be needed to gain deeper mechanistic insight that can be harnessed for therapies aimed at preventing repeat expansion or promoting repeat contraction.
Collapse
Affiliation(s)
- Vanessa C. Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA,Department of Neurology, Harvard Medical School, Boston, MA, USA,Correspondence to: Vanessa C. Wheeler, Center for Genomic Medicine, Massachusetts Hospital, Boston MAA 02115, USA. E-mail: . and Vincent Dion, UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK. E-mail:
| | - Vincent Dion
- UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, UK,Correspondence to: Vanessa C. Wheeler, Center for Genomic Medicine, Massachusetts Hospital, Boston MAA 02115, USA. E-mail: . and Vincent Dion, UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK. E-mail:
| |
Collapse
|
5
|
Barakate A, Arrieta M, Macaulay M, Vivera S, Davidson D, Stephens J, Orr J, Schreiber M, Ramsay L, Halpin C, Waugh R. Downregulation of Barley Regulator of Telomere Elongation Helicase 1 Alters the Distribution of Meiotic Crossovers. FRONTIERS IN PLANT SCIENCE 2021; 12:745070. [PMID: 34659314 PMCID: PMC8515186 DOI: 10.3389/fpls.2021.745070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Programmed meiotic DNA double-strand breaks (DSBs), necessary for proper chromosomal segregation and viable gamete formation, are repaired by homologous recombination (HR) as crossovers (COs) or non-crossovers (NCOs). The mechanisms regulating the number and distribution of COs are still poorly understood. The regulator of telomere elongation helicase 1 (RTEL1) DNA helicase was previously shown to enforce the number of meiotic COs in Caenorhabditis elegans but its function in plants has been studied only in the vegetative phase. Here, we characterised barley RTEL1 gene structure and expression using RNA-seq data previously obtained from vegetative and reproductive organs and tissues. Using RNAi, we downregulated RTEL1 expression specifically in reproductive tissues and analysed its impact on recombination using a barley 50k iSelect SNP Array. Unlike in C. elegans, in a population segregating for RTEL1 downregulated by RNAi, high resolution genome-wide genetic analysis revealed a significant increase of COs at distal chromosomal regions of barley without a change in their total number. Our data reveal the important role of RTEL1 helicase in plant meiosis and control of recombination.
Collapse
Affiliation(s)
- Abdellah Barakate
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mikel Arrieta
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sebastian Vivera
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Diane Davidson
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Jennifer Stephens
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Jamie Orr
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Claire Halpin
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- School of Agriculture and Wine, University of Adelaide, Waite Campus, Adelaide, SA, Australia
| |
Collapse
|
6
|
Gadgil RY, Romer EJ, Goodman CC, Rider SD, Damewood FJ, Barthelemy JR, Shin-Ya K, Hanenberg H, Leffak M. Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication. J Biol Chem 2020; 295:15378-15397. [PMID: 32873711 DOI: 10.1074/jbc.ra120.013495] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/23/2020] [Indexed: 12/12/2022] Open
Abstract
Short tandemly repeated DNA sequences, termed microsatellites, are abundant in the human genome. These microsatellites exhibit length instability and susceptibility to DNA double-strand breaks (DSBs) due to their tendency to form stable non-B DNA structures. Replication-dependent microsatellite DSBs are linked to genome instability signatures in human developmental diseases and cancers. To probe the causes and consequences of microsatellite DSBs, we designed a dual-fluorescence reporter system to detect DSBs at expanded (CTG/CAG) n and polypurine/polypyrimidine (Pu/Py) mirror repeat structures alongside the c-myc replication origin integrated at a single ectopic chromosomal site. Restriction cleavage near the (CTG/CAG)100 microsatellite leads to homology-directed single-strand annealing between flanking AluY elements and reporter gene deletion that can be detected by flow cytometry. However, in the absence of restriction cleavage, endogenous and exogenous replication stressors induce DSBs at the (CTG/CAG)100 and Pu/Py microsatellites. DSBs map to a narrow region at the downstream edge of the (CTG)100 lagging-strand template. (CTG/CAG) n chromosome fragility is repeat length-dependent, whereas instability at the (Pu/Py) microsatellites depends on replication polarity. Strikingly, restriction-generated DSBs and replication-dependent DSBs are not repaired by the same mechanism. Knockdown of DNA damage response proteins increases (Rad18, polymerase (Pol) η, Pol κ) or decreases (Mus81) the sensitivity of the (CTG/CAG)100 microsatellites to replication stress. Replication stress and DSBs at the ectopic (CTG/CAG)100 microsatellite lead to break-induced replication and high-frequency mutagenesis at a flanking thymidine kinase gene. Our results show that non-B structure-prone microsatellites are susceptible to replication-dependent DSBs that cause genome instability.
