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Distribution of the CAG Triplet Repeat in ATXN1, ATXN3, and CACNA1A Loci in Peruvian Population. THE CEREBELLUM 2020; 19:527-535. [PMID: 32285347 DOI: 10.1007/s12311-020-01129-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Spinocerebellar ataxia subtypes 1, 3, and 6 (SCA1, MJD/SCA3, and SCA6) are among the most prevalent autosomal dominant cerebellar ataxias worldwide, but their relative frequencies in Peru are low. Frequency of large normal (LN) alleles at spinocerebellar ataxia-causative genes has been proposed to be associated with disease prevalence. To investigate the allelic distribution of the CAG repeat in ATXN1, ATXN3, and CACNA1A genes in a Peruvian mestizo population and examine their association with the relative frequency of SCA1, MJD/SCA3, and SCA6 across populations. We genotyped 213 healthy mestizo individuals from Northern Lima, Peru, for ATXN1, ATXN3, and CACNA1A using polymerase chain reaction (PCR) and polyacrylamide gel electrophoresis (PAGE). We compared the frequency of LN alleles and relative disease frequency between populations. We also tested 40 samples for CAT repeat interruptions within the CAG tract of ATXN1. We found no association between disease frequency and population frequency of LN alleles at ATXN1 and ATXN3. All 40 ATXN1 samples tested for CAT interruptions were positive. Frequency of LN alleles at CACNA1A correlates with SCA6 frequency across several populations, but this effect was largely driven by data from a single population. Low frequency of SCA1 and MJD/SCA3 in Peru is not explained by frequency of LN alleles at ATXN1 and ATXN3, respectively. The observed correlation between CACNA1A LN alleles and SCA6 frequency requires further assessment.
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Flower M, Lomeikaite V, Holmans P, Jones L, Tabrizi SJ, Monckton DG. Reply: The repeat variant in MSH3 is not a genetic modifier for spinocerebellar ataxia type 3 and Friedreich's ataxia. Brain 2020; 143:e26. [PMID: 32154840 DOI: 10.1093/brain/awaa044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Michael Flower
- Department of Neurodegenerative Disease and Dementia Research Institute, UCL, UK
| | - Vilija Lomeikaite
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, UK
| | - Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, UK
| | - Sarah J Tabrizi
- Department of Neurodegenerative Disease and Dementia Research Institute, UCL, UK
| | - Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, UK
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Origins and Spread of Machado-Joseph Disease Ancestral Mutations Events. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1049:243-254. [PMID: 29427107 DOI: 10.1007/978-3-319-71779-1_12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Machado-Joseph disease (MJD) is the most common autosomal dominant spinocerebellar ataxia reported worldwide, but it shows marked geographic differences in prevalence. The study of ancestral origins and spreading routes of MJD mutational events has contributed to explain such differences. During human evolution, at least two independent de novo MJD expansions occurred in distinct haplotype backgrounds: TTACAC and GTGGCA (named Joseph and Machado lineages). The most ancient Joseph lineage, probably of Asian origin, has been introduced recently in Europe, where founder effects are responsible for the high MJD prevalence, as occurs in the Portuguese/Azorean island of Flores and Northeastern mainland. The Machado lineage is geographically more restricted, with most known families in Portugal (island of São Miguel and along the Tagus valley). The hypothesis of other mutational origins has been raised, namely to explain the disease among Australian aborigines; however, a comprehensive haplotype study suggested the introduction of the Joseph lineage in that community via Asia. Also, additional SNP-based haplotypes (TTAGAC, TTGGAC and GTGCCA) were observed in other MJD families, but phylogenetic analysis with more polymorphic flanking markers did not point to independent mutational events, reinforcing the hypothesis of a very low mutation rate underlying this repeat expansion locus.
