1
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Uppili B, Faruq M. STRIDE-DB: a comprehensive database for exploration of instability and phenotypic relevance of short tandem repeats in the human genome. Database (Oxford) 2024; 2024:baae020. [PMID: 38602506 PMCID: PMC11008502 DOI: 10.1093/database/baae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/10/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
Short Tandem Repeats (STRs) are genetic markers made up of repeating DNA sequences. The variations of the STRs are widely studied in forensic analysis, population studies and genetic testing for a variety of neuromuscular disorders. Understanding polymorphic STR variation and its cause is crucial for deciphering genetic information and finding links to various disorders. In this paper, we present STRIDE-DB, a novel and unique platform to explore STR Instability and its Phenotypic Relevance, and a comprehensive database of STRs in the human genome. We utilized RepeatMasker to identify all the STRs in the human genome (hg19) and combined it with frequency data from the 1000 Genomes Project. STRIDE-DB, a user-friendly resource, plays a pivotal role in investigating the relationship between STR variation, instability and phenotype. By harnessing data from genome-wide association studies (GWAS), ClinVar database, Alu loci, Haploblocks in genome and Conservation of the STRs, it serves as an important tool for researchers exploring the variability of STRs in the human genome and its direct impact on phenotypes. STRIDE-DB has its broad applicability and significance in various research domains like forensic sciences and other repeat expansion disorders. Database URL: https://stridedb.igib.res.in.
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Affiliation(s)
- Bharathram Uppili
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India
- CSIR-HRDC Campus, Academy for Scientific and Innovative Research, Ghaziabad 201002, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India
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2
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Bonnet C. Unraveling the Missing Heritability in Late-Onset Cerebellar Ataxia. Mov Disord 2023. [PMID: 37157870 DOI: 10.1002/mds.29437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Affiliation(s)
- Céline Bonnet
- Laboratoire de génétique médicale, CHRU Nancy, Nancy, France
- Université de Lorraine, INSERM UMR_S1256, NGERE, Nancy, France
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3
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Zattera ML, Bruschi DP. Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome. Cells 2022; 11:cells11213373. [PMID: 36359770 PMCID: PMC9659126 DOI: 10.3390/cells11213373] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 12/02/2022] Open
Abstract
The impact of transposable elements (TEs) on the evolution of the eukaryote genome has been observed in a number of biological processes, such as the recruitment of the host’s gene expression network or the rearrangement of genome structure. However, TEs may also provide a substrate for the emergence of novel repetitive elements, which contribute to the generation of new genomic components during the course of the evolutionary process. In this review, we examine published descriptions of TEs that give rise to tandem sequences in an attempt to comprehend the relationship between TEs and the emergence of de novo satellite DNA families in eukaryotic organisms. We evaluated the intragenomic behavior of the TEs, the role of their molecular structure, and the chromosomal distribution of the paralogous copies that generate arrays of repeats as a substrate for the emergence of new repetitive elements in the genome. We highlight the involvement and importance of TEs in the eukaryote genome and its remodeling processes.
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Affiliation(s)
- Michelle Louise Zattera
- Departamento de Genética, Programa de Pós-Graduação em Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba 81530-000, PR, Brazil
| | - Daniel Pacheco Bruschi
- Departamento de Genética, Laboratorio de Citogenética Evolutiva e Conservação Animal, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba 81530-000, PR, Brazil
- Correspondence:
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4
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Masnovo C, Lobo AF, Mirkin SM. Replication dependent and independent mechanisms of GAA repeat instability. DNA Repair (Amst) 2022; 118:103385. [PMID: 35952488 PMCID: PMC9675320 DOI: 10.1016/j.dnarep.2022.103385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 11/20/2022]
Abstract
Trinucleotide repeat instability is a driver of human disease. Large expansions of (GAA)n repeats in the first intron of the FXN gene are the cause Friedreich's ataxia (FRDA), a progressive degenerative disorder which cannot yet be prevented or treated. (GAA)n repeat instability arises during both replication-dependent processes, such as cell division and intergenerational transmission, as well as in terminally differentiated somatic tissues. Here, we provide a brief historical overview on the discovery of (GAA)n repeat expansions and their association to FRDA, followed by recent advances in the identification of triplex H-DNA formation and replication fork stalling. The main body of this review focuses on the last decade of progress in understanding the mechanism of (GAA)n repeat instability during DNA replication and/or DNA repair. We propose that the discovery of additional mechanisms of (GAA)n repeat instability can be achieved via both comparative approaches to other repeat expansion diseases and genome-wide association studies. Finally, we discuss the advances towards FRDA prevention or amelioration that specifically target (GAA)n repeat expansions.
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Affiliation(s)
- Chiara Masnovo
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Ayesha F Lobo
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
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5
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Loureiro JR, Castro AF, Figueiredo AS, Silveira I. Molecular Mechanisms in Pentanucleotide Repeat Diseases. Cells 2022; 11:cells11020205. [PMID: 35053321 PMCID: PMC8773600 DOI: 10.3390/cells11020205] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 02/01/2023] Open
Abstract
The number of neurodegenerative diseases resulting from repeat expansion has increased extraordinarily in recent years. In several of these pathologies, the repeat can be transcribed in RNA from both DNA strands producing, at least, one toxic RNA repeat that causes neurodegeneration by a complex mechanism. Recently, seven diseases have been found caused by a novel intronic pentanucleotide repeat in distinct genes encoding proteins highly expressed in the cerebellum. These disorders are clinically heterogeneous being characterized by impaired motor function, resulting from ataxia or epilepsy. The role that apparently normal proteins from these mutant genes play in these pathologies is not known. However, recent advances in previously known spinocerebellar ataxias originated by abnormal non-coding pentanucleotide repeats point to a gain of a toxic function by the pathogenic repeat-containing RNA that abnormally forms nuclear foci with RNA-binding proteins. In cells, RNA foci have been shown to be formed by phase separation. Moreover, the field of repeat expansions has lately achieved an extraordinary progress with the discovery that RNA repeats, polyglutamine, and polyalanine proteins are crucial for the formation of nuclear membraneless organelles by phase separation, which is perturbed when they are expanded. This review will cover the amazing advances on repeat diseases.
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Affiliation(s)
- Joana R. Loureiro
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
| | - Ana F. Castro
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Ana S. Figueiredo
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Isabel Silveira
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence: ; Tel.: +351-2240-8800
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6
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Li J, Li Y, Wang J, Gonzalez TJ, Asokan A, Napierala JS, Napierala M. Defining Transcription Regulatory Elements in the Human Frataxin Gene: Implications for Gene Therapy. Hum Gene Ther 2020; 31:839-851. [PMID: 32527155 PMCID: PMC7462031 DOI: 10.1089/hum.2020.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022] Open
Abstract
Friedreich's ataxia (FRDA) is the most common inherited form of ataxia in humans. It is caused by severe downregulation of frataxin (FXN) expression instigated by hyperexpansion of the GAA repeats located in intron 1 of the FXN gene. Despite numerous studies focused on identifying compounds capable of stimulating FXN expression, current knowledge regarding cis-regulatory elements involved in FXN gene expression is lacking. Using a combination of episomal and genome-integrated constructs, we defined a minimal endogenous promoter sequence required to efficiently drive FXN expression in human cells. We generated 19 constructs varying in length of the DNA sequences upstream and downstream of the ATG start codon. Using transient transfection, we evaluated the capability of these constructs to drive FXN expression. These analyses allowed us to identify a region of the gene indispensable for FXN expression. Subsequently, selected constructs containing the FXN expression control regions of varying lengths were site specifically integrated into the genome of HEK293T and human-induced pluripotent stem cells (iPSCs). FXN expression was detected in iPSCs and persisted after differentiation to neuronal and cardiac cells, indicating lineage independent function of defined regulatory DNA sequences. Finally, based on these results, we generated AAV encoding miniFXN genes and demonstrated in vivo FXN expression in mice. Results of these studies identified FXN sequences necessary to express FXN in human and mouse cells and provided rationale for potential use of endogenous FXN sequence in gene therapy strategies for FRDA.