Collapse
Affiliation(s)
- Rujuta Yashodhan Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Eric J Romer
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Caitlin C Goodman
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - S Dean Rider
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - French J Damewood
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Joanna R Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Kazuo Shin-Ya
- Biomedical Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, Düsseldorf, Germany; Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA.
| |
Collapse
|
7
|
Bai G, Kermi C, Stoy H, Schiltz CJ, Bacal J, Zaino AM, Hadden MK, Eichman BF, Lopes M, Cimprich KA. HLTF Promotes Fork Reversal, Limiting Replication Stress Resistance and Preventing Multiple Mechanisms of Unrestrained DNA Synthesis. Mol Cell 2020; 78:1237-1251.e7. [PMID: 32442397 PMCID: PMC7305998 DOI: 10.1016/j.molcel.2020.04.031] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/12/2020] [Accepted: 04/24/2020] [Indexed: 01/06/2023]
Abstract
DNA replication stress can stall replication forks, leading to genome instability. DNA damage tolerance pathways assist fork progression, promoting replication fork reversal, translesion DNA synthesis (TLS), and repriming. In the absence of the fork remodeler HLTF, forks fail to slow following replication stress, but underlying mechanisms and cellular consequences remain elusive. Here, we demonstrate that HLTF-deficient cells fail to undergo fork reversal in vivo and rely on the primase-polymerase PRIMPOL for repriming, unrestrained replication, and S phase progression upon limiting nucleotide levels. By contrast, in an HLTF-HIRAN mutant, unrestrained replication relies on the TLS protein REV1. Importantly, HLTF-deficient cells also exhibit reduced double-strand break (DSB) formation and increased survival upon replication stress. Our findings suggest that HLTF promotes fork remodeling, preventing other mechanisms of replication stress tolerance in cancer cells. This remarkable plasticity of the replication fork may determine the outcome of replication stress in terms of genome integrity, tumorigenesis, and response to chemotherapy.
Collapse
Affiliation(s)
- Gongshi Bai
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Chames Kermi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Carl J Schiltz
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Julien Bacal
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Angela M Zaino
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06029-3092, USA
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06029-3092, USA
| | - Brandt F Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
| |
Collapse
|
8
|
Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
Collapse
Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
| |
Collapse
|
9
|
Chiu V, Hogen R, Sher L, Wadé N, Conti D, Martynova A, Li H, Liang G, O'Connell C. Telomerase Variants in Patients with Cirrhosis Awaiting Liver Transplantation. Hepatology 2019; 69:2652-2663. [PMID: 30964210 PMCID: PMC6594079 DOI: 10.1002/hep.30557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 01/27/2019] [Indexed: 12/16/2022]
Abstract
Telomeres are repetitive DNA sequences that protect the ends of linear chromosomes, and they are maintained by a ribonucleoprotein complex called telomerase. Variants in genes encoding for telomerase components have been associated with a spectrum of disease in the lung, skin, bone marrow, and liver. Mutations in the telomerase reverse transcriptase and telomerase RNA component genes have been observed at a higher prevalence in patients with liver disease compared with the general population; however, the presence of variants in other components of the telomerase complex and their impact on clinical outcomes has not been explored. We evaluated 86 patients with end-stage liver disease for variants in an expanded panel of eight genes, and found that 17 patients (20%) had likely deleterious variants by in silico analysis. Seven unique likely deleterious variants were identified in the regulator of telomere elongation helicase 1 (RTEL1) gene that encodes for a DNA helicase important in telomere maintenance and genomic stability. In gene burden association analysis of their clinical data, the presence of any RTEL1 variant was associated with a 29% lower baseline white blood cell count (95% confidence interval [CI], -7% to -46%; P Value = 0.01) compared with patients without RTEL1 variants, and the presence of any exonic missense RTEL1 variant was associated with a 42% lower baseline platelet count (95% CI, -5% to -65%: P Value = 0.03). The presence of any telomerase variant was associated with an increased number of readmissions within 1 year after transplantation demonstrated by an incident rate ratio (IRR) of 3.15 (95% CI, 1.22 to 8.57). No association with survival was observed. Conclusion: Among patients who underwent liver transplantation, the presence of any exonic missense variant was associated with a longer postoperative length of stay with an IRR of 2.16 (95% CI, 1.31 to 3.68).
