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Dong YN, Mercado-Ayón E, Coulman J, Flatley L, Ngaba LV, Adeshina MW, Lynch DR. The Regulation of the Disease-Causing Gene FXN. Cells 2024; 13:1040. [PMID: 38920668 PMCID: PMC11202134 DOI: 10.3390/cells13121040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Friedreich's ataxia (FRDA) is a progressive neurodegenerative disease caused in almost all patients by expanded guanine-adenine-adenine (GAA) trinucleotide repeats within intron 1 of the FXN gene. This results in a relative deficiency of frataxin, a small nucleus-encoded mitochondrial protein crucial for iron-sulfur cluster biogenesis. Currently, there is only one medication, omaveloxolone, available for FRDA patients, and it is limited to patients 16 years of age and older. This necessitates the development of new medications. Frataxin restoration is one of the main strategies in potential treatment options as it addresses the root cause of the disease. Comprehending the control of frataxin at the transcriptional, post-transcriptional, and post-translational stages could offer potential therapeutic approaches for addressing the illness. This review aims to provide a general overview of the regulation of frataxin and its implications for a possible therapeutic treatment of FRDA.
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Affiliation(s)
- Yi Na Dong
- Departments of Pediatrics and Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Jennifer Coulman
- Departments of Pediatrics and Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Liam Flatley
- The Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lucie Vanessa Ngaba
- Departments of Pediatrics and Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Miniat W. Adeshina
- Departments of Pediatrics and Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David R. Lynch
- Departments of Pediatrics and Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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2
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Matos-Rodrigues G, Hisey JA, Nussenzweig A, Mirkin SM. Detection of alternative DNA structures and its implications for human disease. Mol Cell 2023; 83:3622-3641. [PMID: 37863029 DOI: 10.1016/j.molcel.2023.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 10/22/2023]
Abstract
Around 3% of the genome consists of simple DNA repeats that are prone to forming alternative (non-B) DNA structures, such as hairpins, cruciforms, triplexes (H-DNA), four-stranded guanine quadruplexes (G4-DNA), and others, as well as composite RNA:DNA structures (e.g., R-loops, G-loops, and H-loops). These DNA structures are dynamic and favored by the unwinding of duplex DNA. For many years, the association of alternative DNA structures with genome function was limited by the lack of methods to detect them in vivo. Here, we review the recent advancements in the field and present state-of-the-art technologies and methods to study alternative DNA structures. We discuss the limitations of these methods as well as how they are beginning to provide insights into causal relationships between alternative DNA structures, genome function and stability, and human disease.
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Affiliation(s)
| | - Julia A Hisey
- Department of Biology, Tufts University, Medford, MA, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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3
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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: 7] [Impact Index Per Article: 7.0] [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.
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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
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4
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Pellerin D, Iruzubieta P, Tekgül Ş, Danzi MC, Ashton C, Dicaire MJ, Wandzel M, Roth V, Lamont PJ, Bonnet C, Renaud M, Synofzik M, Zuchner S, Brais B, Başak NA, Houlden H. Non-GAA Repeat Expansions in FGF14 Are Likely Not Pathogenic-Reply to: "Shaking Up Ataxia: FGF14 and RFC1 Repeat Expansions in Affected and Unaffected Members of a Chilean Family". Mov Disord 2023; 38:1575-1577. [PMID: 37565404 DOI: 10.1002/mds.29552] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 08/12/2023] Open
Affiliation(s)
- David Pellerin
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, University College London, London, United Kingdom
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, Quebec, Canada
| | - Pablo Iruzubieta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, University College London, London, United Kingdom
- Department of Neurology, Donostia University Hospital, San Sebastian, Spain
- Neuroscience Department, Biodonostia Health Research Institute, San Sebastian, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Şeyma Tekgül
- Department of Molecular Biology and Genetics, Koç University, School of Medicine, KUTTAM-NDAL, Istanbul, Turkey
| | - Matt C Danzi
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Catherine Ashton
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, Quebec, Canada
- Department of Neurology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Marie-Josée Dicaire
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, Quebec, Canada
| | - Marion Wandzel
- Laboratoire de Génétique Médicale, Hôpitaux de Brabois - CHRU de Nancy, Nancy, France
| | - Virginie Roth
- Laboratoire de Génétique Médicale, Hôpitaux de Brabois - CHRU de Nancy, Nancy, France
| | - Phillipa J Lamont
- Department of Neurology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Céline Bonnet
- Laboratoire de Génétique Médicale, Hôpitaux de Brabois - CHRU de Nancy, Nancy, France
- INSERM-U1256 NGERE, Université de Lorraine, Nancy, France
| | - Mathilde Renaud
- INSERM-U1256 NGERE, Université de Lorraine, Nancy, France
- Service de Neurologie, CHRU de Nancy, Nancy, France
- Service de Génétique Clinique, Hôpitaux de Brabois - CHRU de Nancy, Nancy, France
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Bernard Brais
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Centre de Réadaptation Lucie-Bruneau, Montreal, Quebec, Canada
| | - Nazlı A Başak
- Department of Molecular Biology and Genetics, Koç University, School of Medicine, KUTTAM-NDAL, Istanbul, Turkey
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, University College London, London, United Kingdom
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5
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Arning L, Nguyen HP. Huntington disease update: new insights into the role of repeat instability in disease pathogenesis. MED GENET-BERLIN 2021; 33:293-300. [PMID: 38835439 PMCID: PMC11006308 DOI: 10.1515/medgen-2021-2101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/16/2021] [Indexed: 06/06/2024]
Abstract
The causative mutation for Huntington disease (HD), an expanded trinucleotide repeat sequence in the first exon of the huntingtin gene (HTT) is naturally polymorphic and inevitably associated with disease symptoms above 39 CAG repeats. Although symptomatic medical therapies for HD can improve the motor and non-motor symptoms for affected patients, these drugs do not stop the ongoing neurodegeneration and progression of the disease, which results in severe motor and cognitive disability and death. To date, there is still an urgent need for the development of effective disease-modifying therapies to slow or even stop the progression of HD. The increasing ability to intervene directly at the roots of the disease, namely HTT transcription and translation of its mRNA, makes it necessary to understand the pathogenesis of HD as precisely as possible. In addition to the long-postulated toxicity of the polyglutamine-expanded mutant HTT protein, there is increasing evidence that the CAG repeat-containing RNA might also be directly involved in toxicity. Recent studies have identified cis- (DNA repair genes) and trans- (loss/duplication of CAA interruption) acting variants as major modifiers of age at onset (AO) and disease progression. More and more extensive data indicate that somatic instability functions as a driver for AO as well as disease progression and severity, not only in HD but also in other polyglutamine diseases. Thus, somatic expansions of repetitive DNA sequences may be essential to promote respective repeat lengths to reach a threshold leading to the overt neurodegenerative symptoms of trinucleotide diseases. These findings support somatic expansion as a potential therapeutic target in HD and related repeat expansion disorders.