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Gan SR, Ni W, Dong Y, Wang N, Wu ZY. Population genetics and new insight into range of CAG repeats of spinocerebellar ataxia type 3 in the Han Chinese population. PLoS One 2015; 10:e0134405. [PMID: 26266536 PMCID: PMC4534407 DOI: 10.1371/journal.pone.0134405] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/08/2015] [Indexed: 12/21/2022] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3), also called Machado-Joseph disease (MJD), is one of the most common SCAs worldwide and caused by a CAG repeat expansion located in ATXN3 gene. Based on the CAG repeat numbers, alleles of ATXN3 can be divided into normal alleles (ANs), intermediate alleles (AIs) and expanded alleles (AEs). It was controversial whether the frequency of large normal alleles (large ANs) is related to the prevalence of SCA3 or not. And there were huge chaos in the comprehension of the specific numbers of the range of CAG repeats which is fundamental for genetic analysis of SCA3. To illustrate these issues, we made a novel CAG repeat ladder to detect CAG repeats of ATXN3 in 1003 unrelated Chinese normal individuals and studied haplotypes defined by three single nucleotide polymorphisms (SNPs) closed to ATXN3. We found that the number of CAG repeats ranged from 13 to 49, among them, 14 was the most common number. Positive skew, the highest frequency of large ANs and 4 AIs which had never been reported before were found. Also, AEs and large ANs shared the same haplotypes defined by the SNPs. Based on these data and other related studies, we presumed that de novo mutations of ATXN3 emerging from large ANs are at least one survival mechanisms of mutational ATXN3 and we can redefine the range of CAG repeats as: ANs≤44, 45 ≤AIs ≤49 and AEs≥50.
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Affiliation(s)
- Shi-Rui Gan
- Department of Neurology and Research center of Neurology in Second Affiliated Hospital, and the Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, China; Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wang Ni
- Department of Neurology and Research center of Neurology in Second Affiliated Hospital, and the Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zhi-Ying Wu
- Department of Neurology and Research center of Neurology in Second Affiliated Hospital, and the Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, China; Department of Neurology and Institute of Neurology, Huashan Hospital, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, China
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Gispert S, Kurz A, Waibel S, Bauer P, Liepelt I, Geisen C, Gitler AD, Becker T, Weber M, Berg D, Andersen PM, Krüger R, Riess O, Ludolph AC, Auburger G. The modulation of Amyotrophic Lateral Sclerosis risk by ataxin-2 intermediate polyglutamine expansions is a specific effect. Neurobiol Dis 2011; 45:356-61. [PMID: 21889984 DOI: 10.1016/j.nbd.2011.08.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/10/2011] [Accepted: 08/18/2011] [Indexed: 12/13/2022] Open
Abstract
Full expansions of the polyglutamine domain (polyQ≥34) within the polysome-associated protein ataxin-2 (ATXN2) are the cause of a multi-system neurodegenerative disorder, which usually presents as a Spino-Cerebellar Ataxia and is therefore known as SCA2, but may rarely manifest as Levodopa-responsive Parkinson syndrome or as motor neuron disease. Intermediate expansions (27≤polyQ≤33) were reported to modify the risk of Amyotrophic Lateral Sclerosis (ALS). We have now tested the reproducibility and the specificity of this observation. In 559 independent ALS patients from Central Europe, the association of ATXN2 expansions (30≤polyQ≤35) with ALS was highly significant. The study of 1490 patients with Parkinson's disease (PD) showed an enrichment of ATXN2 alleles 27/28 in a subgroup with familial cases, but the overall risk of sporadic PD was unchanged. No association was found between polyQ expansions in Ataxin-3 (ATXN3) and ALS risk. These data indicate a specific interaction between ATXN2 expansions and the causes of ALS, possibly through altered RNA-processing as a common pathogenic factor.
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Affiliation(s)
- Suzana Gispert
- Experimental Neurology, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
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Freund AA, Scola RH, Teive HAG, Arndt RC, da Costa-Ribeiro MCV, Alle LF, Werneck LC. Spinocerebellar ataxias: microsatellite and allele frequency in unaffected and affected individuals. ARQUIVOS DE NEURO-PSIQUIATRIA 2010; 67:1124-32. [PMID: 20069235 DOI: 10.1590/s0004-282x2009000600034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 08/14/2009] [Indexed: 02/05/2023]
Abstract
The diagnosis and incidence of spinocerebelar ataxias (SCA) is sometimes difficult to analyze due the overlap of phenotypes subtypes and are disorders of mutations caused by CAG trinucleotide repeat expansion. To investigate the incidence of the SCA in Southern Brazil, we analyzed the trinucleotide repeats (CAG)n at the SCA1, SCA2, SCA3, SCA6 and SCA7 loci to identify allele size ranges and frequencies. We examined blood sample from 154 asymptomatic blood donors and 115 individuals with progressive ataxias. PCR products were submitted to capillary electrophoresis. In the blood donors, the ranges of the five loci were: SCA1, 19 to 36 (CAG)n; SCA2, 6 to 28 (CAG)n; SCA3, 12 to 34 (CAG)n; SCA6, 2 to 13 (CAG)n; and SCA7, 2 to 10 (CAG)n. No deviations from Hardy-Weinberg equilibrium were detected. In the ataxia group, we found (CAG)n above the range of the asymptomatic blood donors in SCA3 (21.74%) followed by SCA2 (5.22%), SCA7 (2.61%), SCA6 (0.87%), and no cases of SCA1. The remaining 80 cases (69.56%) have different diagnoses from the type here studied. These data defined the alleles and their frequencies, as well as demonstrated their stability in the population not affected. The molecular diagnosis test confirmed the clinical diagnosis in 28/45 cases and classified another 7/70 from the clinical unclassified ataxias group.
