1
|
Krasikova YS, Maltseva EA, Khodyreva SN, Evdokimov AN, Rechkunova NI, Lavrik OI. Does the XPA-FEN1 Interaction Concern to Nucleotide Excision Repair or Beyond? Biomolecules 2024; 14:814. [PMID: 39062528 PMCID: PMC11274875 DOI: 10.3390/biom14070814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/28/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Nucleotide excision repair (NER) is the most universal repair pathway, which removes a wide range of DNA helix-distorting lesions caused by chemical or physical agents. The final steps of this repair process are gap-filling repair synthesis and subsequent ligation. XPA is the central NER scaffolding protein factor and can be involved in post-incision NER stages. Replication machinery is loaded after the first incision of the damaged strand that is performed by the XPF-ERCC1 nuclease forming a damaged 5'-flap processed by the XPG endonuclease. Flap endonuclease I (FEN1) is a critical component of replication machinery and is absolutely indispensable for the maturation of newly synthesized strands. FEN1 also contributes to the long-patch pathway of base excision repair. Here, we use a set of DNA substrates containing a fluorescently labeled 5'-flap and different size gap to analyze possible repair factor-replication factor interactions. Ternary XPA-FEN1-DNA complexes with each tested DNA are detected. Furthermore, we demonstrate XPA-FEN1 complex formation in the absence of DNA due to protein-protein interaction. Functional assays reveal that XPA moderately inhibits FEN1 catalytic activity. Using fluorescently labeled XPA, formation of ternary RPA-XPA-FEN1 complex, where XPA accommodates FEN1 and RPA contacts simultaneously, can be proposed. We discuss possible functional roles of the XPA-FEN1 interaction in NER related DNA resynthesis and/or other DNA metabolic processes where XPA can be involved in the complex with FEN1.
Collapse
Affiliation(s)
- Yuliya S. Krasikova
- Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (Y.S.K.); (E.A.M.); (S.N.K.); (A.N.E.); (N.I.R.)
| | - Ekaterina A. Maltseva
- Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (Y.S.K.); (E.A.M.); (S.N.K.); (A.N.E.); (N.I.R.)
| | - Svetlana N. Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (Y.S.K.); (E.A.M.); (S.N.K.); (A.N.E.); (N.I.R.)
| | - Alexey N. Evdokimov
- Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (Y.S.K.); (E.A.M.); (S.N.K.); (A.N.E.); (N.I.R.)
| | - Nadejda I. Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (Y.S.K.); (E.A.M.); (S.N.K.); (A.N.E.); (N.I.R.)
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (Y.S.K.); (E.A.M.); (S.N.K.); (A.N.E.); (N.I.R.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| |
Collapse
|
2
|
Adil O, Eddington SB, Gagnon KT, Shamsi MH. Microprobes for Label-Free Detection of Short Tandem Repeats: An Insight into Alleviating Secondary Structure Effects. Anal Chem 2023; 95:13528-13536. [PMID: 37651633 DOI: 10.1021/acs.analchem.3c01886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Overgrowth of short tandem repeat sequences in our genes can cause various neurodegenerative disorders. Such repeat sequences are ideal targets for the label-free electrochemical detection of such potential expansions. However, their length- and sequence-dependent secondary structures may interfere with the interfacial charge transfer of a detection platform, making them complex targets. In addition, the gene contains sporadic repeats that may result in false-positive signals. Therefore, it is necessary to design a platform capable of mitigating these effects and ultimately enhancing the specificity of tandem repeats. Here, we analyzed three different backbones of nucleic acid microprobes [DNA, peptide nucleic acid, and lock-nucleic acid (LNA)] to detect in vitro transcribed RNA carrying CAG repeats, which are associated with Huntington's disease, based on the charge-transfer resistance of the interface. We found that the LNA microprobe can distinguish lengths down to the attomolar concentration level and alleviate the effect of secondary structures and sporadic repeats in the sequence, thus distinguishing the "tandem repeats" specifically. Additionally, the control experiments conducted with and without Mg2+ demonstrated the LNA microprobe to perform better in the presence of the divalent cation. The results suggest that the LNA-based platform may eventually lead to the development of a reliable and straightforward biosensor for genetic neurodegenerative disorders.