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Affiliation(s)
- Larissa Arning
- Department of Human Genetics, Medical Faculty, Ruhr-University Bochum, Bochum 44780, Germany
| | - Huu Phuc Nguyen
- Department of Human Genetics, Medical Faculty, Ruhr-University Bochum, Bochum 44780, Germany
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6
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Nethisinghe S, Kesavan M, Ging H, Labrum R, Polke JM, Islam S, Garcia-Moreno H, Callaghan MF, Cavalcanti F, Pook MA, Giunti P. Interruptions of the FXN GAA Repeat Tract Delay the Age at Onset of Friedreich's Ataxia in a Location Dependent Manner. Int J Mol Sci 2021; 22:7507. [PMID: 34299126 PMCID: PMC8307455 DOI: 10.3390/ijms22147507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/12/2021] [Accepted: 06/18/2021] [Indexed: 12/03/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a comparatively rare autosomal recessive neurological disorder primarily caused by the homozygous expansion of a GAA trinucleotide repeat in intron 1 of the FXN gene. The repeat expansion causes gene silencing that results in deficiency of the frataxin protein leading to mitochondrial dysfunction, oxidative stress and cell death. The GAA repeat tract in some cases may be impure with sequence variations called interruptions. It has previously been observed that large interruptions of the GAA repeat tract, determined by abnormal MboII digestion, are very rare. Here we have used triplet repeat primed PCR (TP PCR) assays to identify small interruptions at the 5' and 3' ends of the GAA repeat tract through alterations in the electropherogram trace signal. We found that contrary to large interruptions, small interruptions are more common, with 3' interruptions being most frequent. Based on detection of interruptions by TP PCR assay, the patient cohort (n = 101) was stratified into four groups: 5' interruption, 3' interruption, both 5' and 3' interruptions or lacking interruption. Those patients with 3' interruptions were associated with shorter GAA1 repeat tracts and later ages at disease onset. The age at disease onset was modelled by a group-specific exponential decay model. Based on this modelling, a 3' interruption is predicted to delay disease onset by approximately 9 years relative to those lacking 5' and 3' interruptions. This highlights the key role of interruptions at the 3' end of the GAA repeat tract in modulating the disease phenotype and its impact on prognosis for the patient.
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Affiliation(s)
- Suran Nethisinghe
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; (S.N.); (M.K.); (H.G.); (H.G.-M.)
| | - Maheswaran Kesavan
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; (S.N.); (M.K.); (H.G.); (H.G.-M.)
| | - Heather Ging
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; (S.N.); (M.K.); (H.G.); (H.G.-M.)
| | - Robyn Labrum
- Neurogenetics Service, Rare and Inherited Disease Laboratory, London North Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3BH, UK; (R.L.); (J.M.P.)
| | - James M. Polke
- Neurogenetics Service, Rare and Inherited Disease Laboratory, London North Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3BH, UK; (R.L.); (J.M.P.)
| | - Saiful Islam
- UCL Queen Square Institute of Neurology, London WC1N 3BG, UK;
| | - Hector Garcia-Moreno
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; (S.N.); (M.K.); (H.G.); (H.G.-M.)
| | - Martina F. Callaghan
- Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, University College London, London WC1N 3AR, UK;
| | - Francesca Cavalcanti
- Institute for Biomedical Research and Innovation (IRIB), Italian National Research Council (CNR), 87050 Mangone, Italy;
| | - Mark A. Pook
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK;
- Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London, Uxbridge UB8 3PH, UK
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; (S.N.); (M.K.); (H.G.); (H.G.-M.)
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Petrillo S, Santoro M, La Rosa P, Perna A, Gallo MG, Bertini ES, Silvestri G, Piemonte F. Nuclear Factor Erythroid 2-Related Factor 2 Activation Might Mitigate Clinical Symptoms in Friedreich's Ataxia: Clues of an "Out-Brain Origin" of the Disease From a Family Study. Front Neurosci 2021; 15:638810. [PMID: 33708070 PMCID: PMC7940825 DOI: 10.3389/fnins.2021.638810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/22/2021] [Indexed: 11/25/2022] Open
Abstract
Friedreich’s ataxia (FRDA) is the most frequent autosomal recessive ataxia in western countries, with a mean age of onset at 10–15 years. Patients manifest progressive cerebellar and sensory ataxia, dysarthria, lower limb pyramidal weakness, and other systemic manifestations. Previously, we described a family displaying two expanded GAA alleles not only in the proband affected by late-onset FRDA but also in the two asymptomatic family members: the mother and the younger sister. Both of them showed a significant reduction of frataxin levels, without any disease manifestation. Here, we analyzed if a protective mechanism might contribute to modulate the phenotype in this family. We particularly focused on the transcription factor nuclear factor erythroid 2-related factor 2 (NRF2), the first line of antioxidant defense in cells, and on the glutathione (GSH) system, an index of reactive oxygen species (ROS) detoxification ability. Our findings show a great reactivity of the GSH system to the frataxin deficiency, particularly in the asymptomatic mother, where the genes of GSH synthesis [glutamate–cysteine ligase (GCL)] and GSSG detoxification [GSH S-reductase (GSR)] were highly responsive. The GSR was activated even in the asymptomatic sister and in the proband, reflecting the need of buffering the GSSG increase. Furthermore, and contrasting the NRF2 expression documented in FRDA tissues, NRF2 was highly activated in the mother and in the younger sister, while it was constitutively low in the proband. This suggests that, also under frataxin depletion, the endogenous stimulation of NRF2 in asymptomatic FRDA subjects may contribute to protect against the progressive oxidative damage, helping to prevent the onset of neurological symptoms and highlighting an “out-brain origin” of the disease.
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Affiliation(s)
- Sara Petrillo
- Unit of Muscular and Neurodegenerative Diseases, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, Rome, Italy
| | - Alessia Perna
- Department of Neurosciences, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maria Giovanna Gallo
- Unit of Muscular and Neurodegenerative Diseases, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Enrico Silvio Bertini
- Unit of Muscular and Neurodegenerative Diseases, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Gabriella Silvestri
- Department of Neurosciences, Università Cattolica del Sacro Cuore, Rome, Italy.,UOC of Neurology, Area of Neuroscience, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Fiorella Piemonte
- Unit of Muscular and Neurodegenerative Diseases, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
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Santoro M, Perna A, La Rosa P, Petrillo S, Piemonte F, Rossi S, Riso V, Nicoletti TF, Modoni A, Pomponi MG, Chiurazzi P, Silvestri G. Compound heterozygosity for an expanded (GAA) and a (GAAGGA) repeat at FXN locus: from a diagnostic pitfall to potential clues to the pathogenesis of Friedreich ataxia. Neurogenetics 2020; 21:279-287. [PMID: 32638185 DOI: 10.1007/s10048-020-00620-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/14/2020] [Indexed: 12/23/2022]
Abstract
Friedreich's ataxia (FRDA) is usually due to a homozygous GAA expansion in intron 1 of the frataxin (FXN) gene. Rarely, uncommon molecular rearrangements at the FXN locus can cause pitfalls in the molecular diagnosis of FRDA. Here we describe a family whose proband was affected by late-onset Friedreich's ataxia (LOFA); long-range PCR (LR-PCR) documented two small expanded GAA alleles both in the proband and in her unaffected younger sister, who therefore received a diagnosis of pre-symptomatic LOFA. Later studies, however, revealed that the proband's unaffected sister, as well as their healthy mother, were both carriers of an expanded GAA allele and an uncommon (GAAGGA)66-67 repeat mimicking a GAA expansion at the LR-PCR that was the cause of the wrong initial diagnosis of pre-symptomatic LOFA. Extensive studies in tissues from all the family members, including LR-PCR, assessment of methylation status of FXN locus, MboII restriction analysis and direct sequencing of LR-PCR products, analysis of FXN mRNA, and frataxin protein expression, support the virtual lack of pathogenicity of the rare (GAAGGA)66-67 repeat, also providing significant data about the modulation of epigenetic modifications at the FXN locus. Overall, this report highlights a rare but possible pitfall in FRDA molecular diagnosis, emphasizing the need of further analysis in case of discrepancy between clinical and molecular data.
