1
|
Deshmukh AL, Caron MC, Mohiuddin M, Lanni S, Panigrahi GB, Khan M, Engchuan W, Shum N, Faruqui A, Wang P, Yuen RKC, Nakamori M, Nakatani K, Masson JY, Pearson CE. FAN1 exo- not endo-nuclease pausing on disease-associated slipped-DNA repeats: A mechanism of repeat instability. Cell Rep 2021; 37:110078. [PMID: 34879276 DOI: 10.1016/j.celrep.2021.110078] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/02/2021] [Accepted: 11/09/2021] [Indexed: 12/19/2022] Open
Abstract
Ongoing inchworm-like CAG and CGG repeat expansions in brains, arising by aberrant processing of slipped DNAs, may drive Huntington's disease, fragile X syndrome, and autism. FAN1 nuclease modifies hyper-expansion rates by unknown means. We show that FAN1, through iterative cycles, binds, dimerizes, and cleaves slipped DNAs, yielding striking exo-nuclease pauses along slip-outs: 5'-C↓A↓GC↓A↓G-3' and 5'-C↓T↓G↓C↓T↓G-3'. CAG excision is slower than CTG and requires intra-strand A·A and T·T mismatches. Fully paired hairpins arrested excision, whereas disease-delaying CAA interruptions further slowed excision. Endo-nucleolytic cleavage is insensitive to slip-outs. Rare FAN1 variants are found in individuals with autism with CGG/CCG expansions, and CGG/CCG slip-outs show exo-nuclease pauses. The slip-out-specific ligand, naphthyridine-azaquinolone, which induces contractions of expanded repeats in vivo, requires FAN1 for its effect, and protects slip-outs from FAN1 exo-, but not endo-, nucleolytic digestion. FAN1's inchworm pausing of slip-out excision rates is well suited to modify inchworm expansion rates, which modify disease onset and progression.
Collapse
Affiliation(s)
- Amit Laxmikant Deshmukh
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Marie-Christine Caron
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, QC G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec City, QC G1R 3S3, Canada
| | - Mohiuddin Mohiuddin
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Stella Lanni
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Gagan B Panigrahi
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Mahreen Khan
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Worrawat Engchuan
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Natalie Shum
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Aisha Faruqui
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Peixiang Wang
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Ryan K C Yuen
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, the Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, QC G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec City, QC G1R 3S3, Canada
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
2
|
Kacher R, Lejeune FX, Noël S, Cazeneuve C, Brice A, Humbert S, Durr A. Propensity for somatic expansion increases over the course of life in Huntington disease. eLife 2021; 10:64674. [PMID: 33983118 PMCID: PMC8118653 DOI: 10.7554/elife.64674] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/27/2021] [Indexed: 12/03/2022] Open
Abstract
Recent work on Huntington disease (HD) suggests that somatic instability of CAG repeat tracts, which can expand into the hundreds in neurons, explains clinical outcomes better than the length of the inherited allele. Here, we measured somatic expansion in blood samples collected from the same 50 HD mutation carriers over a twenty-year period, along with post-mortem tissue from 15 adults and 7 fetal mutation carriers, to examine somatic expansions at different stages of life. Post-mortem brains, as previously reported, had the greatest expansions, but fetal cortex had virtually none. Somatic instability in blood increased with age, despite blood cells being short-lived compared to neurons, and was driven mostly by CAG repeat length, then by age at sampling and by interaction between these two variables. Expansion rates were higher in symptomatic subjects. These data lend support to a previously proposed computational model of somatic instability-driven disease.
Collapse
Affiliation(s)
- Radhia Kacher
- Sorbonne Université, Paris Brain Institute (ICM Institut du Cerveau), AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, Paris, France.,Univ. Grenoble Alpes, INSERM, U 1216, Grenoble Institut Neurosciences, Grenoble, France
| | - François-Xavier Lejeune
- Sorbonne Université, Paris Brain Institute (ICM Institut du Cerveau), AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, Paris, France.,Paris Brain Institute's Data and Analysis Core, University Hospital Pitié-Salpêtrière, Paris, France
| | - Sandrine Noël
- Neurogenetics Laboratory, Department of Genetics, Assistance Publique-Hôpitaux de Paris, University Hospital Pitié-Salpêtrière, Paris, France
| | - Cécile Cazeneuve
- Neurogenetics Laboratory, Department of Genetics, Assistance Publique-Hôpitaux de Paris, University Hospital Pitié-Salpêtrière, Paris, France
| | - Alexis Brice
- Sorbonne Université, Paris Brain Institute (ICM Institut du Cerveau), AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, Paris, France
| | - Sandrine Humbert
- Univ. Grenoble Alpes, INSERM, U 1216, Grenoble Institut Neurosciences, Grenoble, France
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute (ICM Institut du Cerveau), AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, Paris, France.,Neurogenetics Laboratory, Department of Genetics, Assistance Publique-Hôpitaux de Paris, University Hospital Pitié-Salpêtrière, Paris, France
| |
Collapse
|
3
|
Pešović J, Perić S, Brkušanin M, Brajušković G, Rakočević-Stojanović V, Savić-Pavićević D. Repeat Interruptions Modify Age at Onset in Myotonic Dystrophy Type 1 by Stabilizing DMPK Expansions in Somatic Cells. Front Genet 2018; 9:601. [PMID: 30546383 PMCID: PMC6278776 DOI: 10.3389/fgene.2018.00601] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/15/2018] [Indexed: 12/19/2022] Open
Abstract
CTG expansions in DMPK gene, causing myotonic dystrophy type 1 (DM1), are characterized by pronounced somatic instability. A large proportion of variability of somatic instability is explained by expansion size and patient's age at sampling, while individual-specific differences are attributed to additional factors. The age at onset is extremely variable in DM1, and inversely correlates with the expansion size and individual-specific differences in somatic instability. Three to five percent of DM1 patients carry repeat interruptions and some appear with later age at onset than expected for corresponding expansion size. Herein, we characterized somatic instability of interrupted DMPK expansions and the effect on age at onset in our previously described patients. Repeat-primed PCR showed stable structures of different types and patterns of repeat interruptions in blood cells over time and buccal cells. Single-molecule small-pool PCR quantification of somatic instability and mathematical modeling showed that interrupted expansions were characterized by lower level of somatic instability accompanied by slower progression over time. Mathematical modeling demonstrated that individual-specific differences in somatic instability had greater influence on age at onset in patients with interrupted expansions. Therefore, repeat interruptions have clinical importance for disease course in DM1 patients due to stabilizing effect on DMPK expansions in somatic cells.