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Affiliation(s)
- Jixue Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yanjie Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jun Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Trevor J. Gonzalez
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Aravind Asokan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jill S. Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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7
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Paço A, Freitas R, Vieira-da-Silva A. Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene. Genes (Basel) 2019; 10:E1014. [PMID: 31817529 PMCID: PMC6947457 DOI: 10.3390/genes10121014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 11/18/2019] [Accepted: 11/29/2019] [Indexed: 01/24/2023] Open
Abstract
Eukaryotic genomes are rich in repetitive DNA sequences grouped in two classes regarding their genomic organization: tandem repeats and dispersed repeats. In tandem repeats, copies of a short DNA sequence are positioned one after another within the genome, while in dispersed repeats, these copies are randomly distributed. In this review we provide evidence that both tandem and dispersed repeats can have a similar organization, which leads us to suggest an update to their classification based on the sequence features, concretely regarding the presence or absence of retrotransposons/transposon specific domains. In addition, we analyze several studies that show that a repetitive element can be remodeled into repetitive non-coding or coding sequences, suggesting (1) an evolutionary relationship among DNA sequences, and (2) that the evolution of the genomes involved frequent repetitive sequence reshuffling, a process that we have designated as a "DNA remodeling mechanism". The alternative classification of the repetitive DNA sequences here proposed will provide a novel theoretical framework that recognizes the importance of DNA remodeling for the evolution and plasticity of eukaryotic genomes.
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Affiliation(s)
- Ana Paço
- MED-Mediterranean Institute for Agriculture, Environment and Development, University of Évora, 7002–554 Évora, Portugal;
| | - Renata Freitas
- IBMC-Institute for Molecular and Cell Biology, University of Porto, R. Campo Alegre 823, 4150–180 Porto, Portugal;
- I3S-Institute for Innovation and Health Research, University of Porto, Rua Alfredo Allen, 208, 4200–135 Porto, Portugal
- ICBAS-Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Ana Vieira-da-Silva
- MED-Mediterranean Institute for Agriculture, Environment and Development, University of Évora, 7002–554 Évora, Portugal;
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8
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Loureiro JR, Oliveira CL, Mota C, Castro AF, Costa C, Loureiro JL, Coutinho P, Martins S, Sequeiros J, Silveira I. Mutational mechanism for DAB1 (ATTTC) n insertion in SCA37: ATTTT repeat lengthening and nucleotide substitution. Hum Mutat 2019; 40:404-412. [PMID: 30588707 DOI: 10.1002/humu.23704] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/28/2018] [Accepted: 12/22/2018] [Indexed: 12/20/2022]
Abstract
Dynamic mutations by microsatellite instability are the molecular basis of a growing number of neuromuscular and neurodegenerative diseases. Repetitive stretches in the human genome may drive pathogenicity, either by expansion above a given threshold, or by insertion of abnormal tracts in nonpathogenic polymorphic repetitive regions, as is the case in spinocerebellar ataxia type 37 (SCA37). We have recently established that this neurodegenerative disease is caused by an (ATTTC)n insertion within an (ATTTT)n in a noncoding region of DAB1. We now investigated the mutational mechanism that originated the (ATTTC)n insertion within an ancestral (ATTTT)n . Approximately 3% of nonpathogenic (ATTTT)n alleles are interspersed by AT-rich motifs, contrarily to mutant alleles that are composed of pure (ATTTT)n and (ATTTC)n stretches. Haplotype studies in unaffected chromosomes suggested that the primary mutational mechanism, leading to the (ATTTC)n insertion, was likely one or more T>C substitutions in an (ATTTT)n pure allele of approximately 200 repeats. Then, the (ATTTC)n expanded in size, originating a deleterious allele in DAB1 that leads to SCA37. This is likely the mutational mechanism in three similar (TTTCA)n insertions responsible for familial myoclonic epilepsy. Because (ATTTT)n tracts are frequent in the human genome, many loci could be at risk for this mutational process.
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Affiliation(s)
- Joana R Loureiro
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal.,ICBAS, Universidade do Porto, Porto, Portugal
| | - Cláudia L Oliveira
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal
| | - Carolina Mota
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal
| | - Ana F Castro
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal
| | - Cristina Costa
- Department of Neurology, Hospital Prof. Doutor Fernando Fonseca, Amadora, Portugal
| | - José L Loureiro
- IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal.,UnIGENe, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Department of Neurology, Hospital São Sebastião, Feira, Portugal
| | - Paula Coutinho
- IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal.,UnIGENe, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sandra Martins
- Population Genetics & Evolution, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Jorge Sequeiros
- IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal.,ICBAS, Universidade do Porto, Porto, Portugal.,UnIGENe, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Isabel Silveira
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal
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9
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Barcia G, Rachid M, Magen M, Assouline Z, Koenig M, Funalot B, Barnerias C, Rötig A, Munnich A, Bonnefont JP, Steffann J. Pitfalls in molecular diagnosis of Friedreich ataxia. Eur J Med Genet 2018; 61:455-458. [PMID: 29530802 DOI: 10.1016/j.ejmg.2018.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 11/27/2022]
Abstract
Freidreich ataxia (FRDA) is the most common hereditary ataxia, nearly 98% of patients harbouring homozygous GAA expansions in intron 1 of the FXN gene (NM_000144.4). The remaining patients are compound heterozygous for an expansion and a point mutation or an exonic deletion. Molecular screening for FXN expansion is therefore focused on (GAA)n expansion analysis, commonly performed by triplet repeat primed PCR (PT-PCR). We report on an initial pitfall in the molecular characterization of a 15 year-old girl with Freidreich ataxia (FRDA) who carried a rare deletion in intron 1 of the FXN gene. Due to this deletion TP-PCR failed to amplify the GAA expansion. This exceptional configuration induced misinterpretation of the molecular defect in this patient, who was first reported as having no FXN expansion. NGS analysis of a panel of 212 genes involved in nuclear mitochondrial disorders further revealed an intragenic deletion encompassing exons 4-5 of the FXN gene. Modified TP-PCR analysis confirmed the presence of a classical (GAA)n expansion located in trans. This case points out the possible pitfalls in molecular diagnosis of FRDA in affected patients and their relatives: detection of the FXN expansion may be impaired by several non-pathological or pathological variants around the FXN (GAA)n repeat. We propose a new molecular strategy to accurately detect expansion by TP-PCR in FRDA patients.
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Affiliation(s)
- Giulia Barcia
- Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, INSERM UMR1163, Laboratoire des Maladies Mitochondriales, Paris, France; Service de Génétique, Groupe hospitalier Necker Enfants Malades, Assistance Publique -Hôpitaux de Paris, Paris, France
| | - Myriam Rachid
- Service de Génétique, Groupe hospitalier Necker Enfants Malades, Assistance Publique -Hôpitaux de Paris, Paris, France
| | - Maryse Magen
- Service de Génétique, Groupe hospitalier Necker Enfants Malades, Assistance Publique -Hôpitaux de Paris, Paris, France
| | - Zahra Assouline
- Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, INSERM UMR1163, Laboratoire des Maladies Mitochondriales, Paris, France; Service de Génétique, Groupe hospitalier Necker Enfants Malades, Assistance Publique -Hôpitaux de Paris, Paris, France
| | - Michel Koenig
- Laboratoire de Génétique de Maladies Rares, Institut Universitaire de Recherche Clinique, EA7402 Université de Montpellier, Montpellier Cedex, France
| | - Benoit Funalot
- Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, INSERM UMR1163, Laboratoire des Maladies Mitochondriales, Paris, France; Service de Génétique, Groupe hospitalier Necker Enfants Malades, Assistance Publique -Hôpitaux de Paris, Paris, France
| | - Christine Barnerias
- Service de neurologie pédiatrique et maladies métaboliques, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Agnès Rötig
- Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, INSERM UMR1163, Laboratoire des Maladies Mitochondriales, Paris, France
| | - Arnold Munnich
- Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, INSERM UMR1163, Laboratoire des Maladies Mitochondriales, Paris, France; Service de Génétique, Groupe hospitalier Necker Enfants Malades, Assistance Publique -Hôpitaux de Paris, Paris, France
| | - Jean-Paul Bonnefont
- Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, INSERM UMR1163, Laboratoire des Maladies Mitochondriales, Paris, France; Service de Génétique, Groupe hospitalier Necker Enfants Malades, Assistance Publique -Hôpitaux de Paris, Paris, France
| | - Julie Steffann
- Université Paris Descartes - Sorbonne Paris Cité, Institut Imagine, INSERM UMR1163, Laboratoire des Maladies Mitochondriales, Paris, France; Service de Génétique, Groupe hospitalier Necker Enfants Malades, Assistance Publique -Hôpitaux de Paris, Paris, France.