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Affiliation(s)
- Massimo Santoro
- IRCCS Fondazione Don Carlo Gnocchi, Piazzale Morandi, 6, 20121, Milan, Italy
| | - Alessia Perna
- Dept of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Scaro Cuore, L.go F. Vito 1, 000168, Rome, Italy
| | - Piergiorgio La Rosa
- Unit of Muscular and Neurodegenerative Diseases, Ospedale Pediatrico Bambino Gesù, IRCCS, Viale San Paolo, 15, 00146, Rome, Italy
| | - Sara Petrillo
- Unit of Muscular and Neurodegenerative Diseases, Ospedale Pediatrico Bambino Gesù, IRCCS, Viale San Paolo, 15, 00146, Rome, Italy
| | - Fiorella Piemonte
- Unit of Muscular and Neurodegenerative Diseases, Ospedale Pediatrico Bambino Gesù, IRCCS, Viale San Paolo, 15, 00146, Rome, Italy
| | - Salvatore Rossi
- Dept of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Scaro Cuore, L.go F. Vito 1, 000168, Rome, Italy
| | - Vittorio Riso
- Dept of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Scaro Cuore, L.go F. Vito 1, 000168, Rome, Italy
- Institute of Neurology, Neuroscience Area, Neurology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168, Rome, Italy
| | - Tommaso Filippo Nicoletti
- Dept of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Scaro Cuore, L.go F. Vito 1, 000168, Rome, Italy
- Institute of Neurology, Neuroscience Area, Neurology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168, Rome, Italy
| | - Anna Modoni
- Institute of Neurology, Neuroscience Area, Neurology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168, Rome, Italy
| | - Maria Grazia Pomponi
- Institute of Genomic Medicine, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168, Rome, Italy
| | - Pietro Chiurazzi
- Institute of Genomic Medicine, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168, Rome, Italy
| | - Gabriella Silvestri
- Dept of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Scaro Cuore, L.go F. Vito 1, 000168, Rome, Italy.
- Institute of Neurology, Neuroscience Area, Neurology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168, Rome, Italy.
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9
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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: 155] [Impact Index Per Article: 38.8] [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?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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10
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Hashem V, Tiwari A, Bewick B, Teive HAG, Moscovich M, Schüele B, Bushara K, Bower M, Rasmussen A, Tsai YC, Clark T, McFarland K, Ashizawa T. Pulse-Field capillary electrophoresis of repeat-primed PCR amplicons for analysis of large repeats in Spinocerebellar Ataxia Type 10. PLoS One 2020; 15:e0228789. [PMID: 32160188 PMCID: PMC7065784 DOI: 10.1371/journal.pone.0228789] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/23/2020] [Indexed: 12/13/2022] Open
Abstract
Large expansions of microsatellite DNA cause several neurological diseases. In Spinocerebellar ataxia type 10 (SCA10), the repeat interruptions change disease phenotype; an (ATTCC)n or a (ATCCT)n/(ATCCC)n interruption within the (ATTCT)n repeat is associated with the robust phenotype of ataxia and epilepsy while mostly pure (ATTCT)n may have reduced penetrance. Large repeat expansions of SCA10, and many other microsatellite expansions, can exceed 10,000 base pairs (bp) in size. Conventional next generation sequencing (NGS) technologies are ineffective in determining internal sequence contents or size of these expanded repeats. Using repeat primed PCR (RP-PCR) in conjunction with a high-sensitivity pulsed-field capillary electrophoresis fragment analyzer (FEMTO-Pulse, Agilent, Santa Clara, CA) (RP-FEMTO hereafter), we successfully determined sequence content of large expansion repeats in genomic DNA of SCA10 patients and transformed yeast artificial chromosomes containing SCA10 repeats. This RP-FEMTO is a simple and economical methodology which could complement emerging NGS for very long sequence reads such as Single Molecule, Real-Time (SMRT) and nanopore sequencing technologies.
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Affiliation(s)
- Vera Hashem
- Department of Neurology, Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Anjana Tiwari
- Department of Neurology, Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Brittani Bewick
- Department of Neurology, Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Helio A. G. Teive
- Movement Disorders Unit, Neurology Service, Department of Internal Medicine, Hospital de Clinicas, Federal University of Paraná, Curitiba, PR, Brazil
| | - Mariana Moscovich
- Department of Internal Medicine, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Birgitt Schüele
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Khalaf Bushara
- Department of Neurology, University of Minnesota Medical Center, Minneapolis, Minnesota, United States of America
| | - Matt Bower
- Institute of Human Genetics, University of Minnesota Medical Center, Minneapolis, Minnesota, United States of America
| | - Astrid Rasmussen
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, CDMX, Mexico
| | - Yu-Chih Tsai
- Pacific Biosciences of California, Inc, Menlo Park, California, United States of America
| | - Tyson Clark
- Pacific Biosciences of California, Inc, Menlo Park, California, United States of America
| | - Karen McFarland
- Department of Neurology and The McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Tetsuo Ashizawa
- Department of Neurology, Houston Methodist Research Institute, Houston, Texas, United States of America
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11
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Large-scale contractions of Friedreich's ataxia GAA repeats in yeast occur during DNA replication due to their triplex-forming ability. Proc Natl Acad Sci U S A 2020; 117:1628-1637. [PMID: 31911468 PMCID: PMC6983365 DOI: 10.1073/pnas.1913416117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Expansions of GAA repeats cause a severe hereditary neurodegenerative disease, Friedreich’s ataxia. In this study, we characterized the mechanisms of GAA repeat contractions in a yeast experimental system. These mechanisms might, in the long run, aid development of a therapy for this currently incurable disease. We show that GAA repeats contract during DNA replication, which can explain the high level of somatic instability of this repeat in patient tissues. We also provided evidence that a triple-stranded DNA structure is at the heart of GAA repeat instability. This discovery highlights the role of triplex DNA in genome instability and human disease. Friedreich’s ataxia (FRDA) is a human hereditary disease caused by the presence of expanded (GAA)n repeats in the first intron of the FXN gene [V. Campuzano et al., Science 271, 1423–1427 (1996)]. In somatic tissues of FRDA patients, (GAA)n repeat tracts are highly unstable, with contractions more common than expansions [R. Sharma et al., Hum. Mol. Genet. 11, 2175–2187 (2002)]. Here we describe an experimental system to characterize GAA repeat contractions in yeast and to conduct a genetic analysis of this process. We found that large-scale contraction is a one-step process, resulting in a median loss of ∼60 triplet repeats. Our genetic analysis revealed that contractions occur during DNA replication, rather than by various DNA repair pathways. Repeats contract in the course of lagging-strand synthesis: The processivity subunit of DNA polymerase δ, Pol32, and the catalytic domain of Rev1, a translesion polymerase, act together in the same pathway to counteract contractions. Accumulation of single-stranded DNA (ssDNA) in the lagging-strand template greatly increases the probability that (GAA)n repeats contract, which in turn promotes repeat instability in rfa1, rad27, and dna2 mutants. Finally, by comparing contraction rates for homopurine-homopyrimidine repeats differing in their mirror symmetry, we found that contractions depend on a repeat’s triplex-forming ability. We propose that accumulation of ssDNA in the lagging-strand template fosters the formation of a triplex between the nascent and fold-back template strands of the repeat. Occasional jumps of DNA polymerase through this triplex hurdle, result in repeat contractions in the nascent lagging strand.