Collapse
Affiliation(s)
- Jovan Pešović
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Stojan Perić
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Neurology Clinic, Clinical Center of Serbia, Belgrade, Serbia
| | - Miloš Brkušanin
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Goran Brajušković
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Vidosava Rakočević-Stojanović
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Neurology Clinic, Clinical Center of Serbia, Belgrade, Serbia
| | - Dušanka Savić-Pavićević
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| |
Collapse
|
4
|
Tomé S, Dandelot E, Dogan C, Bertrand A, Geneviève D, Péréon Y, Simon M, Bonnefont JP, Bassez G, Gourdon G. Unusual association of a unique CAG interruption in 5' of DM1 CTG repeats with intergenerational contractions and low somatic mosaicism. Hum Mutat 2018; 39:970-982. [PMID: 29664219 DOI: 10.1002/humu.23531] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/23/2018] [Accepted: 04/10/2018] [Indexed: 11/11/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a dominant multisystemic disorder associated with high variability of symptoms and anticipation. DM1 is caused by an unstable CTG repeat expansion that usually increases in successive generations and tissues. DM1 family pedigrees have shown that ∼90% and 10% of transmissions result in expansions and contractions of the CTG repeat, respectively. To date, the mechanisms of CTG repeat contraction remain poorly documented in DM1. In this report, we identified two new DM1 families with apparent contractions and no worsening of DM1 symptoms in two and three successive maternal transmissions. A new and unique CAG interruption was found in 5' of the CTG expansion in one family, whereas multiple 5' CCG interruptions were detected in the second family. We showed that these interruptions are associated with maternal intergenerational contractions and low somatic mosaicism in blood. By specific triplet-prime PCR, we observed that CTG repeat changes (contractions/expansions) occur preferentially in 3' of the interruptions for both families.
Collapse
Affiliation(s)
- Stéphanie Tomé
- Laboratory CTGDM, Inserm UMR1163, Paris, France; Institut Imagine, Université Paris-Descartes-Sorbonne Paris-Cité, Paris, France
| | - Elodie Dandelot
- Laboratory CTGDM, Inserm UMR1163, Paris, France; Institut Imagine, Université Paris-Descartes-Sorbonne Paris-Cité, Paris, France
| | - Céline Dogan
- Neuromuscular Reference Center, AP-HP, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Alexis Bertrand
- Laboratory CTGDM, Inserm UMR1163, Paris, France; Institut Imagine, Université Paris-Descartes-Sorbonne Paris-Cité, Paris, France
| | - David Geneviève
- Molecular Genetic Laboratory, Necker Hospital, Paris, France.,Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Université Montpellier, Montpellier, France
| | - Yann Péréon
- Centre for Neuromuscular Diseases, Hôtel-Dieu Hospital, Nantes, France
| | -
- Pauline Arnaud: Department of genetic, Bichat Hospital, Paris, France, Raphaële Chasserieau: Centre for Neuromuscular Diseases, Hôtel-Dieu Hospital, Nantes, France, Pascal Cintas: Neuromuscular Reference Center, Purpan Hospital, Toulouse, France, Ana-maria Cobo Esteban: Neuromuscular Reference Center, Marin Hospital, Hendaye, France, Marie-Carmen Cruz: Neuromuscular Reference Center, Purpan Hospital, Toulouse, France, Dalil Hamroun: Centre Hospitalo-Universitaire de Montpellier, Montpellier, France, Armelle Magot: Neuromuscular Reference Center, Hôtel-Dieu Hospital, Nantes, France, Alexandra Nadaj-Pakleza Neuromuscular Reference Center, Larrey Hospital, Angers, France, Anne-catherine Aube-Gauthier Neuromuscular Reference Center, Larrey Hospital, Angers, France, Andoni Urtizberea: Neuromuscular Reference Center, Marin Hospital, Hendaye, France
| | - Marie Simon
- Molecular Genetic Laboratory, Necker Hospital, Paris, France
| | | | - Guillaume Bassez
- Sorbonne Université, Inserm, UMRS974, Neuromuscular Reference center, AP-HP, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Geneviève Gourdon
- Laboratory CTGDM, Inserm UMR1163, Paris, France; Institut Imagine, Université Paris-Descartes-Sorbonne Paris-Cité, Paris, France
| |
Collapse
|
5
|
Landrian I, McFarland KN, Liu J, Mulligan CJ, Rasmussen A, Ashizawa T. Inheritance patterns of ATCCT repeat interruptions in spinocerebellar ataxia type 10 (SCA10) expansions. PLoS One 2017; 12:e0175958. [PMID: 28423040 PMCID: PMC5397023 DOI: 10.1371/journal.pone.0175958] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 04/03/2017] [Indexed: 11/18/2022] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10), an autosomal dominant cerebellar ataxia disorder, is caused by a non-coding ATTCT microsatellite repeat expansion in the ataxin 10 gene. In a subset of SCA10 families, the 5’-end of the repeat expansion contains a complex sequence of penta- and heptanucleotide interruption motifs which is followed by a pure tract of tandem ATCCT repeats of unknown length at its 3’-end. Intriguingly, expansions that carry these interruption motifs correlate with an epileptic seizure phenotype and are unstable despite the theory that interruptions are expected to stabilize expanded repeats. To examine the apparent contradiction of unstable, interruption-positive SCA10 expansion alleles and to determine whether the instability originates outside of the interrupted region, we sequenced approximately 1 kb of the 5’-end of SCA10 expansions using the ATCCT-PCR product in individuals across multiple generations from four SCA10 families. We found that the greatest instability within this region occurred in paternal transmissions of the allele in stretches of pure ATTCT motifs while the intervening interrupted sequences were stable. Overall, the ATCCT interruption changes by only one to three repeat units and therefore cannot account for the instability across the length of the disease allele. We conclude that the AT-rich interruptions locally stabilize the SCA10 expansion at the 5’-end but do not completely abolish instability across the entire span of the expansion. In addition, analysis of the interruption alleles across these families support a parsimonious single origin of the mutation with a shared distant ancestor.