Collapse
Affiliation(s)
- Victor Chiu
- Norris Comprehensive Cancer Center and Hospital, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA,Division of Hematology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Rachel Hogen
- Department of Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Linda Sher
- Department of Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Niquelle Wadé
- Department of Preventive Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - David Conti
- Department of Preventive Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Anastasia Martynova
- Norris Comprehensive Cancer Center and Hospital, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA,Division of Hematology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Hongtao Li
- Department of Urology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Gangning Liang
- Norris Comprehensive Cancer Center and Hospital, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA,Department of Urology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| | - Casey O'Connell
- Norris Comprehensive Cancer Center and Hospital, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA,Division of Hematology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA
| |
Collapse
|
10
|
Gallo D, Brown GW. Post-replication repair: Rad5/HLTF regulation, activity on undamaged templates, and relationship to cancer. Crit Rev Biochem Mol Biol 2019; 54:301-332. [PMID: 31429594 DOI: 10.1080/10409238.2019.1651817] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/12/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022]
Abstract
The eukaryotic post-replication repair (PRR) pathway allows completion of DNA replication when replication forks encounter lesions on the DNA template and are mediated by post-translational ubiquitination of the DNA sliding clamp proliferating cell nuclear antigen (PCNA). Monoubiquitinated PCNA recruits translesion synthesis (TLS) polymerases to replicate past DNA lesions in an error-prone manner while addition of K63-linked polyubiquitin chains signals for error-free template switching to the sister chromatid. Central to both branches is the E3 ubiquitin ligase and DNA helicase Rad5/helicase-like transcription factor (HLTF). Mutations in PRR pathway components lead to genomic rearrangements, cancer predisposition, and cancer progression. Recent studies have challenged the notion that the PRR pathway is involved only in DNA lesion tolerance and have shed new light on its roles in cancer progression. Molecular details of Rad5/HLTF recruitment and function at replication forks have emerged. Mounting evidence indicates that PRR is required during lesion-less replication stress, leading to TLS polymerase activity on undamaged templates. Analysis of PRR mutation status in human cancers and PRR function in cancer models indicates that down regulation of PRR activity is a viable strategy to inhibit cancer cell growth and reduce chemoresistance. Here, we review these findings, discuss how they change our views of current PRR models, and look forward to targeting the PRR pathway in the clinic.
Collapse
Affiliation(s)
- David Gallo
- Department of Biochemistry and Donnelly Centre, University of Toronto , Toronto , Canada
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto , Toronto , Canada
| |
Collapse
|
11
|
Dorn A, Feller L, Castri D, Röhrig S, Enderle J, Herrmann NJ, Block-Schmidt A, Trapp O, Köhler L, Puchta H. An Arabidopsis FANCJ helicase homologue is required for DNA crosslink repair and rDNA repeat stability. PLoS Genet 2019; 15:e1008174. [PMID: 31120885 PMCID: PMC6550410 DOI: 10.1371/journal.pgen.1008174] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/05/2019] [Accepted: 05/03/2019] [Indexed: 11/18/2022] Open
Abstract
Proteins of the Fanconi Anemia (FA) complementation group are required for crosslink (CL) repair in humans and their loss leads to severe pathological phenotypes. Here we characterize a homolog of the Fe-S cluster helicase FANCJ in the model plant Arabidopsis, AtFANCJB, and show that it is involved in interstrand CL repair. It acts at a presumably early step in concert with the nuclease FAN1 but independently of the nuclease AtMUS81, and is epistatic to both error-prone and error-free post-replicative repair in Arabidopsis. The simultaneous knock out of FANCJB and the Fe-S cluster helicase RTEL1 leads to induced cell death in root meristems, indicating an important role of the enzymes in replicative DNA repair. Surprisingly, we found that AtFANCJB is involved in safeguarding rDNA stability in plants. In the absence of AtRTEL1 and AtFANCJB, we detected a synergetic reduction to about one third of the original number of 45S rDNA copies. It is tempting to speculate that the detected rDNA instability might be due to deficiencies in G-quadruplex structure resolution and might thus contribute to pathological phenotypes of certain human genetic diseases.
Collapse
Affiliation(s)
- Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Laura Feller
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Dominique Castri
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sarah Röhrig
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Janina Enderle
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Natalie J. Herrmann
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Astrid Block-Schmidt
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Oliver Trapp
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Laura Köhler
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| |
Collapse
|
12
|
Borie R, Bouvry D, Cottin V, Gauvain C, Cazes A, Debray MP, Cadranel J, Dieude P, Degot T, Dominique S, Gamez AS, Jaillet M, Juge PA, Londono-Vallejo A, Mailleux A, Mal H, Boileau C, Menard C, Nunes H, Prevot G, Quetant S, Revy P, Traclet J, Wemeau-Stervinou L, Wislez M, Kannengiesser C, Crestani B. Regulator of telomere length 1 ( RTEL1) mutations are associated with heterogeneous pulmonary and extra-pulmonary phenotypes. Eur Respir J 2019; 53:13993003.00508-2018. [PMID: 30523160 DOI: 10.1183/13993003.00508-2018] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 11/06/2018] [Indexed: 01/10/2023]
Abstract
Regulator of telomere length 1 (RTEL1) mutations have been evidenced in 5-9% of familial pulmonary fibrosis; however, the phenotype of patients with interstitial lung disease (ILD) and RTEL1 mutations is poorly understood.Whole exome sequencing was performed in 252 probands with ILD and we included all patients with ILD and RTEL1 mutation. RTEL1 expression was evaluated by immunochemistry in the lungs of controls, as well as in RTEL1 and telomerase reverse transcriptase (TERT) mutation carriers.We identified 35 subjects from 17 families. Median age at diagnosis of ILD was 53.1 years (range 28.0-80.6). The most frequent pulmonary diagnoses were idiopathic pulmonary fibrosis (n=20, 57%), secondary ILD (n=7, 20%) and unclassifiable fibrosis or interstitial pneumonia with autoimmune features (n=7, 20%). The median transplant-free and overall survival periods were 39.2 months and 45.3 months, respectively. Forced vital capacity at diagnosis was the only factor associated with decreased transplant-free survival. Extra-pulmonary manifestations were less frequent as compared to other telomere-related gene mutation carriers. A systematic analysis of the literature identified 110 patients with ILD and RTEL1 mutations (including this series) and confirmed the heterogeneity of the pulmonary phenotype, the prevalence of non-idiopathic diseases and the low prevalence of extra-pulmonary manifestations.Immunohistochemistry showed that RTEL1 was expressed by bronchial and alveolar epithelial cells, as well as by alveolar macrophages and lymphocytes, but not by fibroblasts.