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12
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Al-Mahdawi S, Ging H, Bayot A, Cavalcanti F, La Cognata V, Cavallaro S, Giunti P, Pook MA. Large Interruptions of GAA Repeat Expansion Mutations in Friedreich Ataxia Are Very Rare. Front Cell Neurosci 2018; 12:443. [PMID: 30519163 PMCID: PMC6258883 DOI: 10.3389/fncel.2018.00443] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/05/2018] [Indexed: 12/19/2022] Open
Abstract
Friedreich ataxia is a multi-system autosomal recessive inherited disorder primarily caused by homozygous GAA repeat expansion mutations within intron 1 of the frataxin gene. The resulting deficiency of frataxin protein leads to progressive mitochondrial dysfunction, oxidative stress, and cell death, with the main affected sites being the large sensory neurons of the dorsal root ganglia and the dentate nucleus of the cerebellum. The GAA repeat expansions may be pure (GAA)n in sequence or may be interrupted with regions of non-GAA sequence. To our knowledge, there has been no large-scale study of FRDA patient DNA samples to determine the frequency of large interruptions in GAA repeat expansions. Therefore, we have investigated a panel of 245 Friedreich ataxia patient and carrier DNA samples using GAA repeat PCR amplification and MboII restriction enzyme digestion. We demonstrate that the vast majority (97.8%) of Friedreich ataxia GAA repeat expansion samples do not contain significant sequence changes that would result in abnormal MboII digestion profiles, indicating that they are primarily pure GAA repeats. These results show for the first time that large interruptions in the GAA repeats are very rare.
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Affiliation(s)
- Sahar Al-Mahdawi
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom.,Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, United Kingdom
| | - Heather Ging
- Ataxia Centre, Department of Molecular Neuroscience, Institute of Neurology, University College London, London, United Kingdom
| | - Aurelien Bayot
- Ataxia Centre, Department of Molecular Neuroscience, Institute of Neurology, University College London, London, United Kingdom
| | | | | | | | - Paola Giunti
- Ataxia Centre, Department of Molecular Neuroscience, Institute of Neurology, University College London, London, United Kingdom
| | - Mark A Pook
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom.,Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, United Kingdom
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13
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Bram E, Javanmardi K, Nicholson K, Culp K, Thibert JR, Kemppainen J, Le V, Schlageter A, Hadd A, Latham GJ. Comprehensive genotyping of the C9orf72 hexanucleotide repeat region in 2095 ALS samples from the NINDS collection using a two-mode, long-read PCR assay. Amyotroph Lateral Scler Frontotemporal Degener 2018; 20:107-114. [PMID: 30430876 DOI: 10.1080/21678421.2018.1522353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Expansion of the G4C2 repeat tract in the C9orf72 gene is linked to frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Here, we provide comprehensive genotyping of the C9orf72 repeat region for the National Institute of Neurological Disorders and Stroke (NINDS) ALS collection (n = 2095), using a novel bimodal PCR assay capable of amplifying nearly 100% GC-rich sequences. METHODS A single-tube 3-primer PCR assay mode, resolved using capillary electrophoresis, was used for sizing up to 145 repeats with single-repeat accuracy, for detecting expansions irrespective of their overall size, and for flagging confounding 3' sequence variations (SVs). A modified two-primer PCR mode, resolved via agarose gel electrophoresis, provided further size information for hyper-expanded samples (>145 repeats) up to ∼5.8 kb amplicons (∼950 G4C2 repeats). RESULTS Within the evaluated cohort, 177 (8.4%) samples were expanded, with 175 (99%) samples being hyper-expanded. 3'-SVs were identified in 64 (3.1%) samples, and were most common in expanded alleles. Genotypes of all 606 (29%) homozygous samples were confirmed using an orthogonal PCR assay. CONCLUSION This study and PCR method may improve and standardize molecular characterization of the C9orf72 locus, and have the potential to inform phenotype-genotype correlations and therapeutic development in ALS/FTD.
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14
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Tomé S, Dandelot E, Dogan C, Bertrand A, Geneviève D, Péréon Y, Simon M, Bonnefont JP, Bassez G, Gourdon G. Unusual association of a unique CAG interruption in 5' of DM1 CTG repeats with intergenerational contractions and low somatic mosaicism. Hum Mutat 2018; 39:970-982. [PMID: 29664219 DOI: 10.1002/humu.23531] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/23/2018] [Accepted: 04/10/2018] [Indexed: 11/11/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a dominant multisystemic disorder associated with high variability of symptoms and anticipation. DM1 is caused by an unstable CTG repeat expansion that usually increases in successive generations and tissues. DM1 family pedigrees have shown that ∼90% and 10% of transmissions result in expansions and contractions of the CTG repeat, respectively. To date, the mechanisms of CTG repeat contraction remain poorly documented in DM1. In this report, we identified two new DM1 families with apparent contractions and no worsening of DM1 symptoms in two and three successive maternal transmissions. A new and unique CAG interruption was found in 5' of the CTG expansion in one family, whereas multiple 5' CCG interruptions were detected in the second family. We showed that these interruptions are associated with maternal intergenerational contractions and low somatic mosaicism in blood. By specific triplet-prime PCR, we observed that CTG repeat changes (contractions/expansions) occur preferentially in 3' of the interruptions for both families.
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Affiliation(s)
- Stéphanie Tomé
- Laboratory CTGDM, Inserm UMR1163, Paris, France; Institut Imagine, Université Paris-Descartes-Sorbonne Paris-Cité, Paris, France
| | - Elodie Dandelot
- Laboratory CTGDM, Inserm UMR1163, Paris, France; Institut Imagine, Université Paris-Descartes-Sorbonne Paris-Cité, Paris, France
| | - Céline Dogan
- Neuromuscular Reference Center, AP-HP, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Alexis Bertrand
- Laboratory CTGDM, Inserm UMR1163, Paris, France; Institut Imagine, Université Paris-Descartes-Sorbonne Paris-Cité, Paris, France
| | - David Geneviève
- Molecular Genetic Laboratory, Necker Hospital, Paris, France.,Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Université Montpellier, Montpellier, France
| | - Yann Péréon
- Centre for Neuromuscular Diseases, Hôtel-Dieu Hospital, Nantes, France
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- Pauline Arnaud: Department of genetic, Bichat Hospital, Paris, France, Raphaële Chasserieau: Centre for Neuromuscular Diseases, Hôtel-Dieu Hospital, Nantes, France, Pascal Cintas: Neuromuscular Reference Center, Purpan Hospital, Toulouse, France, Ana-maria Cobo Esteban: Neuromuscular Reference Center, Marin Hospital, Hendaye, France, Marie-Carmen Cruz: Neuromuscular Reference Center, Purpan Hospital, Toulouse, France, Dalil Hamroun: Centre Hospitalo-Universitaire de Montpellier, Montpellier, France, Armelle Magot: Neuromuscular Reference Center, Hôtel-Dieu Hospital, Nantes, France, Alexandra Nadaj-Pakleza Neuromuscular Reference Center, Larrey Hospital, Angers, France, Anne-catherine Aube-Gauthier Neuromuscular Reference Center, Larrey Hospital, Angers, France, Andoni Urtizberea: Neuromuscular Reference Center, Marin Hospital, Hendaye, France
| | - Marie Simon
- Molecular Genetic Laboratory, Necker Hospital, Paris, France
| | | | - Guillaume Bassez
- Sorbonne Université, Inserm, UMRS974, Neuromuscular Reference center, AP-HP, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Geneviève Gourdon
- Laboratory CTGDM, Inserm UMR1163, Paris, France; Institut Imagine, Université Paris-Descartes-Sorbonne Paris-Cité, Paris, France
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15