Collapse
Affiliation(s)
- Ivette Landrian
- Department of Neurology, College of Medicine, and the McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Karen N. McFarland
- Department of Neurology, College of Medicine, and the McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
- Center for Translational Research in Neurodegenerative Disease, The University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Jilin Liu
- Department of Neurology, College of Medicine, and the McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Connie J. Mulligan
- Department of Anthropology, College of Liberal Arts and Sciences, University of Florida, Gainesville, Florida, United States of America
- Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Astrid Rasmussen
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Tetsuo Ashizawa
- Department of Neurology, College of Medicine, and the McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| |
Collapse
|
6
|
Dogan S, Cilic A, Kurtovic-Kozaric A, Ozturk F. Detection of G-type density in promoter sequence of colon cancer oncogenes and tumor suppressor genes. Bioinformation 2015; 11:290-5. [PMID: 26229289 PMCID: PMC4512003 DOI: 10.6026/97320630011290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 05/13/2015] [Accepted: 06/16/2015] [Indexed: 11/23/2022] Open
Abstract
The guanine rich locations are present in human genome. Previous studies have shown that the presence of G rich sequences and motifs may be significant for gene activity and function. We decided to focus our interest to identify G rich motifs in promoters of oncogenes and tumor suppressor genes. We used a set of 100 most common oncogenes and tumor suppressor genes (TSG) for this analysis. We collected 600nt long promoters with -500 and +100 TSS (transcription start site) from the oncogenes and TSG set. Using a computer program, we calculated the G densities using numbers and locations of G forms with 100nt moving widow. We included G numbers from 2 to 7 guanines. Analysis shows that G density increases from -500 to +100 and more from TSS. G density is found to be maximum within -/+100 of TSS. The results of G densities were compared with the expression data of the selected oncogenes and tumor suppressor genes in patients with colon cancer (n=174).
Collapse
Affiliation(s)
- Senol Dogan
- Department of Genetics and Bioengineering, International Burch University, Francuske revolucije BB, Ilidža 71000
| | - Anis Cilic
- Department of Genetics and Bioengineering, International Burch University, Francuske revolucije BB, Ilidža 71000
| | - Amina Kurtovic-Kozaric
- Department of Genetics and Bioengineering, International Burch University, Francuske revolucije BB, Ilidža 71000
- Department of Clinical Pathology, Clinical Center of the University of Sarajevo, Bosnia and Herzegovina
| | - Fatih Ozturk
- Department of Information Technologies, International Burch University, Francuske revolucije BB, Ilidža 71000, Sarajevo, Bosnia and Herzegovina
| |
Collapse
|
7
|
Diekmann K, Hodkinson TR, Barth S. New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species. ANNALS OF BOTANY 2012; 110:1327-39. [PMID: 22419761 PMCID: PMC3478042 DOI: 10.1093/aob/mcs044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 01/30/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne 'Cashel'. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. METHODS Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. KEY RESULTS All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A(8) mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. CONCLUSIONS The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to their ability to monitor genetic diversity within breeding pools, to trace maternal inheritance and to distinguish closely related species.
Collapse
Affiliation(s)
- Kerstin Diekmann
- Teagasc Crops Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland.
| | | | | |
Collapse
|
8
|
Panigrahi GB, Slean MM, Simard JP, Pearson CE. Human mismatch repair protein hMutLα is required to repair short slipped-DNAs of trinucleotide repeats. J Biol Chem 2012; 287:41844-50. [PMID: 23086927 DOI: 10.1074/jbc.m112.420398] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Mismatch repair (MMR) is required for proper maintenance of the genome by protecting against mutations. The mismatch repair system has also been implicated as a driver of certain mutations, including disease-associated trinucleotide repeat instability. We recently revealed a requirement of hMutSβ in the repair of short slip-outs containing a single CTG repeat unit (1). The involvement of other MMR proteins in short trinucleotide repeat slip-out repair is unknown. Here we show that hMutLα is required for the highly efficient in vitro repair of single CTG repeat slip-outs, to the same degree as hMutSβ. HEK293T cell extracts, deficient in hMLH1, are unable to process single-repeat slip-outs, but are functional when complemented with hMutLα. The MMR-deficient hMLH1 mutant, T117M, which has a point mutation proximal to the ATP-binding domain, is defective in slip-out repair, further supporting a requirement for hMLH1 in the processing of short slip-outs and possibly the involvement of hMHL1 ATPase activity. Extracts of hPMS2-deficient HEC-1-A cells, which express hMLH1, hMLH3, and hPMS1, are only functional when complemented with hMutLα, indicating that neither hMutLβ nor hMutLγ is sufficient to repair short slip-outs. The resolution of clustered short slip-outs, which are poorly repaired, was partially dependent upon a functional hMutLα. The joint involvement of hMutSβ and hMutLα suggests that repeat instability may be the result of aberrant outcomes of repair attempts.
Collapse
Affiliation(s)
- Gagan B Panigrahi
- Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | | |
Collapse
|
9
|
Abstract
In addition to the canonical double helix, DNA can fold into various other inter- and intramolecular secondary structures. Although many such structures were long thought to be in vitro artefacts, bioinformatics demonstrates that DNA sequences capable of forming these structures are conserved throughout evolution, suggesting the existence of non-B-form DNA in vivo. In addition, genes whose products promote formation or resolution of these structures are found in diverse organisms, and a growing body of work suggests that the resolution of DNA secondary structures is critical for genome integrity. This Review focuses on emerging evidence relating to the characteristics of G-quadruplex structures and the possible influence of such structures on genomic stability and cellular processes, such as transcription.