Collapse
Affiliation(s)
- Omair Adil
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, United States
| | - Seth B Eddington
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Keith T Gagnon
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, United States
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Mohtashim H Shamsi
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, United States
| |
Collapse
|
3
|
Abstract
At fifteen different genomic locations, the expansion of a CAG/CTG repeat causes a neurodegenerative or neuromuscular disease, the most common being Huntington's disease and myotonic dystrophy type 1. These disorders are characterized by germline and somatic instability of the causative CAG/CTG repeat mutations. Repeat lengthening, or expansion, in the germline leads to an earlier age of onset or more severe symptoms in the next generation. In somatic cells, repeat expansion is thought to precipitate the rate of disease. The mechanisms underlying repeat instability are not well understood. Here we review the mammalian model systems that have been used to study CAG/CTG repeat instability, and the modifiers identified in these systems. Mouse models have demonstrated prominent roles for proteins in the mismatch repair pathway as critical drivers of CAG/CTG instability, which is also suggested by recent genome-wide association studies in humans. We draw attention to a network of connections between modifiers identified across several systems that might indicate pathway crosstalk in the context of repeat instability, and which could provide hypotheses for further validation or discovery. Overall, the data indicate that repeat dynamics might be modulated by altering the levels of DNA metabolic proteins, their regulation, their interaction with chromatin, or by direct perturbation of the repeat tract. Applying novel methodologies and technologies to this exciting area of research will be needed to gain deeper mechanistic insight that can be harnessed for therapies aimed at preventing repeat expansion or promoting repeat contraction.
Collapse
Affiliation(s)
- Vanessa C. Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA,Department of Neurology, Harvard Medical School, Boston, MA, USA,Correspondence to: Vanessa C. Wheeler, Center for Genomic Medicine, Massachusetts Hospital, Boston MAA 02115, USA. E-mail: . and Vincent Dion, UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK. E-mail:
| | - Vincent Dion
- UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, UK,Correspondence to: Vanessa C. Wheeler, Center for Genomic Medicine, Massachusetts Hospital, Boston MAA 02115, USA. E-mail: . and Vincent Dion, UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK. E-mail:
| |
Collapse
|
4
|
Deshmukh AL, Porro A, Mohiuddin M, Lanni S, Panigrahi GB, Caron MC, Masson JY, Sartori AA, Pearson CE. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. J Huntingtons Dis 2021; 10:95-122. [PMID: 33579867 PMCID: PMC7990447 DOI: 10.3233/jhd-200448] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
FAN1 encodes a DNA repair nuclease. Genetic deficiencies, copy number variants, and single nucleotide variants of FAN1 have been linked to karyomegalic interstitial nephritis, 15q13.3 microdeletion/microduplication syndrome (autism, schizophrenia, and epilepsy), cancer, and most recently repeat expansion diseases. For seven CAG repeat expansion diseases (Huntington's disease (HD) and certain spinocerebellar ataxias), modification of age of onset is linked to variants of specific DNA repair proteins. FAN1 variants are the strongest modifiers. Non-coding disease-delaying FAN1 variants and coding disease-hastening variants (p.R507H and p.R377W) are known, where the former may lead to increased FAN1 levels and the latter have unknown effects upon FAN1 functions. Current thoughts are that ongoing repeat expansions in disease-vulnerable tissues, as individuals age, promote disease onset. Fan1 is required to suppress against high levels of ongoing somatic CAG and CGG repeat expansions in tissues of HD and FMR1 transgenic mice respectively, in addition to participating in DNA interstrand crosslink repair. FAN1 is also a modifier of autism, schizophrenia, and epilepsy. Coupled with the association of these diseases with repeat expansions, this suggests a common mechanism, by which FAN1 modifies repeat diseases. Yet how any of the FAN1 variants modify disease is unknown. Here, we review FAN1 variants, associated clinical effects, protein structure, and the enzyme's attributed functional roles. We highlight how variants may alter its activities in DNA damage response and/or repeat instability. A thorough awareness of the FAN1 gene and FAN1 protein functions will reveal if and how it may be targeted for clinical benefit.