Collapse
Affiliation(s)
- Raphael Borie
- Service de Pneumologie A, Hôpital Bichat, AP-HP, DHU FIRE, Paris, France.,Unité 1152, INSERM, Université Paris Diderot, Paris, France
| | - Diane Bouvry
- Service de Pneumologie, Hôpital Avicenne, AP-HP, Bobigny, France
| | - Vincent Cottin
- Service de Pneumologie, Hôpital Louis Pradel, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Aurélie Cazes
- Unité 1152, INSERM, Université Paris Diderot, Paris, France.,Service d'Anatomopathologie, Hôpital Bichat, AP-HP, Paris, France
| | - Marie-Pierre Debray
- Unité 1152, INSERM, Université Paris Diderot, Paris, France.,Service de Radiologie, Hôpital Bichat, AP-HP, Paris, France
| | | | - Philippe Dieude
- Unité 1152, INSERM, Université Paris Diderot, Paris, France.,Service de Rhumatologie, Hôpital Bichat, AP-HP, Paris, France.,Université Paris Diderot, Paris, France
| | - Tristan Degot
- Service de Pneumologie, CHU Strasbourg, Strasbourg, France
| | | | | | | | | | - Arturo Londono-Vallejo
- UMR 3244 (Telomere and Cancer Lab), CNRS, Institut Curie, PSL Research University, Sorbonne Universités, Paris, France
| | | | - Hervé Mal
- Unité 1152, INSERM, Université Paris Diderot, Paris, France.,Service de Pneumologie B, Hôpital Bichat, AP-HP, Paris, France
| | - Catherine Boileau
- Université Paris Diderot, Paris, France.,Laboratoire de Génétique, Hôpital Bichat, AP-HP, Paris, France
| | | | - Hilario Nunes
- Service de Pneumologie, Hôpital Avicenne, AP-HP, Bobigny, France
| | | | | | - Patrick Revy
- UMR 1163 (Laboratory of Genome Dynamics in the Immune System), INSERM, Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Julie Traclet
- Service de Pneumologie, Hôpital Tenon, AP-HP, Paris, France
| | - Lidwine Wemeau-Stervinou
- Service de Pneumologie, Centre de Compétence des Maladies Pulmonaires Rares, CHRU de Lille, Lille, France
| | - Marie Wislez
- Service de Pneumologie, Unité d'Oncologie Thoracique, Hôpital Cochin, Hôpitaux Universitaires Paris Centre, AP-HP, Paris, France
| | - Caroline Kannengiesser
- Unité 1152, INSERM, Université Paris Diderot, Paris, France.,Université Paris Diderot, Paris, France.,Laboratoire de Génétique, Hôpital Bichat, AP-HP, Paris, France
| | - Bruno Crestani
- Service de Pneumologie A, Hôpital Bichat, AP-HP, DHU FIRE, Paris, France.,Unité 1152, INSERM, Université Paris Diderot, Paris, France.,Université Paris Diderot, Paris, France
| |
Collapse
|
13
|
Kaushal S, Freudenreich CH. The role of fork stalling and DNA structures in causing chromosome fragility. Genes Chromosomes Cancer 2019; 58:270-283. [PMID: 30536896 DOI: 10.1002/gcc.22721] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/13/2018] [Accepted: 12/03/2018] [Indexed: 12/19/2022] Open
Abstract
Alternative non-B form DNA structures, also called secondary structures, can form in certain DNA sequences under conditions that produce single-stranded DNA, such as during replication, transcription, and repair. Direct links between secondary structure formation, replication fork stalling, and genomic instability have been found for many repeated DNA sequences that cause disease when they expand. Common fragile sites (CFSs) are known to be AT-rich and break under replication stress, yet the molecular basis for their fragility is still being investigated. Over the past several years, new evidence has linked both the formation of secondary structures and transcription to fork stalling and fragility of CFSs. How these two events may synergize to cause fragility and the role of nuclease cleavage at secondary structures in rare and CFSs are discussed here. We also highlight evidence for a new hypothesis that secondary structures at CFSs not only initiate fragility but also inhibit healing, resulting in their characteristic appearance.