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Affiliation(s)
- Aline Andrade Freund
- Neurology Division, Internal Medicine Department, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
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Gan SR, Shi SS, Wu JJ, Wang N, Zhao GX, Weng ST, Murong SX, Lu CZ, Wu ZY. High frequency of Machado-Joseph disease identified in southeastern Chinese kindreds with spinocerebellar ataxia. BMC MEDICAL GENETICS 2010; 11:47. [PMID: 20334689 PMCID: PMC2861663 DOI: 10.1186/1471-2350-11-47] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 03/25/2010] [Indexed: 12/23/2022]
Abstract
Background Machado-Joseph disease (MJD), caused by a CAG repeat expansion located in exon10 of the ATXN3 gene, is now regarded as one of the most common spinocerebellar ataxia (SCA) in the world. The relative frequency of MJD among SCA has previously been estimated at about 50% in the Chinese population and has been reported to be related to the frequency of large normal alleles in some populations. Taq polymerase has been used for PCR in nearly all studies reported previously. Methods Normal and expanded alleles of ATXN3 were detected via PCR using LA Taq DNA polymerase (better for GC-rich sequences) and denaturing polyacrylamide gel electrophoresis in 150 normal individuals and 138 unrelated probands from autosomal dominant SCA families. To compare reaction efficiency, 12 MJD patients' expanded alleles were amplified with La Taq and Taq polymerase respectively in the same amplifying systems and reaction conditions. Results Normal alleles ranged from 12 to 42 CAG repeats. The most common allele contained 14 repeats with a frequency of 23.3%, which corroborates previous reports. The frequency of large normal alleles (>27 repeats) was 0.28, which was very high relative to previous reports. The frequency of MJD in SCA patients was 72.5%, which was significantly higher than those in previous reports about the Chinese and other Asian populations. This frequency was one of the highest reported worldwide, with only Portuguese and Brazilian populations exhibiting higher proportions. All 12 expanded alleles were amplified in PCR with La Taq polymerase, whereas only 2 expanded alleles were amplified with Taq polymerase. Conclusion We have first reported the highest relative frequency of MJD in Asia, and we attribute this high frequency to a more efficient PCR using LA Taq polymerase and hypothesized that large ANs may act as a reservoir for expanded alleles in the Southeastern Chinese population.
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Affiliation(s)
- Shi-Rui Gan
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
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10
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Abstract
Trinucleotide repeat expansions are an important cause of inherited neurodegenerative disease. The expanded repeats are unstable, changing in size when transmitted from parents to offspring (intergenerational instability, "meiotic instability") and often showing size variation within the tissues of an affected individual (somatic mosaicism, "mitotic instability"). Repeat instability is a clinically important phenomenon, as increasing repeat lengths correlate with an earlier age of onset and a more severe disease phenotype. The tendency of expanded trinucleotide repeats to increase in length during their transmission from parent to offspring in these diseases provides a molecular explanation for anticipation (increasing disease severity in successive affected generations). In this review, I explore the genetic and molecular basis of trinucleotide repeat instability. Studies of patients and families with trinucleotide repeat disorders have revealed a number of factors that determine the rate and magnitude of trinucleotide repeat change. Analysis of trinucleotide repeat instability in bacteria, yeast, and mice has yielded additional insights. Despite these advances, the pathways and mechanisms underlying trinucleotide repeat instability in humans remain largely unknown. There are many reasons to suspect that this uniquely human phenomenon will significantly impact upon our understanding of development, differentiation and neurobiology.
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Affiliation(s)
- A R La Spada
- Department of Laboratory Medicine and Pharmacology, University of Washington Medical Center, Seattle 98195, USA.