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10
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Krestel H, Meier JC. RNA Editing and Retrotransposons in Neurology. Front Mol Neurosci 2018; 11:163. [PMID: 29875629 PMCID: PMC5974252 DOI: 10.3389/fnmol.2018.00163] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/30/2018] [Indexed: 12/28/2022] Open
Abstract
Compared to sites in protein-coding sequences many more targets undergoing adenosine to inosine (A-to-I) RNA editing were discovered in non-coding regions of human cerebral transcripts, particularly in genetic transposable elements called retrotransposons. We review here the interaction mechanisms of RNA editing and retrotransposons and their impact on normal function and human neurological diseases. Exemplarily, A-to-I editing of retrotransposons embedded in protein-coding mRNAs can contribute to protein abundance and function via circular RNA formation, alternative splicing, and exonization or silencing of retrotransposons. Interactions leading to disease are not very well understood. We describe human diseases with involvement of the central nervous system including inborn errors of metabolism, neurodevelopmental disorders, neuroinflammatory and neurodegenerative and paroxysmal diseases, in which retrotransposons (Alu and/or L1 elements) appear to be causally involved in genetic rearrangements. Sole binding of single-stranded retrotransposon transcripts by RNA editing enzymes rather than enzymatic deamination may have a homeostatic effect on retrotransposon turnover. We also review evidence in support of the emerging pathophysiological function of A-to-I editing of retrotransposons in inflammation and its implication for different neurological diseases including amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer's and Parkinson's disease, and epilepsy.
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Affiliation(s)
- Heinz Krestel
- Department of Neurology, Bern University Hospital and University of Bern, Bern, Switzerland.,Department for BioMedical Research, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Jochen C Meier
- Division Cell Physiology, Zoological Institute, Technical University Braunschweig, Braunschweig, Germany
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11
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Murmann AE, Gao QQ, Putzbach WE, Patel M, Bartom ET, Law CY, Bridgeman B, Chen S, McMahon KM, Thaxton CS, Peter ME. Small interfering RNAs based on huntingtin trinucleotide repeats are highly toxic to cancer cells. EMBO Rep 2018; 19:embr.201745336. [PMID: 29440125 DOI: 10.15252/embr.201745336] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/09/2018] [Accepted: 01/11/2018] [Indexed: 12/13/2022] Open
Abstract
Trinucleotide repeat (TNR) expansions in the genome cause a number of degenerative diseases. A prominent TNR expansion involves the triplet CAG in the huntingtin (HTT) gene responsible for Huntington's disease (HD). Pathology is caused by protein and RNA generated from the TNR regions including small siRNA-sized repeat fragments. An inverse correlation between the length of the repeats in HTT and cancer incidence has been reported for HD patients. We now show that siRNAs based on the CAG TNR are toxic to cancer cells by targeting genes that contain long reverse complementary TNRs in their open reading frames. Of the 60 siRNAs based on the different TNRs, the six members in the CAG/CUG family of related TNRs are the most toxic to both human and mouse cancer cells. siCAG/CUG TNR-based siRNAs induce cell death in vitro in all tested cancer cell lines and slow down tumor growth in a preclinical mouse model of ovarian cancer with no signs of toxicity to the mice. We propose to explore TNR-based siRNAs as a novel form of anticancer reagents.
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Affiliation(s)
- Andrea E Murmann
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Quan Q Gao
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - William E Putzbach
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Monal Patel
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
| | - Calvin Y Law
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Bryan Bridgeman
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Siquan Chen
- Cellular Screening Center, Institute for Genomics & Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Kaylin M McMahon
- Department of Urology, Northwestern University, Chicago, IL, USA.,Simpson Querrey Institute (SQI) for BioNanotechnology, Chicago, IL, USA
| | - C Shad Thaxton
- Department of Urology, Northwestern University, Chicago, IL, USA.,Simpson Querrey Institute (SQI) for BioNanotechnology, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA.,International Institute for Nanotechnology, Evanston, IL, USA
| | - Marcus E Peter
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA .,Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA
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12
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Rohilla KJ, Gagnon KT. RNA biology of disease-associated microsatellite repeat expansions. Acta Neuropathol Commun 2017; 5:63. [PMID: 28851463 PMCID: PMC5574247 DOI: 10.1186/s40478-017-0468-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022] Open
Abstract
Microsatellites, or simple tandem repeat sequences, occur naturally in the human genome and have important roles in genome evolution and function. However, the expansion of microsatellites is associated with over two dozen neurological diseases. A common denominator among the majority of these disorders is the expression of expanded tandem repeat-containing RNA, referred to as xtrRNA in this review, which can mediate molecular disease pathology in multiple ways. This review focuses on the potential impact that simple tandem repeat expansions can have on the biology and metabolism of RNA that contain them and underscores important gaps in understanding. Merging the molecular biology of repeat expansion disorders with the current understanding of RNA biology, including splicing, transcription, transport, turnover and translation, will help clarify mechanisms of disease and improve therapeutic development.
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13
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Seixas AI, Loureiro JR, Costa C, Ordóñez-Ugalde A, Marcelino H, Oliveira CL, Loureiro JL, Dhingra A, Brandão E, Cruz VT, Timóteo A, Quintáns B, Rouleau GA, Rizzu P, Carracedo Á, Bessa J, Heutink P, Sequeiros J, Sobrido MJ, Coutinho P, Silveira I. A Pentanucleotide ATTTC Repeat Insertion in the Non-coding Region of DAB1, Mapping to SCA37, Causes Spinocerebellar Ataxia. Am J Hum Genet 2017; 101:87-103. [PMID: 28686858 DOI: 10.1016/j.ajhg.2017.06.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/13/2017] [Indexed: 01/01/2023] Open
Abstract
Advances in human genetics in recent years have largely been driven by next-generation sequencing (NGS); however, the discovery of disease-related gene mutations has been biased toward the exome because the large and very repetitive regions that characterize the non-coding genome remain difficult to reach by that technology. For autosomal-dominant spinocerebellar ataxias (SCAs), 28 genes have been identified, but only five SCAs originate from non-coding mutations. Over half of SCA-affected families, however, remain without a genetic diagnosis. We used genome-wide linkage analysis, NGS, and repeat analysis to identify an (ATTTC)n insertion in a polymorphic ATTTT repeat in DAB1 in chromosomal region 1p32.2 as the cause of autosomal-dominant SCA; this region has been previously linked to SCA37. The non-pathogenic and pathogenic alleles have the configurations [(ATTTT)7-400] and [(ATTTT)60-79(ATTTC)31-75(ATTTT)58-90], respectively. (ATTTC)n insertions are present on a distinct haplotype and show an inverse correlation between size and age of onset. In the DAB1-oriented strand, (ATTTC)n is located in 5' UTR introns of cerebellar-specific transcripts arising mostly during human fetal brain development from the usage of alternative promoters, but it is maintained in the adult cerebellum. Overexpression of the transfected (ATTTC)58 insertion, but not (ATTTT)n, leads to abnormal nuclear RNA accumulation. Zebrafish embryos injected with RNA of the (AUUUC)58 insertion, but not (AUUUU)n, showed lethal developmental malformations. Together, these results establish an unstable repeat insertion in DAB1 as a cause of cerebellar degeneration; on the basis of the genetic and phenotypic evidence, we propose this mutation as the molecular basis for SCA37.