Collapse
Affiliation(s)
- Simran Kaushal
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, Massachusetts.,Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts
| |
Collapse
|
14
|
Mechanisms of genetic instability caused by (CGG) n repeats in an experimental mammalian system. Nat Struct Mol Biol 2018; 25:669-676. [PMID: 30061600 PMCID: PMC6082162 DOI: 10.1038/s41594-018-0094-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 06/19/2018] [Indexed: 12/17/2022]
Abstract
We describe a new experimental system to study genome instability caused by fragile X (CGG)n repeats in mammalian cells. It is based on a selectable cassette carrying the HyTK gene under the control of the FMR1 promoter with (CGG)n repeats in its 5′-UTR, which was integrated into the unique RL5 site in murine erythroid leukemia cells. Carrier-size (CGG)n repeats dramatically elevate the frequency of the reporter’s inactivation making cells ganciclovir-resistant. These resistant clones have a unique mutational signature: a change in the repeat length concurrent with mutagenesis in the reporter gene. Inactivation of genes implicated in break-induced replication including POLD3, POLD4, RAD52, RAD51 and SMARCAL1, reduced the frequency of ganciclovir-resistant clones to the baseline level that was observed in the absence of (CGG)n repeats. We propose that replication fork collapse at carrier-size (CGG)n repeats can trigger break-induced replication, which result in simultaneous repeat length changes and mutagenesis at a distance.
Collapse
|
15
|
McGinty RJ, Mirkin SM. Cis- and Trans-Modifiers of Repeat Expansions: Blending Model Systems with Human Genetics. Trends Genet 2018; 34:448-465. [PMID: 29567336 PMCID: PMC5959756 DOI: 10.1016/j.tig.2018.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 12/30/2022]
Abstract
Over 30 hereditary diseases are caused by the expansion of microsatellite repeats. The length of the expandable repeat is the main hereditary determinant of these disorders. They are also affected by numerous genomic variants that are either nearby (cis) or physically separated from (trans) the repetitive locus, which we review here. These genetic variants have largely been elucidated in model systems using gene knockouts, while a few have been directly observed as single-nucleotide polymorphisms (SNPs) in patients. There is a notable disconnect between these two bodies of knowledge: knockouts poorly approximate the SNP-level variation in human populations that gives rise to medically relevant cis- and trans-modifiers, while the rarity of these diseases limits the statistical power of SNP-based analysis in humans. We propose that high-throughput SNP-based screening in model systems could become a useful approach to quickly identify and characterize modifiers of clinical relevance for patients.
Collapse
Affiliation(s)
- Ryan J McGinty
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
| |
Collapse
|
16
|
RecQ and Fe-S helicases have unique roles in DNA metabolism dictated by their unwinding directionality, substrate specificity, and protein interactions. Biochem Soc Trans 2017; 46:77-95. [PMID: 29273621 DOI: 10.1042/bst20170044] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/15/2017] [Accepted: 11/17/2017] [Indexed: 12/11/2022]
Abstract
Helicases are molecular motors that play central roles in nucleic acid metabolism. Mutations in genes encoding DNA helicases of the RecQ and iron-sulfur (Fe-S) helicase families are linked to hereditary disorders characterized by chromosomal instabilities, highlighting the importance of these enzymes. Moreover, mono-allelic RecQ and Fe-S helicase mutations are associated with a broad spectrum of cancers. This review will discuss and contrast the specialized molecular functions and biological roles of RecQ and Fe-S helicases in DNA repair, the replication stress response, and the regulation of gene expression, laying a foundation for continued research in these important areas of study.
Collapse
|
17
|
Nguyen JHG, Viterbo D, Anand RP, Verra L, Sloan L, Richard GF, Freudenreich CH. Differential requirement of Srs2 helicase and Rad51 displacement activities in replication of hairpin-forming CAG/CTG repeats. Nucleic Acids Res 2017; 45:4519-4531. [PMID: 28175398 PMCID: PMC5416882 DOI: 10.1093/nar/gkx088] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/31/2017] [Indexed: 12/25/2022] Open
Abstract
Trinucleotide repeats are a source of genome instability, causing replication fork stalling, chromosome fragility, and impaired repair. Specialized helicases play an important role in unwinding DNA structures to maintain genome stability. The Srs2 helicase unwinds DNA hairpins, facilitates replication, and prevents repeat instability and fragility. However, since Srs2 is a multifunctional protein with helicase activity and the ability to displace Rad51 recombinase, it was unclear which functions were required for its various protective roles. Here, using SRS2 separation-of-function alleles, we show that in the absence of Srs2 recruitment to PCNA or in helicase-deficient mutants, breakage at a CAG/CTG repeat increases. We conclude that Srs2 interaction with PCNA allows the helicase activity to unwind fork-blocking CAG/CTG hairpin structures to prevent breaks. Independently of PCNA binding, Srs2 also displaces Rad51 from nascent strands to prevent recombination-dependent repeat expansions and contractions. By 2D gel electrophoresis, we detect two different kinds of structured intermediates or joint molecules (JMs). Some JMs are Rad51-independent and exhibit properties of reversed forks, including being processed by the Exo1 nuclease. In addition, in a helicase-deficient mutant, Rad51-dependent JMs are detected, probably corresponding to recombination between sisters. These results clarify the many roles of Srs2 in facilitating replication through fork-blocking hairpin lesions.