Collapse
|
10
|
Zhao J, Bacolla A, Wang G, Vasquez KM. Non-B DNA structure-induced genetic instability and evolution. Cell Mol Life Sci 2010; 67:43-62. [PMID: 19727556 PMCID: PMC3017512 DOI: 10.1007/s00018-009-0131-2] [Citation(s) in RCA: 310] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 07/22/2009] [Accepted: 08/11/2009] [Indexed: 11/26/2022]
Abstract
Repetitive DNA motifs are abundant in the genomes of various species and have the capacity to adopt non-canonical (i.e., non-B) DNA structures. Several non-B DNA structures, including cruciforms, slipped structures, triplexes, G-quadruplexes, and Z-DNA, have been shown to cause mutations, such as deletions, expansions, and translocations in both prokaryotes and eukaryotes. Their distributions in genomes are not random and often co-localize with sites of chromosomal breakage associated with genetic diseases. Current genome-wide sequence analyses suggest that the genomic instabilities induced by non-B DNA structure-forming sequences not only result in predisposition to disease, but also contribute to rapid evolutionary changes, particularly in genes associated with development and regulatory functions. In this review, we describe the occurrence of non-B DNA-forming sequences in various species, the classes of genes enriched in non-B DNA-forming sequences, and recent mechanistic studies on DNA structure-induced genomic instability to highlight their importance in genomes.
Collapse
Affiliation(s)
- Junhua Zhao
- Department of Carcinogenesis, Science Park-Research Division, The University of Texas M.D. Anderson Cancer Center, 1808 Park Road 1-C, P.O. Box 389, Smithville, TX 78957 USA
| | - Albino Bacolla
- Department of Carcinogenesis, Science Park-Research Division, The University of Texas M.D. Anderson Cancer Center, 1808 Park Road 1-C, P.O. Box 389, Smithville, TX 78957 USA
| | - Guliang Wang
- Department of Carcinogenesis, Science Park-Research Division, The University of Texas M.D. Anderson Cancer Center, 1808 Park Road 1-C, P.O. Box 389, Smithville, TX 78957 USA
| | - Karen M. Vasquez
- Department of Carcinogenesis, Science Park-Research Division, The University of Texas M.D. Anderson Cancer Center, 1808 Park Road 1-C, P.O. Box 389, Smithville, TX 78957 USA
| |
Collapse
|
11
|
Boyer JC, Hawk JD, Stefanovic L, Farber RA. Sequence-dependent effect of interruptions on microsatellite mutation rate in mismatch repair-deficient human cells. Mutat Res 2007; 640:89-96. [PMID: 18242644 DOI: 10.1016/j.mrfmmm.2007.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 11/21/2007] [Accepted: 12/11/2007] [Indexed: 11/18/2022]
Abstract
Although microsatellite mutation rates generally increase with increasing length of the repeat tract, interruptions in a microsatellite may stabilize it. We have performed a direct analysis of the effect of microsatellite interruptions on mutation rate and spectrum in cultured mammalian cells. Two mononucleotide sequences (G(17) and A(17)) and a dinucleotide [(CA)(17)] were compared with interrupted repeats of the same size and with sequences of 8 repeat units. MMR-deficient (MMR(-)) cells were used for these studies to eliminate effects of this repair process. Mutation rates were determined by fluctuation analysis on cells containing a microsatellite sequence at the 5' end of an antibiotic-resistance gene; the vector carrying this sequence was integrated in the genome of the cells. In general, interrupted sequences had lower mutation rates than perfect ones of the same size, but the magnitude of the difference was dependent upon the sequence of the interrupting base(s). Some interrupted repeats had mutation rates that were lower than those of perfect sequences of the same length but similar to those of half the length. This suggests that interrupting bases effectively divide microsatellites into smaller repeat runs with mutational characteristics different from those of the corresponding full-length microsatellite. We conclude that interruptions decrease microsatellite mutation rate and influence the spectrum of frameshift mutations. The sequence of the interrupting base(s) determines the magnitude of the effect on mutation rate.
Collapse
Affiliation(s)
- Jayne C Boyer
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, CB #7525, Chapel Hill, NC 27599, United States.
| | | | | | | |
Collapse
|
12
|
Abstract
Nearly 30 hereditary disorders in humans result from an increase in the number of copies of simple repeats in genomic DNA. These DNA repeats seem to be predisposed to such expansion because they have unusual structural features, which disrupt the cellular replication, repair and recombination machineries. The presence of expanded DNA repeats alters gene expression in human cells, leading to disease. Surprisingly, many of these debilitating diseases are caused by repeat expansions in the non-coding regions of their resident genes. It is becoming clear that the peculiar structures of repeat-containing transcripts are at the heart of the pathogenesis of these diseases.
Collapse
Affiliation(s)
- Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA.
| |
Collapse
|
13
|
|
14
|
Abstract
DNA mismatch repair (MMR) is an evolutionarily conserved process that corrects mismatches generated during DNA replication and escape proofreading. MMR proteins also participate in many other DNA transactions, such that inactivation of MMR can have wide-ranging biological consequences, which can be either beneficial or detrimental. We begin this review by briefly considering the multiple functions of MMR proteins and the consequences of impaired function. We then focus on the biochemical mechanism of MMR replication errors. Emphasis is on structure-function studies of MMR proteins, on how mismatches are recognized, on the process by which the newly replicated strand is identified, and on excision of the replication error.
Collapse
Affiliation(s)
- Thomas A Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA.
| | | |
Collapse
|
15
|
Hebert ML, Wells RD. Roles of double-strand breaks, nicks, and gaps in stimulating deletions of CTG.CAG repeats by intramolecular DNA repair. J Mol Biol 2005; 353:961-79. [PMID: 16213518 DOI: 10.1016/j.jmb.2005.09.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 08/30/2005] [Accepted: 09/09/2005] [Indexed: 11/19/2022]
Abstract
A series of plasmids harboring CTG.CAG repeats with double-strand breaks (DSB), single-strand nicks, or single-strand gaps (15 or 30 nucleotides) within the repeat regions were used to determine their capacity to induce genetic instabilities. These plasmids were introduced into Escherichia coli in the presence of a second plasmid containing a sequence that could support homologous recombination repair between the two plasmids. The transfer of a point mutation from the second to the first plasmid was used to monitor homologous recombination (gene conversion). Only DSBs increased the overall genetic instability. This instability took place by intramolecular repair, which was not dependent on RuvA. Double-strand break-induced instabilities were partially stabilized by a mutation in recF. Gaps of 30 nt formed a distinct 30 nt deletion product, whereas single strand nicks and gaps of 15 nt did not induce expansions or deletions. Formation of this deletion product required the CTG.CAG repeats to be present in the single-stranded region and was stimulated by E.coli DNA ligase, but was not dependent upon the RecFOR pathway. Models are presented to explain the intramolecular repair-induced instabilities and the formation of the 30 nt deletion product.