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Madsen LB, Thomsen B, Sølvsten CAE, Bendixen C, Fredholm M, Jørgensen AL, Nielsen AL. Identification of the porcine homologous of human disease causing trinucleotide repeat sequences. Neurogenetics 2007; 8:207-18. [PMID: 17516099 DOI: 10.1007/s10048-007-0088-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Accepted: 04/05/2007] [Indexed: 12/30/2022]
Abstract
Expansion in the repeat number of intragenic trinucleotide repeats (TNRs) is associated with a variety of inherited human neurodegenerative diseases. To study the composition of TNRs in a mammalian species representing an evolutionary intermediate between humans and rodents, we describe in this paper the identification of porcine noncoding and polyglutamine-encoding TNR regions and the comparison to the homologous TNRs from human, chimpanzee, dog, opossum, rat, and mouse. Several of the porcine TNR regions are highly polymorphic both within and between different breeds. The TNR regions are more conserved in terms of repeat length between humans and pigs than between humans and rodents suggesting that TNR lengths could be implicated in mammalian evolution. The TNRs in the FMR2, SCA6, SCA12, and Huntingtin genes are comparable in length to alleles naturally occurring in humans, and also in FMR1, a long uninterrupted CGG TNR was identified. Most strikingly, we identified a Huntingtin allele with 21 uninterrupted CAG repeats encoding a stretch of 24 polyglutamines. Examination of this particular Huntingtin TNR in 349 porcine offspring showed stable transmission. The presence in the porcine genome of TNRs within genes that, in humans, can undergo pathogenic expansions support the usage of the pig as an alternative animal model for studies of TNR evolution, stability, and functional properties.
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Affiliation(s)
- Lone Bruhn Madsen
- Section for Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Tjele, Denmark
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Andrés-Mateos E, Cruces J, Renart J, Solís-Garrido LM, Serantes R, de Lucas-Cerrillo AM, Montiel C. Bovine CACNA1A gene and comparative analysis of the CAG repeats associated to human spinocerebellar ataxia type-6. Gene 2006; 380:54-61. [PMID: 16876337 DOI: 10.1016/j.gene.2006.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 05/31/2006] [Accepted: 06/02/2006] [Indexed: 12/13/2022]
Abstract
A small expansion of a CAG repeat domain in exon 47 of the human CACNA1A gene, which codes for the pore-forming alpha1A subunit of P/Q-type Ca2+ channels, causes spinocerebellar ataxia type-6. Only the human alpha1A protein has been demonstrated to contain the poly(Q) tract, although this locus has also recently been detected in ape genomes. To our knowledge, no further information has been published on other mammal species. Here, we have cloned the full-length alpha1A subunit in a non-primate species, the cow. The results have made it possible to explore the exon organization of the bovine CACNA1A gene as well as the splice alpha1A isoforms expressed by bovine chromaffin cells. We found a splice variant of the protein that, as in humans, also contains a polymorphic poly(Q) tract. Based on this result and using data from different Genome Databases, we performed an interspecies comparison of exon 47 and discovered that the poly(Q) tract is present in all the species studied, with the exception of primitive fish and rodents. Our results provide insight into the evolution of the CAG repeat tract at the C-terminus coding region of the CACNA1A gene.
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Affiliation(s)
- Eva Andrés-Mateos
- Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, Arzobispo Morcillo 4, 28029-Madrid, Spain
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Martins S, Calafell F, Wong VCN, Sequeiros J, Amorim A. A multistep mutation mechanism drives the evolution of the CAG repeat at MJD/SCA3 locus. Eur J Hum Genet 2006; 14:932-40. [PMID: 16724006 DOI: 10.1038/sj.ejhg.5201643] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Despite the intense debate around the repeat instability reported on the large group of neurological disorders caused by trinucleotide repeat expansions, little is known about the mutation process underlying alleles in the normal range that, ultimately, expand to pathological size. In this study, we assessed the mutation mechanisms by which wild-type Machado-Joseph disease (MJD) alleles have been generated throughout human evolution. Haplotypes including the CAG repeat, six intragenic SNPs and four flanking microsatellites were analysed in 431 normal chromosomes of European, Asian and African origin. A bimodal CAG repeat length frequency distribution was found in the four most frequent wild-type lineages (H1-GCGGCA; H2-GTGGCA; H3-TTAGAC and H4-TTACAC). Based on flanking microsatellite haplotypes, the variance calculated by analysis of molecular variance between modal (CAG)n alleles was little or null in lineages H1, H2 and H4, as were the pairwise differences. Moreover, genetic distances among all the alleles from each lineage did not reflect the allele sizes differences, as expected if a stepwise mutation model was the main process of evolution. On the contrary, when exposed in maximum parsimonious phylogenetic trees, a large number of mutation steps separated same-size alleles, whereas several microsatellite haplotypes were shared by modal CAGs. In conclusion, our results suggest that the main mutation mechanism occurring in the evolution of the polymorphic CAG region at MJD/SCA3 locus is a multistep one, either by gene conversion or DNA slippage; repeats with 14, 21, 23 and 27 CAGs are the main alleles involved in this process.