Collapse
Affiliation(s)
| | - David Viterbo
- Institut Pasteur, Department Genomes & Genetics, CNRS, UMR3525, Université Pierre et Marie Curie, UFR927, 25 rue du Dr Roux, F-75015 Paris, France
| | - Ranjith P Anand
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Lauren Verra
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Laura Sloan
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Guy-Franck Richard
- Institut Pasteur, Department Genomes & Genetics, CNRS, UMR3525, Université Pierre et Marie Curie, UFR927, 25 rue du Dr Roux, F-75015 Paris, France
| | | |
Collapse
|
18
|
Niu H, Klein HL. Multifunctional roles of Saccharomyces cerevisiae Srs2 protein in replication, recombination and repair. FEMS Yeast Res 2017; 17:fow111. [PMID: 28011904 DOI: 10.1093/femsyr/fow111] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 12/22/2016] [Indexed: 11/12/2022] Open
Abstract
The Saccharomyces cerevisiae Srs2 DNA helicase has important roles in DNA replication, recombination and repair. In replication, Srs2 aids in repair of gaps by repair synthesis by preventing gaps from being used to initiate recombination. This is considered to be an anti-recombination role. In recombination, Srs2 plays both prorecombination and anti-recombination roles to promote the synthesis-dependent strand annealing recombination pathway and to inhibit gaps from initiating homologous recombination. In repair, the Srs2 helicase actively promotes gap repair through an interaction with the Exo1 nuclease to enlarge a gap for repair and to prevent Rad51 protein from accumulating on single-stranded DNA. Finally, Srs2 helicase can unwind hairpin-forming repeat sequences to promote replication and prevent repeat instability. The Srs2 activities can be controlled by phosphorylation, SUMO modification and interaction with key partners at DNA damage or lesions sites, which include PCNA and Rad51. These interactions can also limit DNA polymerase function during recombinational repair independent of the Srs2 translocase or helicase activity, further highlighting the importance of the Srs2 protein in regulating recombination. Here we review the myriad roles of Srs2 that have been documented in genome maintenance and distinguish between the translocase, helicase and additional functions of the Srs2 protein.
Collapse
Affiliation(s)
- Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Hannah L Klein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| |
Collapse
|
19
|
Abstract
Eukaryotic genomes contain many repetitive DNA sequences that exhibit size instability. Some repeat elements have the added complication of being able to form secondary structures, such as hairpin loops, slipped DNA, triplex DNA or G-quadruplexes. Especially when repeat sequences are long, these DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks. In turn, repair or replication fork restart attempts within the repeat DNA can lead to addition or removal of repeat elements, which can sometimes lead to disease. One important DNA repair mechanism to maintain genomic integrity is recombination. Though early studies dismissed recombination as a mechanism driving repeat expansion and instability, recent results indicate that mitotic recombination is a key pathway operating within repetitive DNA. The action is two-fold: first, it is an important mechanism to repair nicks, gaps, breaks, or stalled forks to prevent chromosome fragility and protect cell health; second, recombination can cause repeat expansions or contractions, which can be deleterious. In this review, we summarize recent developments that illuminate the role of recombination in maintaining genome stability at DNA repeats.
Collapse
|
20
|
Gadgil R, Barthelemy J, Lewis T, Leffak M. Replication stalling and DNA microsatellite instability. Biophys Chem 2016; 225:38-48. [PMID: 27914716 DOI: 10.1016/j.bpc.2016.11.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/05/2016] [Accepted: 11/05/2016] [Indexed: 01/08/2023]
Abstract
Microsatellites are short, tandemly repeated DNA motifs of 1-6 nucleotides, also termed simple sequence repeats (SRSs) or short tandem repeats (STRs). Collectively, these repeats comprise approximately 3% of the human genome Subramanian et al. (2003), Lander and Lander (2001) [1,2], and represent a large reservoir of loci highly prone to mutations Sun et al. (2012), Ellegren (2004) [3,4] that contribute to human evolution and disease. Microsatellites are known to stall and reverse replication forks in model systems Pelletier et al. (2003), Samadashwily et al. (1997), Kerrest et al. (2009) [5-7], and are hotspots of chromosomal double strand breaks (DSBs). We briefly review the relationship of these repeated sequences to replication stalling and genome instability, and present recent data on the impact of replication stress on DNA fragility at microsatellites in vivo.