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Wedding IM, Kroken M, Henriksen SP, Selmer KK, Fiskerstrand T, Knappskog PM, Berge T, Tallaksen CME. Friedreich ataxia in Norway - an epidemiological, molecular and clinical study. Orphanet J Rare Dis 2015; 10:108. [PMID: 26338206 PMCID: PMC4559212 DOI: 10.1186/s13023-015-0328-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/25/2015] [Indexed: 01/06/2023] Open
Abstract
Background Friedreich ataxia is an autosomal recessive hereditary spinocerebellar disorder, characterized by progressive limb and gait ataxia due to proprioceptive loss, often complicated by cardiomyopathy, diabetes and skeletal deformities. Friedreich ataxia is the most common hereditary ataxia, with a reported prevalence of 1:20 000 – 1:50 000 in Central Europe. Previous reports from south Norway have found a prevalence varying from 1:100 000 – 1:1 350 000; no studies are previously done in the rest of the country. Methods In this cross-sectional study, Friedreich ataxia patients were identified through colleagues in neurological, pediatric and genetic departments, hospital archives searches, patients’ associations, and National Centre for Rare Disorders. All included patients, carriers and controls were investigated clinically and molecularly with genotype characterization including size determination of GAA repeat expansions and frataxin measurements. 1376 healthy blood donors were tested for GAA repeat expansion for carrier frequency analysis. Results Twenty-nine Friedreich ataxia patients were identified in Norway, of which 23 were ethnic Norwegian, corresponding to a prevalence of 1:176 000 and 1:191 000, respectively. The highest prevalence was seen in the north. Carrier frequency of 1:196 (95 % CI = [1:752–1:112]) was found. Homozygous GAA repeat expansions in the FXN gene were found in 27/29, while two patients were compound heterozygous with c.467 T < C, L157P and the deletion (g.120032_122808del) including exon 5a. Two additional patients were heterozygous for GAA repeat expansions only. Significant differences in the level of frataxin were found between the included patients (N = 27), carriers (N = 37) and controls (N = 27). Conclusions In this first thorough study of a complete national cohort of Friedreich ataxia patients, and first nation-wide study of Friedreich ataxia in Norway, the prevalence of Friedreich ataxia in Norway is lower than in Central Europe, but higher than in the last Norwegian report, and as expected from migration studies. A south–north prevalence gradient is present. Based on Hardy Weinberg’s equilibrium, the carrier frequency of 1:196 is consistent with the observed prevalence. All genotypes, and typical and atypical phenotypes were present in the Norwegian population. The patients were phenotypically similar to European cohorts. Frataxin was useful in the diagnostic work-up of heterozygous symptomatic cases. Electronic supplementary material The online version of this article (doi:10.1186/s13023-015-0328-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Iselin Marie Wedding
- Department of Neurology, Oslo University Hospital, Ullevaal, 0407, Oslo, Norway. .,University of Oslo, Faculty of Medicine, Oslo, Norway.
| | - Mette Kroken
- Department of Medical Genetics, Oslo University Hospital, Ullevaal, 0407, Oslo, Norway
| | | | - Kaja Kristine Selmer
- Department of Medical Genetics, Oslo University Hospital, Ullevaal, 0407, Oslo, Norway.,University of Oslo, Faculty of Medicine, Oslo, Norway
| | - Torunn Fiskerstrand
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Per Morten Knappskog
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Tone Berge
- Department of Neurology, Oslo University Hospital, Ullevaal, 0407, Oslo, Norway
| | - Chantal M E Tallaksen
- Department of Neurology, Oslo University Hospital, Ullevaal, 0407, Oslo, Norway.,University of Oslo, Faculty of Medicine, Oslo, Norway
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16
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Affiliation(s)
- Massimo Pandolfo
- Brussels Free University and Erasme Hospital, Brussels, Belgium.
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17
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Holloway TP, Rowley SM, Delatycki MB, Sarsero JP. Detection of interruptions in the GAA trinucleotide repeat expansion in the FXN gene of Friedreich ataxia. Biotechniques 2011; 50:182-6. [PMID: 21486239 DOI: 10.2144/000113615] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 01/06/2011] [Indexed: 11/23/2022] Open
Abstract
Friedreich ataxia is a neurodegenerative disorder caused by the expansion of a GAA trinucleotide repeat sequence within the first intron of the FXN gene. Interruptions in the GAA repeat may serve to alleviate the inhibitory effects of the GAA expansion on FXN gene expression and to decrease pathogenicity. We have developed a simple and rapid PCR- and restriction enzyme-based assay to assess the purity of GAA repeat sequences.
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Affiliation(s)
- Timothy P Holloway
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
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18
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Mancuso M, Sammarco MC, Grabczyk E. Transposon Tn7 preferentially inserts into GAA*TTC triplet repeats under conditions conducive to Y*R*Y triplex formation. PLoS One 2010; 5:e11121. [PMID: 20559546 PMCID: PMC2886061 DOI: 10.1371/journal.pone.0011121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 05/21/2010] [Indexed: 11/26/2022] Open
Abstract
Background Expansion of an unstable GAA•TTC repeat in the first intron of the FXN gene causes Friedreich ataxia by reducing frataxin expression. Structure formation by the repeat has been implicated in both frataxin repression and GAA•TTC instability. The GAA•TTC sequence is capable of adopting multiple non-B DNA structures including Y•R•Y and R•R•Y triplexes. Lower pH promotes the formation of Y•R•Y triplexes by GAA•TTC. Here we used the bacterial transposon Tn7 as an in vitro tool to probe whether GAA•TTC repeats can attract a well-characterized recombinase. Methodology/Principal Findings Tn7 showed a pH-dependent preference for insertion into uninterrupted regions of a Friedreich ataxia patient-derived repeat, inserting 48, 39 and 14 percent of the time at pH 7, pH 8 and pH 9, respectively. Moreover, Tn7 also showed orientation and region specific insertion within the repeat at pH 7 and pH 8, but not at pH 9. In contrast, transposon Tn5 showed no strong preference for or against the repeat during in vitro transposition at any pH tested. Y•R•Y triplex formation was reduced in predictable ways by transposon interruption of the GAA•TTC repeat. However, transposon interruptions in the GAA•TTC repeats did not increase the in vitro transcription efficiency of the templates. Conclusions/Significance We have demonstrated that transposon Tn7 will recognize structures that form spontaneously in GAA•TTC repeats and insert in a specific orientation within the repeat. The conditions used for in vitro transposition span the physiologically relevant range suggesting that long GAA•TTC repeats can form triplex structures in vivo, attracting enzymes involved in DNA repair, recombination and chromatin modification.
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Affiliation(s)
- Miriam Mancuso
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
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19
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Abstract
Friedreich ataxia, the most common inherited ataxia, is caused by the transcriptional silencing of the FXN gene, which codes for the 210 amino acid frataxin, a mitochondrial protein involved in iron-sulfur cluster biosynthesis. The expansion of the GAA x TTC tract in intron 1 to as many as 1700 repeats elicits the transcriptional silencing by the formation of non-B DNA structures (triplexes or sticky DNA), the formation of a persistent DNA x RNA hybrid, or heterochromatin formation. The triplex (sticky DNA) adopted by the long repeat sequence also elicits profound mutagenic, genetic instability, and recombination behaviors. Early stage therapeutic investigations involving polyamides or histone deacetylase inhibitors are being pursued. Friedreich ataxia may be one of the most thoroughly studied hereditary neurological disease from a pathophysiological standpoint.
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Affiliation(s)
- Robert D Wells
- Center for Genome Research, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, The Texas Medical Center, 2121 W. Holcombe Blvd., Houston, TX 77030-3303, USA.