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14
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Tamarit J, Obis È, Ros J. Oxidative stress and altered lipid metabolism in Friedreich ataxia. Free Radic Biol Med 2016; 100:138-146. [PMID: 27296838 DOI: 10.1016/j.freeradbiomed.2016.06.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 06/07/2016] [Accepted: 06/10/2016] [Indexed: 12/31/2022]
Abstract
Friedreich ataxia is a genetic disease caused by the deficiency of frataxin, a mitochondrial protein. Frataxin deficiency impacts in the cell physiology at several levels. One of them is oxidative stress with consequences in terms of protein dysfunctions and metabolic alterations. Among others, alterations in lipid metabolism have been observed in several models of the disease. In this review we summarize the current knowledge of the molecular basis of the disease, the relevance of oxidative stress and the therapeutic strategies based on reduction of mitochondrial reactive oxygen species production. Finally, we will focus the interest in alterations of lipid metabolism as a consequence of mitochondrial dysfunction and describe the therapeutic approaches based on targeting lipid metabolism.
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Affiliation(s)
- Jordi Tamarit
- Departament de Ciències Mèdiques Bàsiques, IRB-Lleida, Universitat de Lleida, Lleida, Spain
| | - Èlia Obis
- Departament de Ciències Mèdiques Bàsiques, IRB-Lleida, Universitat de Lleida, Lleida, Spain
| | - Joaquim Ros
- Departament de Ciències Mèdiques Bàsiques, IRB-Lleida, Universitat de Lleida, Lleida, Spain.
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15
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Chapuis MP, Plantamp C, Streiff R, Blondin L, Piou C. Microsatellite evolutionary rate and pattern in Schistocerca gregaria inferred from direct observation of germline mutations. Mol Ecol 2015; 24:6107-19. [PMID: 26562076 DOI: 10.1111/mec.13465] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 01/21/2023]
Abstract
Unravelling variation among taxonomic orders regarding the rate of evolution in microsatellites is crucial for evolutionary biology and population genetics research. The mean mutation rate of microsatellites tends to be lower in arthropods than in vertebrates, but data are scarce and mostly concern accumulation of mutations in model species. Based on parent-offspring segregations and a hierarchical Bayesian model, the mean rate of mutation in the orthopteran insect Schistocerca gregaria was estimated at 2.1e(-4) per generation per untranscribed dinucleotide locus. This is close to vertebrate estimates and one order of magnitude higher than estimates from species of other arthropod orders, such as Drosophila melanogaster and Daphnia pulex. We also found evidence of a directional bias towards expansions even for long alleles and exceptionally large ranges of allele sizes. Finally, at transcribed microsatellites, the mean rate of mutation was half the rate found at untranscribed loci and the mutational model deviated from that usually considered, with most mutations involving multistep changes that avoid disrupting the reading frame. Our direct estimates of mutation rate were discussed in the light of peculiar biological and genomic features of S. gregaria, including specificities in mismatch repair and the dependence of its activity to allele length. Shedding new light on the mutational dynamics of grasshopper microsatellites is of critical importance for a number of research fields. As an illustration, we showed how our findings improve microsatellite application in population genetics, by obtaining a more precise estimation of S. gregaria effective population size from a published data set based on the same microsatellites.
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Affiliation(s)
- M-P Chapuis
- CIRAD, UMR CBGP, Montpellier, F-34398, France
| | - C Plantamp
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Villeurbanne, 69622, France
| | - R Streiff
- INRA, UMR CBGP, Montpellier, F-34398, France.,INRA, UMR DGIMI, Montpellier, F-34000, France
| | - L Blondin
- CIRAD, UPR B-AMR, Montpellier, F-34398, France
| | - C Piou
- CIRAD, UMR CBGP, Montpellier, F-34398, France
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16
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Faggianelli N, Puglisi R, Veneziano L, Romano S, Frontali M, Vannocci T, Fortuni S, Testi R, Pastore A. Analyzing the Effects of a G137V Mutation in the FXN Gene. Front Mol Neurosci 2015; 8:66. [PMID: 26635519 PMCID: PMC4658817 DOI: 10.3389/fnmol.2015.00066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/23/2015] [Indexed: 12/15/2022] Open
Abstract
Reduced levels of frataxin, an essential mitochondrial protein involved in the regulation of iron-sulfur cluster biogenesis, are responsible for the recessive neurodegenerative Friedreich Ataxia (FRDA). Expansion of a GAA triplet in the first intron of the FRDA is essential for disease development which causes partial silencing of frataxin. In the vast majority of cases, patients are homozygotes for the expansion, but a small number of FRDA patients are heterozygotes for expansion and point mutations in the frataxin coding frame. In this study, we analyze the effects of a point mutation G137V. The patient P94–2, with a history of alcohol and drug abuse, showed a FRDA onset at the border between the classic and late onset phenotype. We applied a combination of biophysical and biochemical methods to characterize its effects on the structure, folding and activity of frataxin. Our study reveals no impairment of the structure or activity of the protein but a reduced folding stability. We suggest that the mutation causes misfolding of the native chain with consequent reduction of the protein concentration in the patient and discuss the possible mechanism of disease.
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Affiliation(s)
- Nathalie Faggianelli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London London, UK
| | - Rita Puglisi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London London, UK
| | | | - Silvia Romano
- Sant'Andrea Hospital, University of Rome La Sapienza Rome, Italy
| | | | - Tommaso Vannocci
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London London, UK
| | - Silvia Fortuni
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata" Rome, Italy
| | - Roberto Testi
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata" Rome, Italy
| | - Annalisa Pastore
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London London, UK
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17
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Abstract
RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics.
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Affiliation(s)
- Viachaslau Bernat
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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18
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Butler JS, Napierala M. Friedreich's ataxia--a case of aberrant transcription termination? Transcription 2015; 6:33-6. [PMID: 25831023 PMCID: PMC4581357 DOI: 10.1080/21541264.2015.1026538] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/02/2015] [Indexed: 11/02/2022] Open
Abstract
Reduced expression of the mitochondrial protein Frataxin (FXN) is the underlying cause of Friedreich's ataxia. We propose a model of premature termination of FXN transcription induced by pathogenic expanded GAA repeats that links R-loop structures, antisense transcription, and heterochromatin formation as a novel mechanism of transcriptional repression in Friedreich's ataxia.
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Affiliation(s)
- Jill Sergesketter Butler
- University of Alabama at Birmingham; Department of Biochemistry and Molecular Genetics; UAB Stem Cell Institute; Birmingham, AL USA
| | - Marek Napierala
- University of Alabama at Birmingham; Department of Biochemistry and Molecular Genetics; UAB Stem Cell Institute; Birmingham, AL USA
- Department of Molecular Biomedicine; Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznan, Poland
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19
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Li Y, Polak U, Bhalla AD, Rozwadowska N, Butler JS, Lynch DR, Dent SYR, Napierala M. Excision of Expanded GAA Repeats Alleviates the Molecular Phenotype of Friedreich's Ataxia. Mol Ther 2015; 23:1055-1065. [PMID: 25758173 DOI: 10.1038/mt.2015.41] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 03/03/2015] [Indexed: 12/21/2022] Open
Abstract
Friedreich's ataxia (FRDA) is an autosomal recessive neurological disease caused by expansions of guanine-adenine-adenine (GAA) repeats in intron 1 of the frataxin (FXN) gene. The expansion results in significantly decreased frataxin expression. We report that human FRDA cells can be corrected by zinc finger nuclease-mediated excision of the expanded GAA repeats. Editing of a single expanded GAA allele created heterozygous, FRDA carrier-like cells and significantly increased frataxin expression. This correction persisted during reprogramming of zinc finger nuclease-edited fibroblasts to induced pluripotent stem cells and subsequent differentiation into neurons. The expression of FRDA biomarkers was normalized in corrected patient cells and disease-associated phenotypes, such as decreases in aconitase activity and intracellular ATP levels, were reversed in zinc finger nuclease corrected neuronal cells. Genetically and phenotypically corrected patient cells represent not only a preferred disease-relevant model system to study pathogenic mechanisms, but also a critical step towards development of cell replacement therapy.