Collapse
Affiliation(s)
- R Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - J Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - T Lewis
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - M Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA.
| |
Collapse
|
21
|
Glousker G, Touzot F, Revy P, Tzfati Y, Savage SA. Unraveling the pathogenesis of Hoyeraal-Hreidarsson syndrome, a complex telomere biology disorder. Br J Haematol 2015; 170:457-71. [PMID: 25940403 DOI: 10.1111/bjh.13442] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hoyeraal-Hreidarsson (HH) syndrome is a multisystem genetic disorder characterized by very short telomeres and considered a clinically severe variant of dyskeratosis congenita. The main cause of mortality, usually in early childhood, is bone marrow failure. Mutations in several telomere biology genes have been reported to cause HH in about 60% of the HH patients, but the genetic defects in the rest of the patients are still unknown. Understanding the aetiology of HH and its diverse manifestations is challenging because of the complexity of telomere biology and the multiple telomeric and non-telomeric functions played by telomere-associated proteins in processes such as telomere replication, telomere protection, DNA damage response and ribosome and spliceosome assembly. Here we review the known clinical complications, molecular defects and germline mutations associated with HH, and elucidate possible mechanistic explanations and remaining questions in our understanding of the disease.
Collapse
Affiliation(s)
- Galina Glousker
- Department of Genetics, The Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Fabien Touzot
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Yehuda Tzfati
- Department of Genetics, The Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| |
Collapse
|
22
|
Richard GF. Shortening trinucleotide repeats using highly specific endonucleases: a possible approach to gene therapy? Trends Genet 2015; 31:177-86. [PMID: 25743488 DOI: 10.1016/j.tig.2015.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 12/31/2022]
Abstract
Trinucleotide repeat expansions are involved in more than two dozen neurological and developmental disorders. Conventional therapeutic approaches aimed at regulating the expression level of affected genes, which rely on drugs, oligonucleotides, and/or transgenes, have met with only limited success so far. An alternative approach is to shorten repeats to non-pathological lengths using highly specific nucleases. Here, I review early experiments using meganucleases, zinc-finger nucleases (ZFN), and transcription-activator like effector nucleases (TALENs) to contract trinucleotide repeats, and discuss the possibility of using CRISPR-Cas nucleases to the same end. Although this is a nascent field, I explore the possibility of designing nucleases and effectively delivering them in the context of gene therapy.
Collapse
Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Department Genomes and Genetics, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 3525, 25 Rue du Dr Roux, 75015 Paris, France
| |
Collapse
|
23
|
Usdin K, House NCM, Freudenreich CH. Repeat instability during DNA repair: Insights from model systems. Crit Rev Biochem Mol Biol 2015; 50:142-67. [PMID: 25608779 DOI: 10.3109/10409238.2014.999192] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The expansion of repeated sequences is the cause of over 30 inherited genetic diseases, including Huntington disease, myotonic dystrophy (types 1 and 2), fragile X syndrome, many spinocerebellar ataxias, and some cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat expansions are dynamic, and disease inheritance and progression are influenced by the size and the rate of expansion. Thus, an understanding of the various cellular mechanisms that cooperate to control or promote repeat expansions is of interest to human health. In addition, the study of repeat expansion and contraction mechanisms has provided insight into how repair pathways operate in the context of structure-forming DNA, as well as insights into non-canonical roles for repair proteins. Here we review the mechanisms of repeat instability, with a special emphasis on the knowledge gained from the various model systems that have been developed to study this topic. We cover the repair pathways and proteins that operate to maintain genome stability, or in some cases cause instability, and the cross-talk and interactions between them.
Collapse
Affiliation(s)
- Karen Usdin
- Laboratory of Cell and Molecular Biology, NIDDK, NIH , Bethesda, MD , USA
| | | | | |
Collapse
|
24
|
Pei S, Zhao F, Liu J, Fu Q, Shang P. Association between regulator of telomere elongation helicase 1 polymorphism and susceptibility to glioma. Int J Clin Exp Med 2015; 8:690-697. [PMID: 25785045 PMCID: PMC4358500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/14/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Glioma is the most devastating type of malignant brain tumors in adults. Genetic factors play important roles in the pathogenesis of glioma. In recent years, some studies found that there were significant association between regulator of telomere elongation helicase 1 rs6010620 polymorphism and glioma susceptibility, however, the results were controversial. The aim of this study was to obtain a more exact estimation of the association between regulator of telomere elongation helicase 1 rs6010620 polymorphism and glioma through a meta-analysis. METHODS The meta-analysis included 19 published case-control studies involving 8541 cases and 14226 controls. The included papers were searched from PubMed and Embase database. Odds ratio (OR) with 95% confidence interval (95% CI) were used to evaluate the association of regulator of telomere elongation helicase 1 rs6010620 polymorphism with glioma. RESULTS A significant association between regulator of telomere elongation helicase 1 rs6010620 polymorphism and glioma susceptibility was observed for GG vs. AA+AG (OR=1.28, 95% CI=1.14-1.43) and G vs. A (OR=1.07, 95% CI=1.03-1.10). Further subgroup analysis based on ethnicity showed similar results in Asians and Caucasians. In the subgroup analysis of source of control, a significant association between the G allele and glioma susceptibility were found in population-based group and hospital-based group. CONCLUSIONS The meta-analysis suggested that regulator of telomere elongation helicase 1 rs6010620 polymorphism was a risk factor for glioma. And this study also suggested that rs6010620 GG genotype and G allele may be indicators for the risk of glioma.