Collapse
Affiliation(s)
- Amit L. Deshmukh
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Antonio Porro
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mohiuddin Mohiuddin
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Stella Lanni
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Gagan B. Panigrahi
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Marie-Christine Caron
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Quebec, Canada
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, Quebec, Canada
| | - Jean-Yves Masson
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Quebec, Canada
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, Quebec, Canada
| | | | - Christopher E. Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- University of Toronto, Program of Molecular Genetics, Toronto, Ontario, Canada
| |
Collapse
|
5
|
Mystery of Expansion: DNA Metabolism and Unstable Repeats. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:101-124. [PMID: 32383118 DOI: 10.1007/978-3-030-41283-8_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The mammalian genome mostly contains repeated sequences. Some of these repeats are in the regulatory elements of genes, and their instability, particularly the propensity to change the repeat unit number, is responsible for 36 well-known neurodegenerative human disorders. The mechanism of repeat expansion has been an unsolved question for more than 20 years. There are a few hypotheses describing models of mutation development. Every hypothesis is based on assumptions about unusual secondary structures that violate DNA metabolism processes in the cell. Some models are based on replication errors, and other models are based on mismatch repair or base excision repair errors. Additionally, it has been shown that epigenetic regulation of gene expression can influence the probability and frequency of expansion. In this review, we consider the molecular bases of repeat expansion disorders and discuss possible mechanisms of repeat expansion during cell metabolism.
Collapse
|
6
|
Park S, Karatayeva N, Demin AA, Munashingha PR, Seo YS. The secondary-structured DNA-binding activity of Dna2 endonuclease/helicase is critical to cell growth under replication stress. FEBS J 2020; 288:1224-1242. [PMID: 32638513 PMCID: PMC7984218 DOI: 10.1111/febs.15475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/11/2020] [Accepted: 06/30/2020] [Indexed: 11/30/2022]
Abstract
Dna2 can efficiently process 5' flaps containing DNA secondary structure using coordinated action of the three biochemical activities: the N-terminally encoded DNA-binding activity and the C-terminally encoded endonuclease and helicase activities. In this study, we investigated the cross talk among the three functional domains using a variety of dna2 mutant alleles and enzymes derived thereof. We found that disruption of the catalytic activities of Dna2 activated Dna2-dependent checkpoint, residing in the N-terminal domain. This checkpoint activity contributed to growth defects of dna2 catalytic mutants, revealing the presence of an intramolecular functional cross talk in Dna2. The N-terminal domain of Dna2 bound specifically to substrates that mimic DNA replication fork intermediates, including Holliday junctions. Using site-directed mutagenesis of the N-terminal domain of Dna2, we discovered that five consecutive basic amino acid residues were essential for the ability of Dna2 to bind hairpin DNA in vitro. Mutant cells expressing the dna2 allele containing all five basic residues substituted with alanine displayed three distinct phenotypes: (i) temperature-sensitive growth defects, (ii) bypass of S-phase arrest, and (iii) increased sensitivity to DNA-damaging agents. Taken together, our results indicate that the interplay between the N-terminal regulatory and C-terminal catalytic domains of Dna2 plays an important role in vivo, especially when cells are placed under replication stress.
Collapse
Affiliation(s)
- Soyeong Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Nargis Karatayeva
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Annie Albert Demin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Palinda Ruvan Munashingha
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Yeon-Soo Seo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| |
Collapse
|
7
|
Svetec Miklenić M, Gatalica N, Matanović A, Žunar B, Štafa A, Lisnić B, Svetec IK. Size-dependent antirecombinogenic effect of short spacers on palindrome recombinogenicity. DNA Repair (Amst) 2020; 90:102848. [PMID: 32388488 DOI: 10.1016/j.dnarep.2020.102848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 03/21/2020] [Accepted: 03/28/2020] [Indexed: 01/01/2023]
Abstract
Palindromic sequences in DNA can instigate genetic recombination and genome instability, which can result in devastating conditions such as the Emmanuel syndrome. Palindrome recombinogenicity increases with its size and sequence similarity between palindrome arms, while quasipalindromes with long spacers are less recombinogenic. However, the minimal spacer length, which could reduce or abolish palindrome recombinogenicity in the eukaryotic genome, was never determined. Therefore, we constructed a series of palindromes containing spacers of lengths ranging from 0 (perfect palindrome) to 10 bp and tested their recombinogenicity in yeast Saccharomyces cerevisiae. We found that a 7 bp spacer significantly reduces 126 bp palindrome recombinogenicity, while a 10 bp spacer completely stabilizes palindromes up to 150 bp long. Additionally, we showed that palindrome stimulated recombination rate is not dependent on Mus81 and Yen1 endonucleases. We also compared the recombinogenicity of a perfect 126 bp palindrome and a corresponding quasipalindrome consisting of the same palindrome arms with a stabilising 10 bp spacer in sgs1Δ and rad27Δ backgrounds, since both Sgs1 helicase and Rad27 endonuclease are implicated in preventing hairpin formation at palindromic sequences during replication.