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Affiliation(s)
- Yanjie Li
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Urszula Polak
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA; Department of Cell Biology, Poznan University of Medical Sciences, Poznan, Poland
| | - Angela D Bhalla
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Natalia Rozwadowska
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA; Institute of Human Genetics, Polish Academy of Science, Poznan, Poland
| | - Jill Sergesketter Butler
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David R Lynch
- Division of Neurology and Pediatrics, Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA; Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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20
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Yandim C, Natisvili T, Festenstein R. Gene regulation and epigenetics in Friedreich's ataxia. J Neurochem 2013; 126 Suppl 1:21-42. [PMID: 23859339 DOI: 10.1111/jnc.12254] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 02/05/2013] [Accepted: 03/06/2013] [Indexed: 12/20/2022]
Abstract
This is an exciting time in the study of Friedreich's ataxia. Over the last 10 years much progress has been made in uncovering the mechanisms, whereby the Frataxin gene is silenced by (GAA)n repeat expansions and several of the findings are now ripe for testing in the clinic. The discovery that the Frataxin gene is heterochromatinised and that this can be antagonised in vivo has led to the tantalizing possibility that the disease might be amenable to a more radical therapeutic approach involving epigenetic modifiers. Here, we set out to review progress in the understanding of the fundamental mechanisms whereby genes are regulated at this level and how these findings have been applied to achieve a deeper understanding of the dysregulation that occurs as the primary genetic lesion in Friedreich's ataxia.
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Affiliation(s)
- Cihangir Yandim
- Gene Control Mechanisms and Disease, Department of Medicine and MRC Clinical Sciences Centre, Imperial College London, London, UK
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21
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Grandi FC, An W. Non-LTR retrotransposons and microsatellites: Partners in genomic variation. Mob Genet Elements 2013; 3:e25674. [PMID: 24195012 PMCID: PMC3812793 DOI: 10.4161/mge.25674] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/07/2013] [Accepted: 07/09/2013] [Indexed: 01/10/2023] Open
Abstract
The human genome is laden with both non-LTR (long-terminal repeat) retrotransposons and microsatellite repeats. Both types of sequences are able to, either actively or passively, mutagenize the genomes of human individuals and are therefore poised to dynamically alter the human genomic landscape across generations. Non-LTR retrotransposons, such as L1 and Alu, are a major source of new microsatellites, which are born both concurrently and subsequently to L1 and Alu integration into the genome. Likewise, the mutation dynamics of microsatellite repeats have a direct impact on the fitness of their non-LTR retrotransposon parent owing to microsatellite expansion and contraction. This review explores the interactions and dynamics between non-LTR retrotransposons and microsatellites in the context of genomic variation and evolution.
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Affiliation(s)
- Fiorella C Grandi
- School of Molecular Biosciences and Center for Reproductive Biology; Washington State University; Pullman, WA USA
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22
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Pascali C, Teichmann M. RNA polymerase III transcription - regulated by chromatin structure and regulator of nuclear chromatin organization. Subcell Biochem 2013; 61:261-287. [PMID: 23150255 DOI: 10.1007/978-94-007-4525-4_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RNA polymerase III (Pol III) transcription is regulated by modifications of the chromatin. DNA methylation and post-translational modifications of histones, such as acetylation, phosphorylation and methylation have been linked to Pol III transcriptional activity. In addition to being regulated by modifications of DNA and histones, Pol III genes and its transcription factors have been implicated in the organization of nuclear chromatin in several organisms. In yeast, the ability of the Pol III transcription system to contribute to nuclear organization seems to be dependent on direct interactions of Pol III genes and/or its transcription factors TFIIIC and TFIIIB with the structural maintenance of chromatin (SMC) protein-containing complexes cohesin and condensin. In human cells, Pol III genes and transcription factors have also been shown to colocalize with cohesin and the transcription regulator and genome organizer CCCTC-binding factor (CTCF). Furthermore, chromosomal sites have been identified in yeast and humans that are bound by partial Pol III machineries (extra TFIIIC sites - ETC; chromosome organizing clamps - COC). These ETCs/COC as well as Pol III genes possess the ability to act as boundary elements that restrict spreading of heterochromatin.
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Affiliation(s)
- Chiara Pascali
- Institut Européen de Chimie et Biologie (IECB), Université Bordeaux Segalen / INSERM U869, 2, rue Robert Escarpit, 33607, Pessac, France
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23
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Zhang Y, Shishkin AA, Nishida Y, Marcinkowski-Desmond D, Saini N, Volkov KV, Mirkin SM, Lobachev KS. Genome-wide screen identifies pathways that govern GAA/TTC repeat fragility and expansions in dividing and nondividing yeast cells. Mol Cell 2012; 48:254-65. [PMID: 22959270 DOI: 10.1016/j.molcel.2012.08.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 07/06/2012] [Accepted: 08/02/2012] [Indexed: 12/20/2022]
Abstract
Triplex structure-forming GAA/TTC repeats pose a dual threat to the eukaryotic genome integrity. Their potential to expand can lead to gene inactivation, the cause of Friedreich's ataxia disease in humans. In model systems, long GAA/TTC tracts also act as chromosomal fragile sites that can trigger gross chromosomal rearrangements. The mechanisms that regulate the metabolism of GAA/TTC repeats are poorly understood. We have developed an experimental system in the yeast Saccharomyces cerevisiae that allows us to systematically identify genes crucial for maintaining the repeat stability. Two major groups of mutants defective in DNA replication or transcription initiation are found to be prone to fragility and large-scale expansions. We demonstrate that problems imposed by the repeats during DNA replication in actively dividing cells and during transcription initiation in nondividing cells can culminate in genome instability. We propose that similar mechanisms can mediate detrimental metabolism of GAA/TTC tracts in human cells.
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Affiliation(s)
- Yu Zhang
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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24
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Kurosaki T, Ueda S, Ishida T, Abe K, Ohno K, Matsuura T. The unstable CCTG repeat responsible for myotonic dystrophy type 2 originates from an AluSx element insertion into an early primate genome. PLoS One 2012; 7:e38379. [PMID: 22723857 PMCID: PMC3378579 DOI: 10.1371/journal.pone.0038379] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 05/04/2012] [Indexed: 02/02/2023] Open
Abstract
Myotonic dystrophy type 2 (DM2) is a subtype of the myotonic dystrophies, caused by expansion of a tetranucleotide CCTG repeat in intron 1 of the zinc finger protein 9 (ZNF9) gene. The expansions are extremely unstable and variable, ranging from 75–11,000 CCTG repeats. This unprecedented repeat size and somatic heterogeneity make molecular diagnosis of DM2 difficult, and yield variable clinical phenotypes. To better understand the mutational origin and instability of the ZNF9 CCTG repeat, we analyzed the repeat configuration and flanking regions in 26 primate species. The 3′-end of an AluSx element, flanked by target site duplications (5′-ACTRCCAR-3′or 5′-ACTRCCARTTA-3′), followed the CCTG repeat, suggesting that the repeat was originally derived from the Alu element insertion. In addition, our results revealed lineage-specific repetitive motifs: pyrimidine (CT)-rich repeat motifs in New World monkeys, dinucleotide (TG) repeat motifs in Old World monkeys and gibbons, and dinucleotide (TG) and tetranucleotide (TCTG and/or CCTG) repeat motifs in great apes and humans. Moreover, these di- and tetra-nucleotide repeat motifs arose from the poly (A) tail of the AluSx element, and evolved into unstable CCTG repeats during primate evolution. Alu elements are known to be the source of microsatellite repeats responsible for two other repeat expansion disorders: Friedreich ataxia and spinocerebellar ataxia type 10. Taken together, these findings raise questions as to the mechanism(s) by which Alu-mediated repeats developed into the large, extremely unstable expansions common to these three disorders.