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Affiliation(s)
- Sandra Martins
- IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.
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Abstract
Nine dominantly inherited neurodegenerative diseases are caused by expansion of a CAG repeat encoding glutamine. An important development in the study of such "polyglutamine" diseases was the realization that merely shutting off expression of a disease-encoding transgene could arrest progression in animal models with significant disease pathology. Such studies opened the door to a powerful new therapeutic approach now being pioneered: silencing of the dominant disease allele by RNA-mediated interference (RNAi), for the arrest--and potential reversal--of the disease process.
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Affiliation(s)
- Nancy M Bonini
- Department of Biology and University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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Bauer PO, Zumrova A, Matoska V, Marikova T, Krilova S, Boday A, Singh B, Goetz P. Absence of spinocerebellar ataxia type 3/Machado-Joseph disease within ataxic patients in the Czech population. Eur J Neurol 2005; 12:851-7. [PMID: 16241973 DOI: 10.1111/j.1468-1331.2005.01090.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Although spinocerebellar ataxia type 3 (SCA3)/Machado-Joseph disease is the most common type of SCA worldwide, we did not identify any cases of the disease amongst SCA patients in the Czech population. It has been proposed that the prevalence of large normal alleles correlates with the frequency of various types of SCA. We have therefore attempted to resolve the absence of SCA3 in our population by investigating, within 204 normal chromosomes, the frequency and nature of CAG repeats as well as two intragenic polymorphisms. We found that large normal alleles with more than 33 CAG repeats were observed at a frequency of only 0.49%. Whereas most of the expanded alleles worldwide have the CA haplotype, this was the least common (5.4%) variant observed in our study, although it was associated with a larger mean CAG repeat length (26.9). We postulate that the absence of SCA3 in the Czech population might be explained by the lack of large normal alleles and consequently a relatively small reservoir for aberrant CAG expansions at the SCA3 locus.
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Affiliation(s)
- P O Bauer
- Neurogenetic Centre of the Institute of Biology and Medical Genetics, Department of Child Neurology, 2nd Medical Faculty of Charles University and Faculty Hospital Motol, Prague, Czech Republic.
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Andrés AM, Soldevila M, Lao O, Volpini V, Saitou N, Jacobs HT, Hayasaka I, Calafell F, Bertranpetit J. Comparative genetics of functional trinucleotide tandem repeats in humans and apes. J Mol Evol 2005; 59:329-39. [PMID: 15553088 DOI: 10.1007/s00239-004-2628-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Several human neurodegenerative disorders are caused by the expansion of polymorphic trinucleotide repeat regions. Many of these loci are functional short tandem repeats (STRs) located in brain-expressed genes, and their study is thus relevant from both a medical and an evolutionary point of view. The aims of our study are to infer the comparative pattern of variation and evolution of this set of loci in order to show species-specific features in this group of STRs and on their potential for expansion (therefore, an insight into evolutionary medicine) and to unravel whether any human-specific feature may be identified in brain-expressed genes involved in human disease. We analyzed the variability of the normal range of seven expanding STR CAG/CTG loci (SCA1, SCA2, SCA3-MJD, SCA6, SCA8, SCA12, and DRPLA) and two nonexpanding polymorphic CAG loci (KCNN3 and NCOA3) in humans, chimpanzees, gorillas, and orangutans. The study showed a general conservation of the repetitive tract and of the polymorphism in the four species and high heterogeneity among loci distributions. Humans present slightly larger alleles than the rest of species but a more relevant difference appears in variability levels: Humans are the species with the largest variance, although only for the expanding loci, suggesting a relationship between variability levels and expansion potential. The sequence analysis shows high levels of sequence conservation among species, a lack of correspondence between interruption patterns and variability levels, and signs of conservative selective pressure for some of the STR loci. Only two loci (SCA1 and SCA8) show a human specific distribution, with larger alleles than the rest of species. This could account, at the same time, for a human-specific trait and a predisposition to disease through expansion.