Collapse
Affiliation(s)
- Micheal L Hebert
- Center for Genome Research, Institute of Biosciences and Technology, Texas A and M University System Health Science Center, 2121 W. Holcombe Blvd., Houston, TX 77030-3303, USA
| | | |
Collapse
|
16
|
Napierala M, Bacolla A, Wells RD. Increased negative superhelical density in vivo enhances the genetic instability of triplet repeat sequences. J Biol Chem 2005; 280:37366-76. [PMID: 16166072 DOI: 10.1074/jbc.m508065200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The influence of negative superhelical density on the genetic instabilities of long GAA.TTC, CGG.CCG, and CTG.CAG repeat sequences was studied in vivo in topologically constrained plasmids in Escherichia coli. These repeat tracts are involved in the etiologies of Friedreich ataxia, fragile X syndrome, and myotonic dystrophy type 1, respectively. The capacity of these DNA tracts to undergo deletions-expansions was explored with three genetic-biochemical approaches including first, the utilization of topoisomerase I and/or DNA gyrase mutants, second, the specific inhibition of DNA gyrase by novobiocin, and third, the genetic removal of the HU protein, thus lowering the negative supercoil density (-sigma). All three strategies revealed that higher -sigma in vivo enhanced the formation of deleted repeat sequences. The effects were most pronounced for the Friedreich ataxia and the fragile X triplet repeat sequences. Higher levels of -sigma stabilize non-B DNA conformations (i.e. triplexes, sticky DNA, flexible and writhed DNA, slipped structures) at appropriate repeat tracts; also, numerous prior genetic instability investigations invoke a role for these structures in promoting the slippage of the DNA complementary strands. Thus, we propose that the in vivo modulation of the DNA structure, localized to the repeat tracts, is responsible for these behaviors. Presuming that these interrelationships are also found in humans, dynamic alterations in the chromosomal nuclear matrix may modulate the -sigma of certain DNA regions and, thus, stabilize/destabilize certain non-B conformations which regulate the genetic expansions-deletions responsible for the diseases.
Collapse
Affiliation(s)
- Marek Napierala
- Institute of Biosciences and Technology, Center for Genome Research, Texas A&M University System Health Science Center, Houston, 77030-3303, USA
| | | | | |
Collapse
|
17
|
Bhattacharyya S, Lahue RS. Srs2 Helicase of Saccharomyces cerevisiae Selectively Unwinds Triplet Repeat DNA. J Biol Chem 2005; 280:33311-7. [PMID: 16085654 DOI: 10.1074/jbc.m503325200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trinucleotide repeat expansions are the mutational cause of at least 15 genetic diseases. In vitro, single-stranded triplet repeat DNA forms highly stable hairpins, depending on repeat sequence, and a strong correlation exists between hairpin-forming ability and the risk of expansion in vivo. Hairpins are viewed, therefore, as likely mutagenic precursors to expansions. If a helicase unwinds the hairpin, it would be less likely to expand. Previous work indicated that yeast Srs2 DNA helicase selectively blocks expansions in vivo (Bhattacharyya, S., and Lahue, R. S. (2004) Mol. Cell. Biol. 24, 7324-7330). For example, srs2 mutants, including an ATPase-defective point mutant, exhibit substantially higher expansion rates than wild type controls. In contrast, mutation of another helicase gene, SGS1, had little effect on expansion rates. These findings prompted the idea that Srs2 might selectively unwind triplet repeat hairpins. In this study, DNA helicase assays were performed with purified Srs2, Sgs1, and Escherichia coli UvrD (DNA helicase II). Srs2 shows substantially faster unwinding than Sgs1 or UvrD on partial duplex substrates containing (CTG) x (CTG) sequences, provided that Srs2 encounters the triplet repeat DNA immediately on entering the duplex. Srs2 was also faster at unwinding (CAG) x (CAG)- and (CCG) x (CCG)-containing substrates and an intramolecular (CTG) x (CTG) hairpin. In contrast, all three enzymes unwind about equally well control substrates with either Watson-Crick base pairs or mismatched substrates with non-CNG repeats. Overall, the selective unwinding activity of Srs2 on triplet repeat hairpin DNA helps explain the genetic evidence that Srs2, not the RecQ homolog Sgs1, is a preferred helicase for preventing expansions.
Collapse
Affiliation(s)
- Saumitri Bhattacharyya
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-6805, USA
| | | |
Collapse
|
18
|
Subramanian J, Vijayakumar S, Tomkinson AE, Arnheim N. Genetic instability induced by overexpression of DNA ligase I in budding yeast. Genetics 2005; 171:427-41. [PMID: 15965249 PMCID: PMC1456761 DOI: 10.1534/genetics.105.042861] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recombination and microsatellite mutation in humans contribute to disorders including cancer and trinucleotide repeat (TNR) disease. TNR expansions in wild-type yeast may arise by flap ligation during lagging-strand replication. Here we show that overexpression of DNA ligase I (CDC9) increases the rates of TNR expansion, of TNR contraction, and of mitotic recombination. Surprisingly, this effect is observed with catalytically inactive forms of Cdc9p protein, but only if they possess a functional PCNA-binding site. Furthermore, in vitro analysis indicates that the interaction of PCNA with Cdc9p and Rad27p (Fen1) is mutually exclusive. Together our genetic and biochemical analysis suggests that, although DNA ligase I seals DNA nicks during replication, repair, and recombination, higher than normal levels can yield genetic instability by disrupting the normal interplay of PCNA with other proteins such as Fen1.