Collapse
Affiliation(s)
- Marina Svetec Miklenić
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Nikolina Gatalica
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Angela Matanović
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Bojan Žunar
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Anamarija Štafa
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Berislav Lisnić
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ivan Krešimir Svetec
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia.
| |
Collapse
|
8
|
Hibino M, Aiba Y, Shoji O. Cationic guanine: positively charged nucleobase with improved DNA affinity inhibits self-duplex formation. Chem Commun (Camb) 2020; 56:2546-2549. [PMID: 32040115 DOI: 10.1039/d0cc00169d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligonucleotides represent powerful DNA-recognition tools, but the formation of undesirable "self-duplexes" becomes more probable with increasing DNA affinity. Herein, we have developed a modified nucleobase with "self-avoiding" properties. Facile methylation of guanine yields a cationic N7-methylguanine, which suppresses the formation of self-duplexes whilst improving DNA affinity through electrostatic interaction.
Collapse
Affiliation(s)
- Masaki Hibino
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| |
Collapse
|
9
|
Mitchell ML, Leveille MP, Solecki RS, Tran T, Cannon B. Sequence-Dependent Effects of Monovalent Cations on the Structural Dynamics of Trinucleotide-Repeat DNA Hairpins. J Phys Chem B 2018; 122:11841-11851. [PMID: 30441902 DOI: 10.1021/acs.jpcb.8b07994] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Repetitive trinucleotide DNA sequences at specific genetic loci are associated with numerous hereditary, neurodegenerative diseases. The propensity of single-stranded domains containing these sequences to form secondary structure via extensive self-complementarity disrupts normal DNA processing to create genetic instabilities. To investigate these intrastrand structural dynamics, a DNA hairpin system was devised for single-molecule fluorescence study of the folding kinetics and energetics for secondary structure formation between two interacting, repetitive domains with specific numbers of the same trinucleotide motif (CXG), where X = T or A. Single-molecule fluorescence resonance energy transfer (smFRET) data show discrete conformational transitions between unstructured and closed hairpin states. The lifetimes of the closed hairpin states correlate with the number of repeats, with (CTG) N/(CTG) N domains maintaining longer-lived, closed states than equivalent-sized (CAG) N/(CAG) N domains. NaCl promotes similar degree of stabilization for the closed hairpin states of both repeat sequences. Temperature-based, smFRET experiments reveal that NaCl favors hairpin closing for (CAG) N/(CAG) N by preordering single-stranded repeat domains to accelerate the closing transition. In contrast, NaCl slows the opening transition of CTG hairpins; however, it promotes misfolded conformations that require unfolding. Energy diagrams illustrate the distinct folding pathways of (CTG) N and (CAG) N repeat domains and identify features that may contribute to their gene-destabilizing effects.
Collapse
Affiliation(s)
- Marisa L Mitchell
- Department of Physics , Loyola University Chicago , Chicago , Illinois 60660 , United States
| | - Michael P Leveille
- Department of Physics , Loyola University Chicago , Chicago , Illinois 60660 , United States
| | - Roman S Solecki
- Department of Physics , Loyola University Chicago , Chicago , Illinois 60660 , United States
| | - Thao Tran
- Department of Physics , Loyola University Chicago , Chicago , Illinois 60660 , United States
| | - Brian Cannon
- Department of Physics , Loyola University Chicago , Chicago , Illinois 60660 , United States
| |
Collapse
|
10
|
da Silva MS, Hovel-Miner GA, Briggs EM, Elias MC, McCulloch R. Evaluation of mechanisms that may generate DNA lesions triggering antigenic variation in African trypanosomes. PLoS Pathog 2018; 14:e1007321. [PMID: 30440029 PMCID: PMC6237402 DOI: 10.1371/journal.ppat.1007321] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Antigenic variation by variant surface glycoprotein (VSG) coat switching in African trypanosomes is one of the most elaborate immune evasion strategies found among pathogens. Changes in the identity of the transcribed VSG gene, which is always flanked by 70-bp and telomeric repeats, can be achieved either by transcriptional or DNA recombination mechanisms. The major route of VSG switching is DNA recombination, which occurs in the bloodstream VSG expression site (ES), a multigenic site transcribed by RNA polymerase I. Recombinogenic VSG switching is frequently catalyzed by homologous recombination (HR), a reaction normally triggered by DNA breaks. However, a clear understanding of how such breaks arise-including whether there is a dedicated and ES-focused mechanism-is lacking. Here, we synthesize data emerging from recent studies that have proposed a range of mechanisms that could generate these breaks: action of a nuclease or nucleases; repetitive DNA, most notably the 70-bp repeats, providing an intra-ES source of instability; DNA breaks derived from the VSG-adjacent telomere; DNA breaks arising from high transcription levels at the active ES; and DNA lesions arising from replication-transcription conflicts in the ES. We discuss the evidence that underpins these switch-initiation models and consider what features and mechanisms might be shared or might allow the models to be tested further. Evaluation of all these models highlights that we still have much to learn about the earliest acting step in VSG switching, which may have the greatest potential for therapeutic intervention in order to undermine the key reaction used by trypanosomes for their survival and propagation in the mammalian host.