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Affiliation(s)
- Tatsuaki Kurosaki
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takafumi Ishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Koji Abe
- Department of Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tohru Matsuura
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- * E-mail:
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25
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Kumari D, Usdin K. Is Friedreich ataxia an epigenetic disorder? Clin Epigenetics 2012; 4:2. [PMID: 22414340 PMCID: PMC3305337 DOI: 10.1186/1868-7083-4-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 01/30/2012] [Indexed: 12/16/2022] Open
Abstract
Friedreich ataxia (FRDA) is a debilitating and frequently fatal neurological disorder that is recessively inherited. It belongs to the group of genetic disorders known as the Repeat Expansion Diseases, in which pathology arises from the deleterious consequences of the inheritance of a tandem repeat array whose repeat number exceeds a critical threshold. In the case of FRDA, the repeat unit is the triplet GAA•TTC and the tandem array is located in the first intron of the frataxin (FXN) gene. Pathology arises because expanded alleles make lower than normal levels of mature FXN mRNA and thus reduced levels of frataxin, the FXN gene product. The repeats form a variety of unusual DNA structures that have the potential to affect gene expression in a number of ways. For example, triplex formation in vitro and in bacteria leads to the formation of persistent RNA:DNA hybrids that block transcription. In addition, these repeats have been shown to affect splicing in model systems. More recently, it has been shown that the region flanking the repeats in the FXN gene is enriched for epigenetic marks characteristic of transcriptionally repressed regions of the genome. However, exactly how repeats in an intron cause the FXN mRNA deficit in FRDA has been the subject of much debate. Identifying the mechanism or mechanisms responsible for the FXN mRNA deficit in FRDA is important for the development of treatments for this currently incurable disorder. This review discusses evidence for and against different models for the repeat-mediated mRNA deficit.
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Affiliation(s)
- Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA.
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26
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Kozlowski P, de Mezer M, Krzyzosiak WJ. Trinucleotide repeats in human genome and exome. Nucleic Acids Res 2010; 38:4027-39. [PMID: 20215431 PMCID: PMC2896521 DOI: 10.1093/nar/gkq127] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Trinucleotide repeats (TNRs) are of interest in genetics because they are used as markers for tracing genotype–phenotype relations and because they are directly involved in numerous human genetic diseases. In this study, we searched the human genome reference sequence and annotated exons (exome) for the presence of uninterrupted triplet repeat tracts composed of six or more repeated units. A list of 32 448 TNRs and 878 TNR-containing genes was generated and is provided herein. We found that some triplet repeats, specifically CNG, are overrepresented, while CTT, ATC, AAC and AAT are underrepresented in exons. This observation suggests that the occurrence of TNRs in exons is not random, but undergoes positive or negative selective pressure. Additionally, TNR types strongly determine their localization in mRNA sections (ORF, UTRs). Most genes containing exon-overrepresented TNRs are associated with gene ontology-defined functions. Surprisingly, many groups of genes that contain TNR types coding for different homo-amino acid tracts associate with the same transcription-related GO categories. We propose that TNRs have potential to be functional genetic elements and that their variation may be involved in the regulation of many common phenotypes; as such, TNR polymorphisms should be considered a priority in association studies.
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Affiliation(s)
- Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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Richard GF, Kerrest A, Dujon B. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 2008; 72:686-727. [PMID: 19052325 PMCID: PMC2593564 DOI: 10.1128/mmbr.00011-08] [Citation(s) in RCA: 323] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.
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Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA2171, Université Pierre et Marie Curie, UFR927, 25 rue du Dr. Roux, F-75015, Paris, France.
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Kim HM, Narayanan V, Mieczkowski PA, Petes TD, Krasilnikova MM, Mirkin SM, Lobachev KS. Chromosome fragility at GAA tracts in yeast depends on repeat orientation and requires mismatch repair. EMBO J 2008; 27:2896-906. [PMID: 18833189 DOI: 10.1038/emboj.2008.205] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 09/15/2008] [Indexed: 11/10/2022] Open
Abstract
Expansion of triplex-forming GAA/TTC repeats in the first intron of FXN gene results in Friedreich's ataxia. Besides FXN, there are a number of other polymorphic GAA/TTC loci in the human genome where the size variations thus far have been considered to be a neutral event. Using yeast as a model system, we demonstrate that expanded GAA/TTC repeats represent a threat to eukaryotic genome integrity by triggering double-strand breaks and gross chromosomal rearrangements. The fragility potential strongly depends on the length of the tracts and orientation of the repeats relative to the replication origin, which correlates with their propensity to adopt triplex structure and to block replication progression. We show that fragility is mediated by mismatch repair machinery and requires the MutSbeta and endonuclease activity of MutLalpha. We suggest that the mechanism of GAA/TTC-induced chromosomal aberrations defined in yeast can also operate in human carriers with expanded tracts.
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Affiliation(s)
- Hyun-Min Kim
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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29
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Baralle M, Pastor T, Bussani E, Pagani F. Influence of Friedreich ataxia GAA noncoding repeat expansions on pre-mRNA processing. Am J Hum Genet 2008; 83:77-88. [PMID: 18597733 PMCID: PMC2443835 DOI: 10.1016/j.ajhg.2008.06.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Revised: 06/16/2008] [Accepted: 06/18/2008] [Indexed: 12/27/2022] Open
Abstract
The intronic GAA repeat expansion in the frataxin (FXN) gene causes the hereditary neurodegenerative disorder Friedreich ataxia. Although it is generally believed that GAA repeats block transcription elongation, direct proof in eukaryotic systems is lacking. We tested in hybrid minigenes the effect of GAA and TTC repeats on nascent transcription and pre-mRNA processing. Unexpectedly, disease-causing GAA(100) repeats did not affect transcriptional elongation in a nuclear HeLa Run On assay, nor did they affect pre-mRNA transcript abundance. However, they did result in a complex defect in pre-mRNA processing. The insertion of GAA but not TTC repeats downstream of reporter exons resulted in their partial or complete exclusion from the mature mRNAs and in the generation of a variety of aberrant splicing products. This effect of GAA repeats was observed to be position and context dependent; their insertion at different distances from the reporter exons had a variable effect on splice-site selection. In addition, GAA repeats bind to a multitude of different splicing factors and induced the accumulation of an upstream pre-mRNA splicing intermediate, which is not turned over into mature mRNA. When embedded in the homologous frataxin minigene system, the GAA repeats did not affect the pre-mRNA transcript abundance but did significantly reduce the splicing efficiency of the first intron. These data indicate an association between GAA noncoding repeats and aberrant pre-mRNA processing because binding of transcribed GAA repeats to a multitude of trans-acting splicing factors can interfere with normal turnover of intronic RNA and thus lead to its degradation and a lower abundance of mature mRNA.
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Affiliation(s)
- Marco Baralle
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste 34012, Italy
| | - Tibor Pastor
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste 34012, Italy
| | - Erica Bussani
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste 34012, Italy
| | - Franco Pagani
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste 34012, Italy
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Kelkar YD, Tyekucheva S, Chiaromonte F, Makova KD. The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Res 2007; 18:30-8. [PMID: 18032720 DOI: 10.1101/gr.7113408] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mutation rates of microsatellites vary greatly among loci. The causes of this heterogeneity remain largely enigmatic yet are crucial for understanding numerous human neurological diseases and genetic instability in cancer. In this first genome-wide study, the relative contributions of intrinsic features and regional genomic factors to the variation in mutability among orthologous human-chimpanzee microsatellites are investigated with resampling and regression techniques. As a result, we uncover the intricacies of microsatellite mutagenesis as follows. First, intrinsic features (repeat number, length, and motif size), which all influence the probability and rate of slippage, are the strongest predictors of mutability. Second, mutability increases nonuniformly with length, suggesting that processes additional to slippage, such as faulty repair, contribute to mutations. Third, mutability varies among microsatellites with different motif composition likely due to dissimilarities in secondary DNA structure formed by their slippage intermediates. Fourth, mutability of mononucleotide microsatellites is impacted by their location on sex chromosomes vs. autosomes and inside vs. outside of Alu repeats, the former confirming the importance of replication and the latter suggesting a role for gene conversion. Fifth, transcription status and location in a particular isochore do not influence microsatellite mutability. Sixth, compared with intrinsic features, regional genomic factors have only minor effects. Finally, our regression models explain approximately 90% of variation in microsatellite mutability and can generate useful predictions for the studies of human diseases, forensics, and conservation genetics.