Collapse
Affiliation(s)
- Jaichandar Subramanian
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, 90089-2910, USA
| | | | | | | |
Collapse
|
19
|
Sobczak K, Krzyzosiak WJ. Patterns of CAG repeat interruptions in SCA1 and SCA2 genes in relation to repeat instability. Hum Mutat 2005; 24:236-47. [PMID: 15300851 DOI: 10.1002/humu.20075] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
About 3% of the human genome is composed of simple sequence repeats and many of these sequences occur within genes. These repeats are often polymorphic in a normal population and their expansion in specific genes leads to a number of hereditary neurological diseases. Normal variants of disease-related genes contain either pure or interrupted repeats, and the postulated function of the interruptions is to prevent repeat expansions. Their structural role in the repeat tracts of genes and transcripts awaits detailed characterization. In this study, we have determined the SCA1 and SCA2 genotypes in a Polish population and found significant differences in allele spectra and frequencies from those reported for other populations. They are discussed in relation to the repeat expansion mechanism and disease incidence. We postulate that the dynamic mutation of the genes SCA1 (also ATX1 or ataxin 1) and SCA2 (also ATX2 or ataxin 2) may begin from the expansion of long pure repeat tracts without the prior loss of interruptions. A simple way of cost-effective allelotyping of CAG repeat regions in the SCA1 and SCA2genes is also shown. The reliable SSCP/duplex analysis presented here may be the method of choice for the systematic searching of genes for known and novel interrupted repeats.
Collapse
Affiliation(s)
- Krzysztof Sobczak
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
| | | |
Collapse
|
20
|
Mulvihill DJ, Nichol Edamura K, Hagerman KA, Pearson CE, Wang YH. Effect of CAT or AGG Interruptions and CpG Methylation on Nucleosome Assembly upon Trinucleotide Repeats on Spinocerebellar Ataxia, Type 1 and Fragile X Syndrome*. J Biol Chem 2005; 280:4498-503. [PMID: 15574425 DOI: 10.1074/jbc.m413239200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleosome packaging regulates many aspects of DNA metabolism and is thought to mediate genetic instability and transcription of expanded trinucleotide repeats. Both instability and transcription are sensitive to repeat length, tract purity, and CpG methylation. CAT or AGG interruptions within the (CAG)n or (CGG)n tracts of spinocerebellar ataxia, type 1 or fragile X syndrome, respectively, confer increased genetic stability to the repeats. We report the formation of nucleosomes on sequences containing pure and interrupted (CAG)n and (CGG)n repeats having lengths above and below the genetic stability thresholds. Increased lengths of pure repeats led to increased and decreased propensities for nucleosome assembly on the (CAG)n and (CGG)n repeats, respectively. CpG methylation of the CGG repeat further reduced assembly. CAT interruptions in (CAG)n tracts decreased nucleosome assembly. In contrast, AGG interruptions in (CGG)n tracts did not affect assembly by hypoacetylated histones. The latter observation was unaltered by CpG methylation of the repeats. However, nucleosome assembly by hyperacetylated histones on interrupted CGG tracts was increased relative to pure tracts and this effect was abolished by CpG methylation. Thus, CAT or AGG interruptions can modulate the ability of (CAG)n and (CGG) tracts to assemble into chromatin and the effect of the AGG interruptions is dependent upon both the methylation status of the DNA and the acetylation status of the histones. Compared with the genetically unstable pure repeats, both interruptions permit a propensity of nucleosome assembly closer to that of random (genetically stable) sequences, suggesting an association of nucleosome assembly of trinucleotide repeats and genetic instability.
Collapse
Affiliation(s)
- David J Mulvihill
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
| | | | | | | | | |
Collapse
|
21
|
Gorbunova V, Seluanov A, Mittelman D, Wilson JH. Genome-wide demethylation destabilizes CTG.CAG trinucleotide repeats in mammalian cells. Hum Mol Genet 2004; 13:2979-89. [PMID: 15459182 DOI: 10.1093/hmg/ddh317] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many neurological diseases, including myotonic dystrophy, Huntington's disease and several spinocerebellar ataxias, result from intergenerational increases in the length of a CTG.CAG repeat tract. Although the basis for intergenerational repeat expansion is unclear, repeat tracts are especially unstable during germline development and production of gametes. Mammalian development is characterized by waves of genome-wide demethylation and remethylation. To test whether changes in methylation status might contribute to trinucleotide repeat instability, we examined the effects of DNA methyltransferase inhibitors on trinucleotide repeat stability in mammalian cells. Using a selectable genetic system for detection of repeat contractions in CHO cells, we showed that the rate of contractions increased >1000-fold upon treatment with the DNA methyltransferase inhibitor 5-aza-deoxycytidine (5-aza-CdR). The link between DNA demethylation and repeat instability was strengthened by similar results obtained with hydralazine treatment, which inhibits expression of DNA methyltransferase. In human cells from myotonic dystrophy patients, treatment with 5-aza-CdR strongly destabilized repeat tracts in the DMPK gene, with a clear bias toward expansion. The bias toward expansion events and changes in repeat length that occur in jumps, rather than by accumulation of small changes, are reminiscent of the intergenerational repeat instability observed in human patients. The dramatic destabilizing effect of DNA methyltransferase inhibitors supports the hypothesis that changes in methylation patterns during epigenetic reprogramming may trigger the intergenerational repeat expansions that lead to disease.
Collapse
Affiliation(s)
- Vera Gorbunova
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | |
Collapse
|
22
|
Dixon MJ, Lahue RS. DNA elements important for CAG*CTG repeat thresholds in Saccharomyces cerevisiae. Nucleic Acids Res 2004; 32:1289-97. [PMID: 14982954 PMCID: PMC390281 DOI: 10.1093/nar/gkh292] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Trinucleotide repeat (TNR) instability is of interest because of its central role in human diseases such as Huntington's and its unique genetic features. One distinctive characteristic of TNR instability is a threshold, defined as a minimal repeat length that confers frequent mutations. While thresholds are well established, important risk determinants for disease-causing mutations, their mechanistic analysis has been delayed by the lack of suitably tractable experimental systems. In this study, we directly compared for the first time three DNA elements-TNR sequence, purity and flanking sequence-all of which are suggested in the literature to contribute to thresholds. In a yeast model system, we find that CAG repeats require a substantially longer threshold to contract than CTG tracts, indicating that the lagging template repeat sequence helps determine the threshold. In contrast, ATG interruptions within a CTG run do not inhibit contractions via a threshold mechanism, but by altering the likelihood of forming a hairpin intermediate. The presence of a GC-rich flanking sequence, similar to a haplotype found in some Huntington's patients, does not detectably alter expansions of Okazaki fragment CTG tracts, suggesting no role for this flanking sequence on thresholds. Together these results help better define TNR thresholds by delineating sequence elements that modulate instability.