Collapse
Affiliation(s)
- Marcelo Santos da Silva
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Galadriel A. Hovel-Miner
- The George Washington University, Department of Microbiology Immunology, and Tropical Medicine, Washington, DC, United States of America
| | - Emma M. Briggs
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
11
|
McGinty RJ, Mirkin SM. Cis- and Trans-Modifiers of Repeat Expansions: Blending Model Systems with Human Genetics. Trends Genet 2018; 34:448-465. [PMID: 29567336 PMCID: PMC5959756 DOI: 10.1016/j.tig.2018.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 12/30/2022]
Abstract
Over 30 hereditary diseases are caused by the expansion of microsatellite repeats. The length of the expandable repeat is the main hereditary determinant of these disorders. They are also affected by numerous genomic variants that are either nearby (cis) or physically separated from (trans) the repetitive locus, which we review here. These genetic variants have largely been elucidated in model systems using gene knockouts, while a few have been directly observed as single-nucleotide polymorphisms (SNPs) in patients. There is a notable disconnect between these two bodies of knowledge: knockouts poorly approximate the SNP-level variation in human populations that gives rise to medically relevant cis- and trans-modifiers, while the rarity of these diseases limits the statistical power of SNP-based analysis in humans. We propose that high-throughput SNP-based screening in model systems could become a useful approach to quickly identify and characterize modifiers of clinical relevance for patients.
Collapse
Affiliation(s)
- Ryan J McGinty
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
| |
Collapse
|
12
|
Loo J, Yang C, Tsang HL, Lau PM, Yong KT, Ho HP, Kong SK. An Aptamer Bio-barCode (ABC) assay using SPR, RNase H, and probes with RNA and gold-nanorods for anti-cancer drug screening. Analyst 2017; 142:3579-3587. [PMID: 28852760 DOI: 10.1039/c7an01026e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
With modifications to an ultra-sensitive bio-barcode (BBC) assay, we have developed a next generation aptamer-based bio-barcode (ABC) assay to detect cytochrome-c (Cyto-c), a cell death marker released from cancer cells, for anti-cancer drug screening. An aptamer is a short single-stranded DNA selected from a synthetic DNA library that is capable of binding to its target with high affinity and specificity based on its unique DNA sequence and 3D structure after folding. Similar to the BBC assay, Cyto-c is captured by a micro-magnetic particle (MMP) coated with capturing antibodies (Ab) and an aptamer specifically against Cyto-c to form sandwich structures ([MMP-Ab]-[Cyto-c]-[Aptamer]). After washing and melting, our aptamers, acting as a DNA bio-barcode, are released from the sandwiches and hybridized with the probes specially designed for RNase H for surface plasmon resonance (SPR) sensing. In an aptamer-probe duplex, RNase H digests the RNA in the probe and releases the intact aptamer for another round of hybridization and digestion. With signal enhancement effects from gold-nanorods (Au-NRs) on probes for SPR sensing, the detection limit was found to be 1 nM for the aptamer and 80 pM for Cyto-c. Without the time-consuming DNA amplification steps by PCR, the detection process of this new ABC assay can be completed within three hours. As a proof-of-concept, phenylarsine oxide was found to be a potent agent to kill liver cancer cells with multi-drug resistance at the nano-molar level. This approach thus provides a fast, sensitive and robust tool for anti-cancer drug screening.