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20
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Pandolfo M. Mutations causing Friedreich ataxia. FUTURE NEUROLOGY 2008. [DOI: 10.2217/14796708.3.1.73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Friedreich ataxia (FRDA) is an autosomal recessive degenerative disease primarily affecting the nervous system and the heart. The identification of the FRDA gene (FXN) encoding the mitochondrial protein frataxin allowed to better define the clinical and pathological spectrum of the disease, to investigate pathogenesis and to eventually propose novel treatments for this so far incurable disease. Frataxin has homologs in all eukaryotes and in gram-negative bacteria. Studies in yeast and mouse models and biochemical investigations indicate a role in the assembly of iron–sulfur clusters in the mitochondrion. Frataxin deficiency leads to abnormal mitochondrial iron metabolism, decreased activities of iron–sulfur cluster-containing enzymes, reduced oxidative phosphorylation and possibly increased oxidative stress. Complete absence of frataxin is lethal at an embryonic level in all investigated multicellular organisms, in yeast it leads to loss of mitochondrial function and mitochondrial DNA. Patients with FRDA have a unique mutation that results in low levels of structurally and functionally normal frataxin. The mutation is an unstable hyperexpansion of a GAA triplet-repeat sequence in the first intron of the gene. Pathological lengths of the GAA repeat adopt in vitro a non-B, triple helical DNA structure that inhibits transcription. In the nucleus, chromatin condenses at and around the GAA repeat into a heterochromatic state that is associated with repressed transcription. It is not yet known whether the triple helical structure forms in the nucleus and has a role in triggering chromatin condensation. Rare mutations, always occurring in heterozygosity with the GAA repeat expansion in FRDA patients, alter the coding frataxin sequence and result in non-functional or absent protein. Restoring frataxin transcription is an exciting perspective for treatment. Preliminary results in cell models suggest that some inhibitors of histone deacetylases may have this effect.
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Affiliation(s)
- Massimo Pandolfo
- Chief of Neurology Université Libre de Bruxelles-Hôpital Erasme, Service de Neurologie, Route de Lennik 808, B-1070 Bruxelles, Belgium
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Wells RD, Dere R, Hebert ML, Napierala M, Son LS. Advances in mechanisms of genetic instability related to hereditary neurological diseases. Nucleic Acids Res 2005; 33:3785-98. [PMID: 16006624 PMCID: PMC1174910 DOI: 10.1093/nar/gki697] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Substantial progress has been realized in the past several years in our understanding of the molecular mechanisms responsible for the expansions and deletions (genetic instabilities) of repeating tri-, tetra- and pentanucleotide repeating sequences associated with a number of hereditary neurological diseases. These instabilities occur by replication, recombination and repair processes, probably acting in concert, due to slippage of the DNA complementary strands relative to each other. The biophysical properties of the folded-back repeating sequence strands play a critical role in these instabilities. Non-B DNA structural elements (hairpins and slipped structures, DNA unwinding elements, tetraplexes, triplexes and sticky DNA) are described. The replication mechanisms are influenced by pausing of the replication fork, orientation of the repeat strands, location of the repeat sequences relative to replication origins and the flap endonuclease. Methyl-directed mismatch repair, nucleotide excision repair, and repair of damage caused by mutagens are discussed. Genetic recombination and double-strand break repair advances in Escherichia coli, yeast and mammalian models are reviewed. Furthermore, the newly discovered capacities of certain triplet repeat sequences to cause gross chromosomal rearrangements are discussed.
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Affiliation(s)
- Robert D Wells
- Center for Genome Research, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, Texas Medical Center, 2121 W. Holcombe Blvd, Houston, TX 77030, USA.
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Dere R, Napierala M, Ranum LPW, Wells RD. Hairpin Structure-forming Propensity of the (CCTG·CAGG) Tetranucleotide Repeats Contributes to the Genetic Instability Associated with Myotonic Dystrophy Type 2. J Biol Chem 2004; 279:41715-26. [PMID: 15292165 DOI: 10.1074/jbc.m406415200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The genetic instabilities of (CCTG.CAGG)(n) tetranucleotide repeats were investigated to evaluate the molecular mechanisms responsible for the massive expansions found in myotonic dystrophy type 2 (DM2) patients. DM2 is caused by an expansion of the repeat from the normal allele of 26 to as many as 11,000 repeats. Genetic expansions and deletions were monitored in an African green monkey kidney cell culture system (COS-7 cells) as a function of the length (30, 114, or 200 repeats), orientation, or proximity of the repeat tracts to the origin (SV40) of replication. As found for CTG.CAG repeats related to DM1, the instabilities were greater for the longer tetranucleotide repeat tracts. Also, the expansions and deletions predominated when cloned in orientation II (CAGG on the leading strand template) rather than I and when cloned proximal rather than distal to the replication origin. Biochemical studies on synthetic d(CAGG)(26) and d(CCTG)(26) as models of unpaired regions of the replication fork revealed that d(CAGG)(26) has a marked propensity to adopt a defined base paired hairpin structure, whereas the complementary d(CCTG)(26) lacks this capacity. The effect of orientation described above differs from all previous results with three triplet repeat sequences (including CTG.CAG), which are also involved in the etiologies of other hereditary neurological diseases. However, similar to the triplet repeat sequences, the ability of one of the two strands to form a more stable folded structure, in our case the CAGG strand, explains this unorthodox "reversed" behavior.
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Affiliation(s)
- Ruhee Dere
- Institute of Biosciences and Technology, Center for Genome Research, Texas A and M University System Health Science Center, Texas Medical Center, Houston, Texas 77030-3303, USA
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Napierala M, Dere R, Vetcher A, Wells RD. Structure-dependent Recombination Hot Spot Activity of GAA·TTC Sequences from Intron 1 of the Friedreich's Ataxia Gene. J Biol Chem 2004; 279:6444-54. [PMID: 14625270 DOI: 10.1074/jbc.m309596200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The recombinational properties of long GAA.TTC repeating sequences were analyzed in Escherichia coli to gain further insights into the molecular mechanisms of the genetic instability of this tract as possibly related to the etiology of Friedreich's ataxia. Intramolecular and intermolecular recombination studies showed that the frequency of recombination between the GAA.TTC tracts was as much as 15 times higher than the non-repeating control sequences. Homologous, intramolecular recombination between GAA.TTC tracts and GAAGGA.TCCTTC repeats also occurred with a very high frequency (approximately 0.8%). Biochemical analyses of the recombination products demonstrated the expansions and deletions of the GAA.TTC repeats. These results, together with our previous studies on the CTG.CAG sequences, suggest that the recombinational hot spot characteristics may be a common feature of all triplet repeat sequences. Unexpectedly, we found that the recombination properties of the GAA.TTC tracts were unique, compared with CTG.CAG repeats, because they depended on the DNA secondary structure polymorphism. Increasing the length of the GAA.TTC repeats decreased the intramolecular recombination frequency between these tracts. Also, a correlation was found between the propensity of the GAA.TTC tracts to adopt the sticky DNA conformation and the inhibition of intramolecular recombination. The use of novobiocin to modulate the intracellular DNA topology, i.e. the lowering of the negative superhelical density, repressed the formation of the sticky DNA structure, thereby restoring the expected positive correlation between the length of the GAA.TTC tracts and the frequency of intramolecular recombination. Hence, our results demonstrate that sticky DNA exists and functions in E. coli.