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Affiliation(s)
- Aida M Andrés
- Unitat de Biologia Evolutiva, Facultat de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
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Michlewski G, Krzyzosiak WJ. Molecular Architecture of CAG Repeats in Human Disease Related Transcripts. J Mol Biol 2004; 340:665-79. [PMID: 15223312 DOI: 10.1016/j.jmb.2004.05.021] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2004] [Revised: 05/24/2004] [Accepted: 05/24/2004] [Indexed: 11/26/2022]
Abstract
CAG repeats are present in numerous human transcripts but neither their structures nor physiological functions have been satisfactorily recognized. The expanded CAG repeats are present in transcripts from several mutant genes associated with hereditary neurodegenerative diseases but their contribution to pathogenesis has not been documented convincingly. Here, we show that the structures formed by the repeats and their natural flanking sequences in the spinocerebellar ataxia (SCA) type 3 and type 6, and dentatorubral-palidoluysian atrophy (DRPLA) transcripts have different molecular architectures which may have functional meaning. We provide evidence that the hairpin structure formed by CAG repeats in mRNA fragments is preserved in full-length mRNA. We also demonstrate that the single-nucleotide polymorphism (SNP) that is located immediately adjacent (3') to the repeats of the SCA3 transcript modulates the structures formed by these sequences, and may have functional significance, as only one of its variants is selected in human evolution.
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Affiliation(s)
- Gracjan Michlewski
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 St., 61-704 Poznan, Poland
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Chattopadhyay B, Basu P, Gangopadhyay PK, Mukherjee SC, Sinha KK, Chakraborty A, Roy T, Roychoudhury S, Majumder PP, Bhattacharyya NP. Variation of CAG repeats and two intragenic polymorphisms at SCA3 locus among Machado-Joseph disease/SCA3 patients and diverse normal populations from eastern India. Acta Neurol Scand 2003; 108:407-14. [PMID: 14616293 DOI: 10.1034/j.1600-0404.2003.00167.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVES MJD1/SCA3 is the most common type of spinocerebellar ataxia (SCA) worldwide. To explain the low prevalence of the disease among SCA patients from eastern India, we analysed CAG repeats and two bi-allelic intragenic markers at SCA3 locus among 412 normal individuals and 10 patients. MATERIALS AND METHODS For CAG repeat analysis, PCR amplified fragments were run on polyacrylamide gel, transferred to a membrane, probed with (CAG)10 and detected on an autoradiograph. Bi-allelic markers were analysed using allele specific PCR amplification. RESULTS Large normal alleles (>33 CAG repeats) were 0.015 in pooled populations. All the patients had the common haplotype C-A as observed worldwide. Frequency of C-A haplotype among large normal alleles was 0.75. CONCLUSIONS Observed low prevalence of SCA3 could be because of the low prevalence of large normal alleles that might act as the reservoir for the expanded alleles. SCA3 mutation in Indian populations had the same origin as found worldwide.
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Affiliation(s)
- B Chattopadhyay
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
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Wiezel CEV, Canas MDCT, Simões AL. The SCA1 (Spinocerebellar ataxia type 1) and MJD (Machado-Joseph disease) CAG repeats in normal individuals: segregation analysis and allele frequencies. Genet Mol Biol 2003. [DOI: 10.1590/s1415-47572003000200002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Iughetti P, Otto PA, Zatz M, Bueno MRP, Marie SK. Different behavior in the paternally vs. maternally inherited mutated allele in Brazilian Machado-Joseph (MJD1) Families. ACTA ACUST UNITED AC 1998. [DOI: 10.1002/(sici)1096-8628(19980518)77:3<246::aid-ajmg11>3.0.co;2-g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Maurer DJ, Benzow KA, Schut LJ, Ranum LP, Livingston DM. Comparison of expanded CAG repeat tracts in sperm and lymphocyte DNA from Machado Joseph disease and spinocerebellar ataxia type I patients. Hum Mutat 1998; Suppl 1:S74-7. [PMID: 9452047 DOI: 10.1002/humu.1380110126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- D J Maurer
- Department of Biochemistry, University of Minnesota Medical School, Minneapolis 55455, USA
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Ritchie RJ, Chakrabarti L, Knight SJ, Harding RM, Davies KE. Population genetics of the FRAXE and FRAXF GCC repeats, and a novel CGG repeat, in Xq28. AMERICAN JOURNAL OF MEDICAL GENETICS 1997; 73:463-9. [PMID: 9415475 DOI: 10.1002/(sici)1096-8628(19971231)73:4<463::aid-ajmg16>3.0.co;2-p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Most of the rare folate sensitive fragile sites cloned to date arise from expansion of a CGG:CCG trinucleotide repeat array. Analysis of the CAG repeat at the Huntington Disease (HD) locus showed a positively skewed repeat distribution leading to the proposal that microsatellites are subject to a mutational bias toward expansion. Such a mutational bias predicts an increase in mean repeat size at all microsatellite loci. We present an analysis of repeats at two fragile site loci, FRAXE and FRAXF, and a novel CGG repeat in Xq28, in five different human populations, which suggests that these loci may also be subject to the same mutation process. The novel repeat array may represent the first evidence for the existence of a fourth fragile site in Xq27.3-28.