Collapse
Affiliation(s)
- Jacky Loo
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong
| | - Chengbin Yang
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore
| | - Hing Lun Tsang
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
| | - Pui Man Lau
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
| | - Ken-Tye Yong
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore
| | - Ho Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong
| | - Siu Kai Kong
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
| |
Collapse
|
13
|
Rohilla KJ, Gagnon KT. RNA biology of disease-associated microsatellite repeat expansions. Acta Neuropathol Commun 2017; 5:63. [PMID: 28851463 PMCID: PMC5574247 DOI: 10.1186/s40478-017-0468-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022] Open
Abstract
Microsatellites, or simple tandem repeat sequences, occur naturally in the human genome and have important roles in genome evolution and function. However, the expansion of microsatellites is associated with over two dozen neurological diseases. A common denominator among the majority of these disorders is the expression of expanded tandem repeat-containing RNA, referred to as xtrRNA in this review, which can mediate molecular disease pathology in multiple ways. This review focuses on the potential impact that simple tandem repeat expansions can have on the biology and metabolism of RNA that contain them and underscores important gaps in understanding. Merging the molecular biology of repeat expansion disorders with the current understanding of RNA biology, including splicing, transcription, transport, turnover and translation, will help clarify mechanisms of disease and improve therapeutic development.
Collapse
|
14
|
Polyzos AA, McMurray CT. Close encounters: Moving along bumps, breaks, and bubbles on expanded trinucleotide tracts. DNA Repair (Amst) 2017; 56:144-155. [PMID: 28690053 PMCID: PMC5558859 DOI: 10.1016/j.dnarep.2017.06.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Expansion of simple triplet repeats (TNR) underlies more than 30 severe degenerative diseases. There is a good understanding of the major pathways generating an expansion, and the associated polymerases that operate during gap filling synthesis at these "difficult to copy" sequences. However, the mechanism by which a TNR is repaired depends on the type of lesion, the structural features imposed by the lesion, the assembled replication/repair complex, and the polymerase that encounters it. The relationships among these parameters are exceptionally complex and how they direct pathway choice is poorly understood. In this review, we consider the properties of polymerases, and how encounters with GC-rich or abnormal structures might influence polymerase choice and the success of replication and repair. Insights over the last three years have highlighted new mechanisms that provide interesting choices to consider in protecting genome stability.
Collapse
Affiliation(s)
- Aris A Polyzos
- MBIB Division, Lawrence Berkeley Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, United States
| | - Cynthia T McMurray
- MBIB Division, Lawrence Berkeley Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, United States.
| |
Collapse
|
15
|
Effects of Replication and Transcription on DNA Structure-Related Genetic Instability. Genes (Basel) 2017; 8:genes8010017. [PMID: 28067787 PMCID: PMC5295012 DOI: 10.3390/genes8010017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/21/2016] [Accepted: 12/26/2016] [Indexed: 12/20/2022] Open
Abstract
Many repetitive sequences in the human genome can adopt conformations that differ from the canonical B-DNA double helix (i.e., non-B DNA), and can impact important biological processes such as DNA replication, transcription, recombination, telomere maintenance, viral integration, transposome activation, DNA damage and repair. Thus, non-B DNA-forming sequences have been implicated in genetic instability and disease development. In this article, we discuss the interactions of non-B DNA with the replication and/or transcription machinery, particularly in disease states (e.g., tumors) that can lead to an abnormal cellular environment, and how such interactions may alter DNA replication and transcription, leading to potential conflicts at non-B DNA regions, and eventually result in genetic stability and human disease.
Collapse
|
16
|
Ups and Downs: Mechanisms of Repeat Instability in the Fragile X-Related Disorders. Genes (Basel) 2016; 7:genes7090070. [PMID: 27657135 PMCID: PMC5042400 DOI: 10.3390/genes7090070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 08/30/2016] [Accepted: 09/13/2016] [Indexed: 02/06/2023] Open
Abstract
The Fragile X-related disorders (FXDs) are a group of clinical conditions resulting from the expansion of a CGG/CCG-repeat tract in exon 1 of the Fragile X mental retardation 1 (FMR1) gene. While expansions of the repeat tract predominate, contractions are also seen with the net result being that individuals can show extensive repeat length heterogeneity in different tissues. The mechanisms responsible for expansion and contraction are still not well understood. This review will discuss what is known about these processes and current evidence that supports a model in which expansion arises from the interaction of components of the base excision repair, mismatch repair and transcription coupled repair pathways.