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Affiliation(s)
- Marek Napierala
- Institute of Biosciences and Technology, Center for Genome Research, Texas A&M University System Health Science Center, Texas Medical Center, Houston, Texas 77030-3303, USA
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24
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Abstract
Our discovery that plasmids containing the Friedreich's ataxia (FRDA) expanded GAA.TTC sequence, which forms sticky DNA, are prone to form dimers compared with monomers in vivo is the basis of an intracellular assay in Escherichia coli for this unusual DNA conformation. Sticky DNA is a single long GAA.GAA.TTC triplex formed in plasmids harboring a pair of long GAA.TTC repeat tracts in the direct repeat orientation. This requirement is fulfilled by either plasmid dimers of DNAs with a single trinucleotide repeat sequence tract or by monomeric DNAs containing a pair of direct repeat GAA.TTC sequences. DNAs harboring a single GAA.TTC repeat are unable to form this type of triplex conformation. An excellent correlation was observed between the ability of a plasmid to adopt the sticky triplex conformation as assayed in vitro and its propensity to form plasmid dimers relative to monomers in vivo. The variables measured that strongly influenced these measurements are as follows: length of the GAA.TTC insert; the extent of periodic interruptions within the repeat sequence; the orientation of the repeat inserts; and the in vivo negative supercoil density. Nitrogen mustard cross-linking studies on a family of GAA.TTC-containing plasmids showed the presence of sticky DNA in vivo and, thus, serves as an important bridge between the in vitro and in vivo determinations. Biochemical genetic studies on FRDA containing DNAs grown in recA or nucleotide excision repair or ruv-deficient cells showed that the in vivo properties of sticky DNA play an important role in the monomer-dimer-sticky DNA intracellular intercon-versions. Thus, the sticky DNA triplex exists and functions in living cells, strengthening the likelihood of its role in the etiology of FRDA.
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Affiliation(s)
- Alexandre A Vetcher
- Center for Genome Research, Institute of Biosciences and Technology, Texas A & M University System Health Science Center, Texas Medical Center, Houston, Texas 77030-3303, USA
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25
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Pandolfo M. The molecular basis of Friedreich ataxia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2003; 516:99-118. [PMID: 12611437 DOI: 10.1007/978-1-4615-0117-6_5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Affiliation(s)
- Massimo Pandolfo
- Centre Hospitalier de lé Université de Montréal, Hopital Notre-Dame, 1560 rue Sherbrooke Est, Montréal, Québec H2L 4M1 Canada
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26
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Potaman VN, Bissler JJ, Hashem VI, Oussatcheva EA, Lu L, Shlyakhtenko LS, Lyubchenko YL, Matsuura T, Ashizawa T, Leffak M, Benham CJ, Sinden RR. Unpaired structures in SCA10 (ATTCT)n.(AGAAT)n repeats. J Mol Biol 2003; 326:1095-111. [PMID: 12589756 DOI: 10.1016/s0022-2836(03)00037-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A number of human hereditary diseases have been associated with the instability of DNA repeats in the genome. Recently, spinocerebellar ataxia type 10 has been associated with expansion of the pentanucleotide repeat (ATTCT)(n).(AGAAT)(n) from a normal range of ten to 22 to as many as 4500 copies. The structural properties of this repeat cloned in circular plasmids were studied by a variety of methods. Two-dimensional gel electrophoresis and atomic force microscopy detected local DNA unpairing in supercoiled plasmids. Chemical probing analysis indicated that, at moderate superhelical densities, the (ATTCT)(n).(AGAAT)(n) repeat forms an unpaired region, which further extends into adjacent A+T-rich flanking sequences at higher superhelical densities. The superhelical energy required to initiate duplex unpairing is essentially length-independent from eight to 46 repeats. In plasmids containing five repeats, minimal unpairing of (ATTCT)(5).(AGAAT)(5) occurred while 2D gel analysis and chemical probing indicate greater unpairing in A+T-rich sequences in other regions of the plasmid. The observed experimental results are consistent with a statistical mechanical, computational analysis of these supercoiled plasmids. For plasmids containing 29 repeats, which is just above the normal human size range, flanked by an A+T-rich sequence, atomic force microscopy detected the formation of a locally condensed structure at high superhelical densities. However, even at high superhelical densities, DNA strands within the presumably compact A+T-rich region were accessible to small chemicals and oligonucleotide hybridization. Thus, DNA strands in this "collapsed structure" remain unpaired and accessible for interaction with other molecules. The unpaired DNA structure functioned as an aberrant replication origin, in that it supported complete plasmid replication in a HeLa cell extract. A model is proposed in which unscheduled or aberrant DNA replication is a critical step in the expansion mutation.
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Affiliation(s)
- Vladimir N Potaman
- Laboratory of DNA Structure and Function, Center for Genome Research, Institute of Biosciences and Technology, Texas A and M University System Health Sciences Center, Houston, TX 77030-3303, USA
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27
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Vetcher AA, Napierala M, Wells RD. Sticky DNA: effect of the polypurine.polypyrimidine sequence. J Biol Chem 2002; 277:39228-34. [PMID: 12161438 DOI: 10.1074/jbc.m205210200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The polypurine.polypyrimidine sequence requirements for the formation of sticky DNA were evaluated in Escherichia coli plasmid systems to determine the potential occurrence of this conformation throughout biological systems. A mirror repeat, dinucleotide tract of (GA.TC)(37), which is ubiquitous in eukaryotes, formed sticky DNA, but shorter sequences of 10 or 20 repeats were inert. (GGA.TCC)(n) inserts (where n = 126, 159, and 222 bp) also formed sticky DNA. As shown previously, the control sequence (GAA.TTC)(150) (450 bp) readily adopted the X-shaped sticky structure; however, this structure has never been found for the nonpathogenic (GAAGGA.TCCTTC)(65) of the same approximate length (390 bp). A sequence that is replete with polypurine.polypyrimidine tracts that can form triplexes and slipped structures but lacks long repeating motifs (the 2.5-kbp intron 21 sequence from the polycystic kidney disease gene 1) was also inert. Interestingly, tracts of (GAA.TTC)(n) (where n = 176 or 80) readily formed sticky DNA with (GAAGGA.TCCTTC)(65) cloned into the same plasmid when the pair of inserts was in the direct, but not in the indirect (inverted), orientation. The stabilities of the triple base (Watson-Crick and Hoogsteen) interactions in the DNA/DNA associated triplex region of the sticky conformations account for these observations. Our results have significant chemical and biological implications for the structure and function of this unusual DNA conformation in Friedreich's ataxia.
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Affiliation(s)
- Alexandre A Vetcher
- Center for Genome Research, Institute of Biosciences and Technology, Texas A&M University, Texas Medical Center, Houston, Texas 77030-3303, USA
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28
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Vetcher AA, Napierala M, Iyer RR, Chastain PD, Griffith JD, Wells RD. Sticky DNA, a long GAA.GAA.TTC triplex that is formed intramolecularly, in the sequence of intron 1 of the frataxin gene. J Biol Chem 2002; 277:39217-27. [PMID: 12161437 DOI: 10.1074/jbc.m205209200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Friedreich's ataxia is caused by the massive expansion of GAA.TTC repeats in intron 1 of the frataxin (X25) gene. Our prior investigations showed that long GAA.TTC repeats formed very stable triplex structures which caused two repeat tracts to adhere to each other (sticky DNA). This process was dependent on negative supercoiling and the presence of divalent metal ions. Herein, we have investigated the formation of sticky DNA from plasmid monomers and dimers; sticky DNA is formed only when two tracts of sufficiently long (GAA.TTC)(n) (n = 59-270) are present in a single plasmid DNA and are in the direct repeat orientation. If the inserts are in the indirect (inverted) repeat orientation, no sticky DNA was observed. Furthermore, kinetic studies support the intramolecular nature of sticky DNA formation. Electron microscopy investigations also provide strong data for sticky DNA as a single long triplex. Hence, these results give new insights into our understanding of the capacity of sticky DNA to inhibit transcription and thereby reduce the level of frataxin protein as related to the etiology of Friedreich's ataxia.