Collapse
Affiliation(s)
- Michael J Dixon
- Eppley Institute for Research in Cancer and Allied Diseases and Department of Pathology and Microbiology, University of Nebraska Medical Center, Box 986805, Omaha, NE 68198-6805, USA
| | | |
Collapse
|
23
|
Abstract
DNA mismatch repair (MMR) guards the integrity of the genome in virtually all cells. It contributes about 1000-fold to the overall fidelity of replication and targets mispaired bases that arise through replication errors, during homologous recombination, and as a result of DNA damage. Cells deficient in MMR have a mutator phenotype in which the rate of spontaneous mutation is greatly elevated, and they frequently exhibit microsatellite instability at mono- and dinucleotide repeats. The importance of MMR in mutation avoidance is highlighted by the finding that defects in MMR predispose individuals to hereditary nonpolyposis colorectal cancer. In addition to its role in postreplication repair, the MMR machinery serves to police homologous recombination events and acts as a barrier to genetic exchange between species.
Collapse
Affiliation(s)
- Mark J Schofield
- Genetics and Biochemistry Branch, National Institute of Diabetes, and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
| | | |
Collapse
|
24
|
Hebert ML, Spitz LA, Wells RD. DNA Double-strand Breaks Induce Deletion of CTG·CAG Repeats in an Orientation-dependent Manner in Escherichia coli. J Mol Biol 2004; 336:655-72. [PMID: 15095979 DOI: 10.1016/j.jmb.2003.12.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Revised: 12/11/2003] [Accepted: 12/11/2003] [Indexed: 10/26/2022]
Abstract
The influences of double-strand breaks (DSBs) within a triplet repeat sequence on its genetic instabilities (expansions and deletions) related to hereditary neurological diseases was investigated. Plasmids containing 43 or 70 CTG.CAG repeats or 43 CGG.CCG repeats were linearized in vitro near the center of the repeats and were transformed into parental, RecA-dependent homologous recombination-deficient, or RecBC exonuclease-deficient Escherichia coli. The resulting repair process considerably increased deletion of the repeating sequence compared to the circular DNA controls. Unexpectedly, the orientation of the insert relative to the unidirectional ColE1 origin of replication affected the amount of instability generated during the repair of the DSB. When the CTG strand was the template for lagging-strand synthesis, instability was increased, most markedly in the recA- strain. Results indicated that RecA and/or RecBC might play a role in DSB repair within the triplet repeat. Altering the length, orientation, and sequence composition of the triplet repeat suggested an important role of DNA secondary structures during repair intermediates. Hence, we hypothesize that ColE1 origin-dependent replication was involved during the repair of the DSB. A model is presented to explain the mechanisms of the observed genetic instabilities.
Collapse
Affiliation(s)
- Micheal L Hebert
- Institute of Biosciences and Technology, Center for Genome Research, Texas A and M University System Health Science Center, Texas Medical Center, 2121 W. Holcombe Blavd., Houston, TX 77030-3303, USA
| | | | | |
Collapse
|
25
|
Gorbunova V, Seluanov A, Dion V, Sandor Z, Meservy JL, Wilson JH. Selectable system for monitoring the instability of CTG/CAG triplet repeats in mammalian cells. Mol Cell Biol 2003; 23:4485-93. [PMID: 12808091 PMCID: PMC164839 DOI: 10.1128/mcb.23.13.4485-4493.2003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Despite substantial progress in understanding the mechanism by which expanded CTG/CAG trinucleotide repeats cause neurodegenerative diseases, little is known about the basis for repeat instability itself. By taking advantage of a novel phenomenon, we have developed a selectable assay to detect contractions of CTG/CAG triplets. When inserted into an intron in the APRT gene or the HPRT minigene, long tracts of CTG/CAG repeats (more than about 33 repeat units) are efficiently incorporated into mRNA as a new exon, thereby rendering the encoded protein nonfunctional, whereas short repeat tracts do not affect the phenotype. Therefore, contractions of long repeats can be monitored in large cell populations, by selecting for HPRT(+) or APRT(+) clones. Using this selectable system, we determined the frequency of spontaneous contractions and showed that treatments with DNA-damaging agents stimulate repeat contractions. The selectable system that we have developed provides a versatile tool for the analysis of CTG/CAG repeat instability in mammalian cells. We also discuss how the effect of long CTG/CAG repeat tracts on splicing may contribute to the progression of polyglutamine diseases.
Collapse
Affiliation(s)
- Vera Gorbunova
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | | | | | |
Collapse
|
26
|
Meservy JL, Sargent RG, Iyer RR, Chan F, McKenzie GJ, Wells RD, Wilson JH. Long CTG tracts from the myotonic dystrophy gene induce deletions and rearrangements during recombination at the APRT locus in CHO cells. Mol Cell Biol 2003; 23:3152-62. [PMID: 12697816 PMCID: PMC153196 DOI: 10.1128/mcb.23.9.3152-3162.2003] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expansion of CTG triplet repeats in the 3' untranslated region of the DMPK gene causes the autosomal dominant disorder myotonic dystrophy. Instability of CTG repeats is thought to arise from their capacity to form hairpin DNA structures. How these structures interact with various aspects of DNA metabolism has been studied intensely for Escherichia coli and Saccharomyces cerevisiae but is relatively uncharacterized in mammalian cells. To examine the stability of (CTG)(17), (CTG)(98), and (CTG)(183) repeats during homologous recombination, we placed them in the second intron of one copy of a tandemly duplicated pair of APRT genes. Cells selected for homologous recombination between the two copies of the APRT gene displayed distinctive patterns of change. Among recombinants from cells with (CTG)(98) and (CTG)(183), 5% had lost large numbers of repeats and 10% had suffered rearrangements, a frequency more than 50-fold above normal levels. Analysis of individual rearrangements confirmed the involvement of the CTG repeats. Similar changes were not observed in proliferating (CTG)(98) and (CTG)(183) cells that were not recombinant at APRT. Instead, they displayed high frequencies of small changes in repeat number. The (CTG)(17) repeats were stable in all assays. These studies indicate that homologous recombination strongly destabilizes long tracts of CTG repeats.