Collapse
|
17
|
Cilli P, Ventura I, Minoprio A, Meccia E, Martire A, Wilson SH, Bignami M, Mazzei F. Oxidized dNTPs and the OGG1 and MUTYH DNA glycosylases combine to induce CAG/CTG repeat instability. Nucleic Acids Res 2016; 44:5190-203. [PMID: 26980281 PMCID: PMC4914090 DOI: 10.1093/nar/gkw170] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/03/2016] [Indexed: 12/13/2022] Open
Abstract
DNA trinucleotide repeat (TNR) expansion underlies several neurodegenerative disorders including Huntington's disease (HD). Accumulation of oxidized DNA bases and their inefficient processing by base excision repair (BER) are among the factors suggested to contribute to TNR expansion. In this study, we have examined whether oxidation of the purine dNTPs in the dNTP pool provides a source of DNA damage that promotes TNR expansion. We demonstrate that during BER of 8-oxoguanine (8-oxodG) in TNR sequences, DNA polymerase β (POL β) can incorporate 8-oxodGMP with the formation of 8-oxodG:C and 8-oxodG:A mispairs. Their processing by the OGG1 and MUTYH DNA glycosylases generates closely spaced incisions on opposite DNA strands that are permissive for TNR expansion. Evidence in HD model R6/2 mice indicates that these DNA glycosylases are present in brain areas affected by neurodegeneration. Consistent with prevailing oxidative stress, the same brain areas contained increased DNA 8-oxodG levels and expression of the p53-inducible ribonucleotide reductase. Our in vitro and in vivo data support a model where an oxidized dNTPs pool together with aberrant BER processing contribute to TNR expansion in non-replicating cells.
Collapse
Affiliation(s)
- Piera Cilli
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma, Italy Department of Science, University Roma Tre, 00154 Roma, Italy
| | - Ilenia Ventura
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Anna Minoprio
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Ettore Meccia
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Alberto Martire
- Department of Drug Safety and Evaluation, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Margherita Bignami
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Filomena Mazzei
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma, Italy
| |
Collapse
|
18
|
Zhao XN, Usdin K. The transcription-coupled repair protein ERCC6/CSB also protects against repeat expansion in a mouse model of the fragile X premutation. Hum Mutat 2015; 36:482-7. [PMID: 25726753 DOI: 10.1002/humu.22777] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/20/2015] [Indexed: 12/31/2022]
Abstract
The fragile X-related disorders (FXDs) are members of the group of diseases known as the repeat expansion diseases. The FXDs result from expansion of an unstable CGG/CCG repeat tract in the 5' UTR of the FMR1 gene. Contractions are also seen, albeit at lower frequency. We have previously shown that ERCC6/CSB plays an auxiliary role in promoting germ line and somatic expansions in a mouse model of the FXDs. However, work in model systems of other repeat expansion diseases has suggested that CSB may protect against expansions by promoting contractions. Since FXD mice normally have such a high expansion frequency, it is possible that such a protective effect would have been masked. We thus examined the effect of the loss of CSB in an Msh2(+/-) background where the germ line expansion frequency is reduced and in an Msh2(-/-) background where expansions do not occur, but contractions do. Our data show that in addition to promoting repeat expansion, CSB does in fact protect the genome from germ line expansions in the FXD mouse model. However, it likely does so not by promoting contractions but by promoting an error-free process that preserves the parental allele.
Collapse
Affiliation(s)
- Xiao-Nan Zhao
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | | |
Collapse
|
19
|
Le HP, Masuda Y, Tsurimoto T, Maki S, Katayama T, Furukohri A, Maki H. Short CCG repeat in huntingtin gene is an obstacle for replicative DNA polymerases, potentially hampering progression of replication fork. Genes Cells 2015; 20:817-33. [PMID: 26271349 DOI: 10.1111/gtc.12275] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/22/2015] [Indexed: 01/02/2023]
Abstract
Trinucleotide repeats (TNRs) are highly unstable in genomes, and their expansions are linked to human disorders. DNA replication is reported to be involved in TNR instability, but the current models are insufficient in explaining TNR expansion is induced during replication. Here, we investigated replication fork progression across huntingtin (HTT)-gene-derived fragments using an Escherichia coli oriC plasmid DNA replication system. We found most of the forks to travel smoothly across the HTT fragments even when the fragments had a pathological length of CAG/CTG repeats (approximately 120 repeats). A little fork stalling in the fragments was observed, but it occurred within a short 3'-flanking region downstream of the repeats. This region contains another short TNR, (CCG/CGG)7 , and the sense strand containing CCG repeats appeared to impede the replicative DNA polymerase Pol III. Examining the behavior of the human leading and lagging replicative polymerases Pol epsilon (hPolε) and Pol delta (hPolδ) on this sequence, we found hPolδ replicating DNA across the CCG repeats but hPolε stalling at the CCG repeats even if the secondary structure is eliminated by a single-stranded binding protein. These findings offer insights into the distinct behavior of leading and lagging polymerases at CCG/CGG repeats, which may be important for understanding the process of replication arrest and genome instability at the HTT gene.