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Affiliation(s)
- Alexandre A Vetcher
- Center for Genome Research, Institute of Biosciences and Technology, Texas A&M University, Texas Medical Center, Houston, Texas 77030-3303, USA
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29
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Miranda CJ, Santos MM, Ohshima K, Smith J, Li L, Bunting M, Cossée M, Koenig M, Sequeiros J, Kaplan J, Pandolfo M. Frataxin knockin mouse. FEBS Lett 2002; 512:291-7. [PMID: 11852098 DOI: 10.1016/s0014-5793(02)02251-2] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Friedreich ataxia is the consequence of frataxin deficiency, most often caused by a GAA repeat expansion in intron 1 of the corresponding gene. Frataxin is a mitochondrial protein involved in iron homeostasis. As an attempt to generate a mouse model of the disease, we introduced a (GAA)(230) repeat within the mouse frataxin gene by homologous recombination. GAA repeat knockin mice were crossed with frataxin knockout mice to obtain double heterozygous mice expressing 25-36% of wild-type frataxin levels. These mice were viable and did not develop anomalies of motor coordination, iron metabolism or response to iron loading. Repeats were meiotically and mitotically stable.
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Affiliation(s)
- Carlos J Miranda
- Department of Medicine, Centre Hospitalier de l'Université de Montréal, Hôpital Notre-Dame, Pav de Seve--Y5608, 1560 rue Sherbrooke Est, H2L 4M1, Montréal, QC, Canada
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30
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McDaniel DO, Keats B, Vedanarayanan VV, Subramony SH. Sequence variation in GAA repeat expansions may cause differential phenotype display in Friedreich's ataxia. Mov Disord 2001; 16:1153-8. [PMID: 11748752 DOI: 10.1002/mds.1210] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Friedreich's ataxia, the most common autosomal recessive inherited ataxia, is characterized by progressive gait and limb ataxia. Friedreich's ataxia is known for its occurrence within the first or second decade of life and is associated with hypertrophic cardiomyopathy, and in some cases with diabetes. Genetically, it is identified by the expression of an unstable trinucleotide GAA repeat expansion located in the first intron of the X25 gene on chromosome 9. Two brothers with very late adult-onset ataxia, and their unaffected sister, were examined for the clinical presentation of FA and for the presence of the mutated FA gene. The relationship of the expanded gene sequence to the severity of disease and age of onset were evaluated. Clinical examination revealed that the two brothers had mild ataxia and proprioceptive loss, with age of onset between 60 and 70 years of age. DNA from peripheral blood nucleated cells demonstrated a small homozygous expansion, with approximately 120-130 GAA repeats in the X25 gene in both patients. The expanded repeats were interrupted either with GAAGAG, GAAGGA, or GAAGAAAA sequences. The unaffected sister carried a normal FA genotype with 8-uninterrupted GAA repeat, observed by sequence analysis. In addition, the levels of FA gene transcript in both brothers were relatively lower than that in the unaffected sister. No detectable cardiomyopathy or diabetes was observed. Phenotypic diversity of FA is increasingly expanding. The age of onset and the structure of GAA repeat expansion plays an important role in determining the clinical features and the differential diagnosis of FA. The confirmation of the FA gene mutation in the atypical case, broadens the clinical spectrum of FA, and supports the idea that patients with even a mild form of ataxia of late adult onset should be considered for molecular testing.
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Affiliation(s)
- D O McDaniel
- Department of Surgery, The University of Mississippi Medical Center, Jackson, Mississippi 39216, USA.
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31
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Affiliation(s)
- M Pandolfo
- Département de Médecine, Université de Montréal, Centre Hospitalier de l'Université de Montréal, Hôpital Notre-Dame, Montréal, Québec, Canada.
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32
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Sakamoto N, Larson JE, Iyer RR, Montermini L, Pandolfo M, Wells RD. GGA*TCC-interrupted triplets in long GAA*TTC repeats inhibit the formation of triplex and sticky DNA structures, alleviate transcription inhibition, and reduce genetic instabilities. J Biol Chem 2001; 276:27178-87. [PMID: 11325966 DOI: 10.1074/jbc.m101852200] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Large expansions of GAA.TTC repeats in the first intron of the frataxin (X25) gene are the principal mutation responsible for Friedreich's ataxia (FRDA). Sticky DNA, based on R.R.Y triplexes, was found at the expanded GAA.TTC repeats from FRDA patients. The (GAAGGA.TCCTTC)(65) repeat occurs in the same frataxin locus but is nonpathogenic and does not form sticky DNA. To elucidate the behavior of sticky DNA, we introduced various extents of GGA.TCC interruptions into the long GAA.TTC repeat. More than 20% of GGA.TCC interruptions abolished the formation of sticky DNA. However, the GAA.TTC repeats with less than 11% of GGA.TCC interruptions formed triplexes and/or sticky DNA similar to the uninterrupted repeat sequence. These triplexes showed different P1 nuclease sensitivities, and the GGA.TCC interruptions were slightly more sensitive than the surrounding GAA.TTC repeats. Furthermore, genetic instability investigations in Escherichia coli revealed that a small number (4%) of interruptions substantially stabilized the long GAA.TTC tracts. Furthermore, the greater the extent of interruptions of the GAA.TTC repeats, the less inhibition of in vitro transcription was observed, as expected, based on the capacity of interruptions to inhibit the formation of sticky DNA. We propose that the interruptions introduce base mismatches into the R.R.Y triplex, which explains the observed chemical and biological properties.
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Affiliation(s)
- N Sakamoto
- Institute of Biosciences and Technology, Center for Genome Research, Texas A & M University System Health Science Center, Texas Medical Center, Houston, Texas 77030, USA
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Sakamoto N, Ohshima K, Montermini L, Pandolfo M, Wells RD. Sticky DNA, a self-associated complex formed at long GAA*TTC repeats in intron 1 of the frataxin gene, inhibits transcription. J Biol Chem 2001; 276:27171-7. [PMID: 11340071 DOI: 10.1074/jbc.m101879200] [Citation(s) in RCA: 149] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Friedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disease caused by the expansion of GAA.TTC repeats in the first intron of the frataxin (X25) gene. FRDA patients carrying two expanded GAA.TTC repeats show very low levels of mature frataxin mRNA and protein. A novel type of unusual DNA structure, sticky DNA, was previously found in the expanded GAA.TTC repeats from FRDA patients. To evaluate the effect of sticky DNA on transcription, in vitro transcription studies of (GAA.TTC)(n) repeats (where n = 9-150) were carried out using T7 or SP6 RNA polymerase. When a gel-isolated sticky DNA template was transcribed, the amount of full-length RNA synthesized was significantly reduced compared with the transcription of the linear template. Surprisingly, transcriptional inhibition was observed not only for the sticky DNA template but also another DNA molecule used as an internal control in an orientation-independent manner. The molecular mechanism of transcriptional inhibition by sticky DNA was a sequestration of the RNA polymerases by direct binding to the complex DNA structure. Moreover, plasmids containing the (GAAGGA.TCCTTC)(65) repeat, which does not form sticky DNA, did not inhibit in vitro transcription, as expected. These results suggest that the role of sticky DNA in FRDA may be the sequestration of transcription factors.
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Affiliation(s)
- N Sakamoto
- Institute of Biosciences and Technology, Center for Genome Research, Texas A & M University, Texas Medical Center, Houston, Texas 77030, USA
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34
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Patel PI, Isaya G. Friedreich ataxia: from GAA triplet-repeat expansion to frataxin deficiency. Am J Hum Genet 2001; 69:15-24. [PMID: 11391483 PMCID: PMC1226030 DOI: 10.1086/321283] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2001] [Accepted: 05/14/2001] [Indexed: 12/30/2022] Open
Affiliation(s)
- P I Patel
- Departments of Neurology and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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