Collapse
Affiliation(s)
- Shujun Pei
- Department of Anesthesiology, Chinese PLA 251 HospitalZhangjiakou, China
- Department of Anesthesiology, Chinese PLA General HospitalBeijing, China
| | - Feng Zhao
- Department of Anesthesiology, Chinese PLA General HospitalBeijing, China
| | - Junle Liu
- Department of Anesthesiology, Chinese PLA General HospitalBeijing, China
| | - Qiang Fu
- Department of Anesthesiology, Chinese PLA General HospitalBeijing, China
| | - Peizhong Shang
- Department of General Surgery, Chinese PLA 251 HospitalZhangjiakou, China
| |
Collapse
|
25
|
León-Ortiz AM, Svendsen J, Boulton SJ. Metabolism of DNA secondary structures at the eukaryotic replication fork. DNA Repair (Amst) 2014; 19:152-62. [PMID: 24815912 DOI: 10.1016/j.dnarep.2014.03.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
DNA secondary structures are largely advantageous for numerous cellular processes but can pose specific threats to the progression of the replication machinery and therefore genome duplication and cell division. A number of specialized enzymes dismantle these structures to allow replication fork progression to proceed faithfully. In this review, we discuss the in vitro and in vivo data that has lead to the identification of these enzymes in eukaryotes, and the evidence that suggests that they act specifically at replication forks to resolve secondary structures. We focus on the role of helicases, which catalyze the dissociation of nucleotide complexes, and on the role of nucleases, which cleave secondary structures to allow replication fork progression at the expense of local rearrangements. Finally, we discuss outstanding questions in terms of dismantling DNA secondary structures, as well as the interplay between diverse enzymes that act upon specific types of structures.
Collapse
Affiliation(s)
- Ana María León-Ortiz
- DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms EN6 3LD, UK
| | - Jennifer Svendsen
- DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms EN6 3LD, UK
| | - Simon J Boulton
- DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms EN6 3LD, UK.
| |
Collapse
|
26
|
Ezzatizadeh V, Sandi C, Sandi M, Anjomani-Virmouni S, Al-Mahdawi S, Pook MA. MutLα heterodimers modify the molecular phenotype of Friedreich ataxia. PLoS One 2014; 9:e100523. [PMID: 24971578 PMCID: PMC4074104 DOI: 10.1371/journal.pone.0100523] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/28/2014] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Friedreich ataxia (FRDA), the most common autosomal recessive ataxia disorder, is caused by a dynamic GAA repeat expansion mutation within intron 1 of FXN gene, resulting in down-regulation of frataxin expression. Studies of cell and mouse models have revealed a role for the mismatch repair (MMR) MutS-heterodimer complexes and the PMS2 component of the MutLα complex in the dynamics of intergenerational and somatic GAA repeat expansions: MSH2, MSH3 and MSH6 promote GAA repeat expansions, while PMS2 inhibits GAA repeat expansions. METHODOLOGY/PRINCIPAL FINDINGS To determine the potential role of the other component of the MutLα complex, MLH1, in GAA repeat instability in FRDA, we have analyzed intergenerational and somatic GAA repeat expansions from FXN transgenic mice that have been crossed with Mlh1 deficient mice. We find that loss of Mlh1 activity reduces both intergenerational and somatic GAA repeat expansions. However, we also find that loss of either Mlh1 or Pms2 reduces FXN transcription, suggesting different mechanisms of action for Mlh1 and Pms2 on GAA repeat expansion dynamics and regulation of FXN transcription. CONCLUSIONS/SIGNIFICANCE Both MutLα components, PMS2 and MLH1, have now been shown to modify the molecular phenotype of FRDA. We propose that upregulation of MLH1 or PMS2 could be potential FRDA therapeutic approaches to increase FXN transcription.
Collapse
Affiliation(s)
- Vahid Ezzatizadeh
- Division of Biosciences, School of Health Sciences and Social Care, Brunel University London, Uxbridge, United Kingdom
| | - Chiranjeevi Sandi
- Division of Biosciences, School of Health Sciences and Social Care, Brunel University London, Uxbridge, United Kingdom
| | - Madhavi Sandi
- Division of Biosciences, School of Health Sciences and Social Care, Brunel University London, Uxbridge, United Kingdom
| | - Sara Anjomani-Virmouni
- Division of Biosciences, School of Health Sciences and Social Care, Brunel University London, Uxbridge, United Kingdom
| | - Sahar Al-Mahdawi
- Division of Biosciences, School of Health Sciences and Social Care, Brunel University London, Uxbridge, United Kingdom
| | - Mark A. Pook
- Division of Biosciences, School of Health Sciences and Social Care, Brunel University London, Uxbridge, United Kingdom
| |
Collapse
|