Collapse
Affiliation(s)
- James L Meservy
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | | | | | | | |
Collapse
|
27
|
Feschenko VV, Rajman LA, Lovett ST. Stabilization of perfect and imperfect tandem repeats by single-strand DNA exonucleases. Proc Natl Acad Sci U S A 2003; 100:1134-9. [PMID: 12538867 PMCID: PMC298739 DOI: 10.1073/pnas.0233122100] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rearrangements between tandemly repeated DNA sequences are a common source of genetic instability. Such rearrangements underlie several human genetic diseases. In many organisms, the mismatch-repair (MMR) system functions to stabilize repeats when the repeat unit is short or when sequence imperfections are present between the repeats. We show here that the action of single-stranded DNA (ssDNA) exonucleases plays an additional, important role in stabilizing tandem repeats, independent of their role in MMR. For perfect repeats of approximately 100 bp in Escherichia coli that are not susceptible to MMR, exonuclease (Exo)-I, ExoX, and RecJ exonuclease redundantly inhibit deletion. Our data suggest that >90% of potential deletion events are avoided by the combined action of these three exonucleases. Imperfect tandem repeats, less prone to rearrangements, are stabilized by both the MMR-pathway and ssDNA-specific exonucleases. For 100-bp repeats containing four mispairs, ExoI alone aborts most deletion events, even in the presence of a functional MMR system. By genetic analysis, we show that the inhibitory effect of ssDNA exonucleases on deletion formation is independent of the MutS and UvrD proteins. Exonuclease degradation of DNA displaced during the deletion process may abort slipped misalignment. Exonuclease action is therefore a significant force in genetic stabilization of many forms of repetitive DNA.
Collapse
Affiliation(s)
- Vladimir V Feschenko
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA
| | | | | |
Collapse
|
28
|
Bhattacharyya S, Rolfsmeier ML, Dixon MJ, Wagoner K, Lahue RS. Identification of RTG2 as a modifier gene for CTG*CAG repeat instability in Saccharomyces cerevisiae. Genetics 2002; 162:579-89. [PMID: 12399373 PMCID: PMC1462295 DOI: 10.1093/genetics/162.2.579] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Trinucleotide repeats (TNRs) undergo frequent mutations in families affected by TNR diseases and in model organisms. Much of the instability is conferred in cis by the sequence and length of the triplet tract. Trans-acting factors also modulate TNR instability risk, on the basis of such evidence as parent-of-origin effects. To help identify trans-acting modifiers, a screen was performed to find yeast mutants with altered CTG.CAG repeat mutation frequencies. The RTG2 gene was identified as one such modifier. In rtg2 mutants, expansions of CTG.CAG repeats show a modest increase in rate, depending on the starting tract length. Surprisingly, contractions were suppressed in an rtg2 background. This creates a situation in a model system where expansions outnumber contractions, as in humans. The rtg2 phenotype was apparently specific for CTG.CAG repeat instability, since no changes in mutation rate were observed for dinucleotide repeats or at the CAN1 reporter gene. This feature sets rtg2 mutants apart from most other mutants that affect genetic stability both for TNRs and at other DNA sequences. It was also found that RTG2 acts independently of its normal partners RTG1 and RTG3, suggesting a novel function of RTG2 that helps modify CTG.CAG repeat mutation risk.
Collapse
Affiliation(s)
- Saumitri Bhattacharyya
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha 68198-6805, USA
| | | | | | | | | |
Collapse
|
29
|
Henricksen LA, Veeraraghavan J, Chafin DR, Bambara RA. DNA ligase I competes with FEN1 to expand repetitive DNA sequences in vitro. J Biol Chem 2002; 277:22361-9. [PMID: 11948189 DOI: 10.1074/jbc.m201765200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Repeat sequences in various genomes undergo expansion by poorly understood mechanisms. By using an oligonucleotide system containing such repeats, we recapitulated the last steps in Okazaki fragment processing, which have been implicated in sequence expansion. A template containing either triplet or tandem repeats was annealed to a downstream primer containing complementary repeats at its 5'-end. Overlapping upstream primers, designed to strand-displace varying numbers of repeats in the downstream primer, were annealed. Human DNA ligase I joined overlapping segments of repeats generating an expansion product from the primer strands. Joining efficiency decreased with repeat length. Flap endonuclease 1 (FEN1) cleaved the displaced downstream strand and together with DNA ligase I produced non-expanded products. However, both expanded and non-expanded products formed irrespective of relative nuclease and ligase concentrations tested or enzyme addition order, suggesting the pre-existence and persistence of intermediates leading to both outcomes. FEN1 activity decreased with the length of repeat segment displaced presumably because the flap forms structures that inhibit cleavage. Increased MgCl(2) disfavored ligation of substrate intermediates that result in expansion products. Examination of expansion in vitro enables dissection of substrate and replication enzyme dynamics on repeat sequences.
Collapse
Affiliation(s)
- Leigh A Henricksen
- Department of Biochemistry and Biophysics and the Cancer Center, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | | | | | | |
Collapse
|
30
|
Current Awareness. Yeast 2001. [DOI: 10.1002/yea.686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
31
|
Kovtun IV, Goellner G, McMurray CT. Structural features of trinucleotide repeats associated with DNA expansion. Biochem Cell Biol 2001. [DOI: 10.1139/o01-101] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The mechanism of DNA expansion is not well understood. Recent evidence from genetic, in vivo, and in vitro studies has suggested a link between the formation of alternative DNA secondary structures by trinucleotide repeat tracts and their propensity to undergo expansion. This review will focus on structural features and the mechanism of expansion relevant to human disease.Key words: expansion, hairpin, trinucleotide repeat, polymerase slippage, recombination, repair.
Collapse
|