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Affiliation(s)
- R J Ritchie
- Department of Biochemistry, University of Oxford, United Kingdom
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Andrew SE, Goldberg YP, Hayden MR. Rethinking genotype and phenotype correlations in polyglutamine expansion disorders. Hum Mol Genet 1997; 6:2005-10. [PMID: 9328463 DOI: 10.1093/hmg/6.12.2005] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- S E Andrew
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Vancouver, B.C., Canada
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Cossée M, Schmitt M, Campuzano V, Reutenauer L, Moutou C, Mandel JL, Koenig M. Evolution of the Friedreich's ataxia trinucleotide repeat expansion: founder effect and premutations. Proc Natl Acad Sci U S A 1997; 94:7452-7. [PMID: 9207112 PMCID: PMC23842 DOI: 10.1073/pnas.94.14.7452] [Citation(s) in RCA: 219] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Friedreich's ataxia, the most frequent inherited ataxia, is caused, in the vast majority of cases, by large GAA repeat expansions in the first intron of the frataxin gene. The normal sequence corresponds to a moderately polymorphic trinucleotide repeat with bimodal size distribution. Small normal alleles have approximately eight to nine repeats whereas a more heterogeneous mode of large normal alleles ranges from 16 to 34 GAA. The latter class accounts for approximately 17% of normal alleles. To identify the origin of the expansion mutation, we analyzed linkage disequilibrium between expansion mutations or normal alleles and a haplotype of five polymorphic markers within or close to the frataxin gene; 51% of the expansions were associated with a single haplotype, and the other expansions were associated with haplotypes that could be related to the major one by mutation at a polymorphic marker or by ancient recombination. Of interest, the major haplotype associated with expansion is also the major haplotype associated with the larger alleles in the normal size range and was almost never found associated with the smaller normal alleles. The results indicate that most if not all large normal alleles derive from a single founder chromosome and that they represent a reservoir for larger expansion events, possibly through "premutation" intermediates. Indeed, we found two such alleles (42 and 60 GAA) that underwent cataclysmic expansion to pathological range in a single generation. This stepwise evolution to large trinucleotide expansions already was suggested for myotonic dystrophy and fragile X syndrome and may relate to a common mutational mechanism, despite sequence motif differences.
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Affiliation(s)
- M Cossée
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche Médicale/Centre National de la Recherche Scientifique/Université Louis Pasteur, Strasbourg, France
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Abstract
Seven neurodegenerative disorders are known to be caused by unstable expansions of the trinucleotide CAG within human genes, and more will be discovered in the coming years. These disorders share some clinical similarities, as well as some differences, which are summarized here. These diseases have unusual clinical genetic properties related to the dynamic nature of CAG repeat expansions, including instability of the repeat expansion in meiosis, particularly male meiosis; a strong correlation between onset age and size of the repeat expansion; anticipation (earlier disease onset in succeeding generations); new mutations arising from unstable, mutable alleles with a high-normal CAG repeat number; and reduced penetrance for alleles in the low-affected range. Much more remains to be learned about the molecular biology and clinical pathophysiology of this new class of genetic diseases.
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Affiliation(s)
- M A Nance
- Department of Neurology, Hennepin County Medical Center, Minneapolis, MN 55415, USA.
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