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Affiliation(s)
- Yogeshwar D Kelkar
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
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31
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Greene E, Mahishi L, Entezam A, Kumari D, Usdin K. Repeat-induced epigenetic changes in intron 1 of the frataxin gene and its consequences in Friedreich ataxia. Nucleic Acids Res 2007; 35:3383-90. [PMID: 17478498 PMCID: PMC1904289 DOI: 10.1093/nar/gkm271] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 04/06/2007] [Accepted: 04/09/2007] [Indexed: 11/22/2022] Open
Abstract
Friedreich ataxia (FRDA), the most common hereditary ataxia, is caused by mutations in the frataxin (FXN) gene. The vast majority of FRDA mutations involve expansion of a GAA*TTC-repeat tract in intron 1, which leads to an FXN mRNA deficit. Bisulfite mapping demonstrates that the region adjacent to the repeat was methylated in both unaffected and affected individuals. However, methylation was more extensive in patients. Additionally, three residues were almost completely methylation-free in unaffected individuals but almost always methylated in those with FRDA. One of these residues is located within an E-box whose deletion caused a significant drop in promoter activity in reporter assays. Elevated levels of histone H3 dimethylated on lysine 9 were seen in FRDA cells consistent with a more repressive chromatin organization. Such chromatin is known to reduce transcription elongation. This may be one way in which the expanded repeats contribute to the frataxin deficit in FRDA. Our data also suggest that repeat-mediated chromatin changes may also affect transcription initiation by blocking binding of factors that increase frataxin promoter activity. Our results also raise the possibility that the repeat-mediated increases in DNA methylation in the FXN gene in FRDA patients are secondary to the chromatin changes.
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Affiliation(s)
| | | | | | | | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
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32
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M. Rindler P, Clark RM, Pollard LM, De Biase I, Bidichandani SI. Replication in mammalian cells recapitulates the locus-specific differences in somatic instability of genomic GAA triplet-repeats. Nucleic Acids Res 2006; 34:6352-61. [PMID: 17142224 PMCID: PMC1669776 DOI: 10.1093/nar/gkl846] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 10/09/2006] [Accepted: 10/09/2006] [Indexed: 11/21/2022] Open
Abstract
Friedreich ataxia is caused by an expanded (GAA.TTC)n sequence in intron 1 of the FXN gene. Small pool PCR analysis showed that pure (GAA.TTC)44+ sequences at the FXN locus are unstable in somatic cells in vivo, displaying both expansions and contractions. On searching the entire human and mouse genomes we identified three other genomic loci with pure (GAA.TTC)44+ sequences. Alleles at these loci showed mutation loads of <1% compared with 6.3-30% for FXN alleles of similar length, indicating that somatic instability in vivo is regulated by locus-specific factors. Since distance between the origin of replication and the (CTG.CAG)n sequence modulates repeat instability in mammalian cells, we tested if this could also recapitulate the locus-specific differences for genomic (GAA.TTC)n sequences. Repeat instability was evaluated following replication of a (GAA.TTC)115 sequence in transfected COS1 cells under the control of the SV40 origin of replication located at one of five different distances from the repeat. Indeed, depending on the location of the SV40 origin relative to the (GAA.TTC)n sequence, we noted either no instability, predominant expansion or both expansion and contraction. These data suggest that mammalian DNA replication is a possible mechanism underlying locus-specific differences in instability of GAA triplet-repeat sequences.
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Affiliation(s)
- Paul M. Rindler
- Department of Biochemistry and Molecular BiologyOklahoma City, OK 73104, USA
| | - Rhonda M. Clark
- Department of Biochemistry and Molecular BiologyOklahoma City, OK 73104, USA
| | - Laura M. Pollard
- Department of Biochemistry and Molecular BiologyOklahoma City, OK 73104, USA
| | - Irene De Biase
- Department of Biochemistry and Molecular BiologyOklahoma City, OK 73104, USA
| | - Sanjay I. Bidichandani
- Department of Biochemistry and Molecular BiologyOklahoma City, OK 73104, USA
- Department of Pediatrics, University of Oklahoma Health Sciences CenterOklahoma City, OK 73104, USA
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Buschiazzo E, Gemmell NJ. The rise, fall and renaissance of microsatellites in eukaryotic genomes. Bioessays 2006; 28:1040-50. [PMID: 16998838 DOI: 10.1002/bies.20470] [Citation(s) in RCA: 190] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microsatellites are among the most versatile of genetic markers, being used in an impressive number of biological applications. However, the evolutionary dynamics of these markers remain a source of contention. Almost 20 years after the discovery of these ubiquitous simple sequences, new genomic data are clarifying our understanding of the structure, distribution and variability of microsatellites in genomes, especially for the eukaryotes. While these new data provide a great deal of descriptive information about the nature and abundance of microsatellite sequences within eukaryotic genomes, there have been few attempts to synthesise this information to develop a global concept of evolution. This review provides an up-to-date account of the mutational processes, biases and constraints believed to be involved in the evolution of microsatellites, particularly with respect to the creation and degeneration of microsatellites, which we assert may be broadly viewed as a life cycle. In addition, we identify areas of contention that require further research and propose some possible directions for future investigation.
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Affiliation(s)
- Emmanuel Buschiazzo
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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Burnett R, Melander C, Puckett JW, Son LS, Wells RD, Dervan PB, Gottesfeld JM. DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA.TTC repeats in Friedreich's ataxia. Proc Natl Acad Sci U S A 2006; 103:11497-502. [PMID: 16857735 PMCID: PMC1544198 DOI: 10.1073/pnas.0604939103] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The DNA abnormality found in 98% of Friedreich's ataxia (FRDA) patients is the unstable hyperexpansion of a GAA.TTC triplet repeat in the first intron of the frataxin gene. Expanded GAA.TTC repeats result in decreased transcription and reduced levels of frataxin protein in affected individuals. Beta-alanine-linked pyrrole-imidazole polyamides bind GAA.TTC tracts with high affinity and disrupt the intramolecular DNA.DNA-associated region of the sticky-DNA conformation formed by long GAA.TTC repeats. Fluorescent polyamide-Bodipy conjugates localize in the nucleus of a lymphoid cell line derived from a FRDA patient. The synthetic ligands increase transcription of the frataxin gene in cell culture, resulting in increased levels of frataxin protein. DNA microarray analyses indicate that a limited number of genes are significantly affected in FRDA cells. Polyamides may increase transcription by altering the DNA conformation of genes harboring long GAA.TTC repeats or by chromatin opening.
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Affiliation(s)
- Ryan Burnett
- *Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Christian Melander
- *Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - James W. Puckett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - Leslie S. Son
- Center for Genome Research, Institute for Biosciences and Technology, Texas A&M University System Health Science Center, 2121 West Holcombe Boulevard, Houston, TX 77030
| | - Robert D. Wells
- Center for Genome Research, Institute for Biosciences and Technology, Texas A&M University System Health Science Center, 2121 West Holcombe Boulevard, Houston, TX 77030
| | - Peter B. Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - Joel M. Gottesfeld
- *Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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35
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Zemánek M, Kypr J, Vorlícková M. Conformational properties of DNA containing (CCA)n and (TGG)n trinucleotide repeats. Int J Biol Macromol 2005; 36:23-32. [PMID: 15896838 DOI: 10.1016/j.ijbiomac.2005.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2004] [Revised: 03/11/2005] [Accepted: 03/11/2005] [Indexed: 10/25/2022]
Abstract
We have used CD spectroscopy, polyacrylamide gel electrophoresis, and UV absorption spectroscopy to study conformational properties of DNA fragments containing (CCA)n and (TGG)n repeats, which are the most length-polymorphic microsatellite sequences of the human genome. The (CCA)n fragments are random single strands at neutral and alkaline pH but they fold into intramolecular intercalated cytosine tetraplexes at mildly acid pH values. More acid values stabilize intermolecular tetraplex formation. The behavior of (TGG)n repeats is more complex. They form hairpins or antiparallel homoduplexes in low salt solutions which, however, are transformed into parallel-stranded guanine tetraplexes at physiological KCl concentrations. Their molecularity depends on the repeat number: (TGG)4 associates into an octameric complex, (TGG)8 forms tetramolecular complexes. (TGG)n with odd repeat numbers (5, 7, and 9) generate bimolecular and tetramolecular tetraplexes. The only (TGG)7 folds into an intramolecular tetraplex at low KCl concentrations, which is antiparallel-stranded. Moreover, the (TGG)(n) fragments provide various mutually slipped conformers whose population increases with salt concentration and with the increasing repeat number. However, the self-structures of both strands disappear in the presence of the complementary strand because both (TGG)n and (CCA)n prefer to associate into the classical heteroduplex. We suppose that the extreme conformational variability of the DNA strands stands behind the length polymorphism which the (CCA)n/(TGG)n repeats exhibit in the human genome.
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Affiliation(s)
- Michal Zemánek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
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36
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Clark RM, Bhaskar SS, Miyahara M, Dalgliesh GL, Bidichandani SI. Expansion of GAA trinucleotide repeats in mammals. Genomics 2005; 87:57-67. [PMID: 16316739 DOI: 10.1016/j.ygeno.2005.09.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Revised: 09/04/2005] [Accepted: 09/07/2005] [Indexed: 01/29/2023]
Abstract
We have previously shown that GAA trinucleotide repeats have undergone significant expansion in the human genome. Here we present the analysis of the length distribution of all 10 nonredundant trinucleotide repeat motifs in 20 complete eukaryotic genomes (6 mammalian, 2 nonmammalian vertebrates, 4 arthropods, 4 fungi, and 1 each of nematode, amoebozoa, alveolate, and plant), which showed that the abundance of large expansions of GAA trinucleotide repeats is specific to mammals. Analysis of human-chimpanzee-gorilla orthologs revealed that loci with large expansions are species-specific and have occurred after divergence from the common ancestor. PCR analysis of human controls revealed large expansions at multiple human (GAA)(30+) loci; nine loci showed expanded alleles containing >65 triplets, analogous to disease-causing expansions in Friedreich ataxia, including two that are in introns of genes of unknown function. The abundance of long GAA trinucleotide repeat tracts in mammalian genomes represents a significant mutation potential and source of interindividual variability.
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Affiliation(s)
- Rhonda M Clark
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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37
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Missirlis PI, Mead CLR, Butland SL, Ouellette BFF, Devon RS, Leavitt BR, Holt RA. Satellog: a database for the identification and prioritization of satellite repeats in disease association studies. BMC Bioinformatics 2005; 6:145. [PMID: 15949044 PMCID: PMC1181805 DOI: 10.1186/1471-2105-6-145] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Accepted: 06/10/2005] [Indexed: 11/30/2022] Open
Abstract
Background To date, 35 human diseases, some of which also exhibit anticipation, have been associated with unstable repeats. Anticipation has been reported in a number of diseases in which repeat expansion may have a role in etiology. Despite the growing importance of unstable repeats in disease, currently no resource exists for the prioritization of repeats. Here we present Satellog, a database that catalogs all pure 1–16 repeat unit satellite repeats in the human genome along with supplementary data. Satellog analyzes each pure repeat in UniGene clusters for evidence of repeat polymorphism. Results A total of 5,546 such repeats were identified, providing the first indication of many novel polymorphic sites in the genome. Overall, polymorphic repeats were over-represented within 3'-UTR sequence relative to 5'-UTR and coding sequence. Interestingly, we observed that repeat polymorphism within coding sequence is restricted to trinucleotide repeats whereas UTR sequence tolerated a wider range of repeat period polymorphisms. For each pure repeat we also calculate its repeat length percentile rank, its location either within or adjacent to EnsEMBL genes, and its expression profile in normal tissues according to the GeneNote database. Conclusion Satellog provides the ability to dynamically prioritize repeats based on any of their characteristics (i.e. repeat unit, class, period, length, repeat length percentile rank, genomic co-ordinates), polymorphism profile within UniGene, proximity to or presence within gene regions (i.e. cds, UTR, 15 kb upstream etc.), metadata of the genes they are detected within and gene expression profiles within normal human tissues. Unstable repeats associated with 31 diseases were analyzed in Satellog to evaluate their common repeat properties. The utility of Satellog was highlighted by prioritizing repeats for Huntington's disease and schizophrenia. Satellog is available online at .
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Affiliation(s)
- Perseus I Missirlis
- Genome Sciences Centre, BC Cancer Agency, Suite 100, 570 West 7th Ave, Vancouver, BC, V5Z 4S6, Canada
| | - Carri-Lyn R Mead
- Genome Sciences Centre, BC Cancer Agency, Suite 100, 570 West 7th Ave, Vancouver, BC, V5Z 4S6, Canada
| | - Stefanie L Butland
- UBC Bioinformatics Centre, University of British Columbia, 950 West 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - BF Francis Ouellette
- UBC Bioinformatics Centre, University of British Columbia, 950 West 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Rebecca S Devon
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, B.C., V5Z 4H4, Canada
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, B.C., V5Z 4H4, Canada
| | - Robert A Holt
- Genome Sciences Centre, BC Cancer Agency, Suite 100, 570 West 7th Ave, Vancouver, BC, V5Z 4S6, Canada
- Department of Psychiatry, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 2A1, Canada
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38
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Pollard LM, Sharma R, Gómez M, Shah S, Delatycki MB, Pianese L, Monticelli A, Keats BJB, Bidichandani SI. Replication-mediated instability of the GAA triplet repeat mutation in Friedreich ataxia. Nucleic Acids Res 2004; 32:5962-71. [PMID: 15534367 PMCID: PMC528813 DOI: 10.1093/nar/gkh933] [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] [Received: 07/22/2004] [Revised: 10/22/2004] [Accepted: 10/22/2004] [Indexed: 11/14/2022] Open
Abstract
Friedreich ataxia is caused by the expansion of a polymorphic and unstable GAA triplet repeat in the FRDA gene, but the mechanisms for its instability are poorly understood. Replication of (GAA*TTC)n sequences (9-105 triplets) in plasmids propagated in Escherichia coli displayed length- and orientation-dependent instability. There were small length variations upon replication in both orientations, but large contractions were frequently observed when GAA was the lagging strand template. DNA replication was also significantly slower in this orientation. To evaluate the physiological relevance of our findings, we analyzed peripheral leukocytes from human subjects carrying repeats of similar length (8-107 triplets). Analysis of 9400 somatic FRDA molecules using small-pool PCR revealed a similar mutational spectrum, including large contractions. The threshold length for the initiation of somatic instability in vivo was between 40 and 44 triplets, corresponding to the length of a eukaryotic Okazaki fragment. Consistent with the stabilization of premutation alleles during germline transmission, we also found that instability of somatic cells in vivo and repeats propagated in E.coli were abrogated by (GAGGAA)n hexanucleotide interruptions. Our data demonstrate that the GAA triplet repeat mutation in Friedreich ataxia is destabilized, frequently undergoing large contractions, during DNA replication.
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Affiliation(s)
- Laura M Pollard
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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