Collapse
Affiliation(s)
- Hang Phuong Le
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Nara, Japan
| | - Yuji Masuda
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, 464-8601, Japan.,Department of Toxicogenomics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Toshiki Tsurimoto
- Department of Biology, School of Sciences, Kyushu University, Fukuoka, 812-8581, Japan
| | - Satoko Maki
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Nara, Japan
| | - Tsutomu Katayama
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Asako Furukohri
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Nara, Japan
| | - Hisaji Maki
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Nara, Japan
| |
Collapse
|
20
|
Tarantino ME, Bilotti K, Huang J, Delaney S. Rate-determining Step of Flap Endonuclease 1 (FEN1) Reflects a Kinetic Bias against Long Flaps and Trinucleotide Repeat Sequences. J Biol Chem 2015; 290:21154-21162. [PMID: 26160176 DOI: 10.1074/jbc.m115.666438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Indexed: 11/06/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is a structure-specific nuclease responsible for removing 5'-flaps formed during Okazaki fragment maturation and long patch base excision repair. In this work, we use rapid quench flow techniques to examine the rates of 5'-flap removal on DNA substrates of varying length and sequence. Of particular interest are flaps containing trinucleotide repeats (TNR), which have been proposed to affect FEN1 activity and cause genetic instability. We report that FEN1 processes substrates containing flaps of 30 nucleotides or fewer at comparable single-turnover rates. However, for flaps longer than 30 nucleotides, FEN1 kinetically discriminates substrates based on flap length and flap sequence. In particular, FEN1 removes flaps containing TNR sequences at a rate slower than mixed sequence flaps of the same length. Furthermore, multiple-turnover kinetic analysis reveals that the rate-determining step of FEN1 switches as a function of flap length from product release to chemistry (or a step prior to chemistry). These results provide a kinetic perspective on the role of FEN1 in DNA replication and repair and contribute to our understanding of FEN1 in mediating genetic instability of TNR sequences.
Collapse
Affiliation(s)
- Mary E Tarantino
- Department of Chemistry, Brown University, Providence, Rhode Island 02912
| | - Katharina Bilotti
- Department of Chemistry, Brown University, Providence, Rhode Island 02912
| | - Ji Huang
- Department of Chemistry, Brown University, Providence, Rhode Island 02912
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912.
| |
Collapse
|
21
|
Abstract
DNA repair normally protects the genome against mutations that threaten genome integrity and thus cell viability. However, growing evidence suggests that in the case of the Repeat Expansion Diseases, disorders that result from an increase in the size of a disease-specific microsatellite, the disease-causing mutation is actually the result of aberrant DNA repair. A variety of proteins from different DNA repair pathways have thus far been implicated in this process. This review will summarize recent findings from patients and from mouse models of these diseases that shed light on how these pathways may interact to cause repeat expansion.
Collapse
Affiliation(s)
- Xiao-Nan Zhao
- Section on Genomic Structure and Function Laboratory of Cell and Molecular Biology National Institute of Diabetes, Digestive and Kidney Diseases National Institutes of Health, Bethesda, MD 20892-0830, USA
| | - Karen Usdin
- Section on Genomic Structure and Function Laboratory of Cell and Molecular Biology National Institute of Diabetes, Digestive and Kidney Diseases National Institutes of Health, Bethesda, MD 20892-0830, USA.
| |
Collapse
|
22
|
Crespan E, Hübscher U, Maga G. Expansion of CAG triplet repeats by human DNA polymerases λ and β in vitro, is regulated by flap endonuclease 1 and DNA ligase 1. DNA Repair (Amst) 2015; 29:101-11. [PMID: 25687118 DOI: 10.1016/j.dnarep.2015.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/16/2015] [Accepted: 01/19/2015] [Indexed: 11/20/2022]
Abstract
Huntington's disease (HD) is a neurological genetic disorder caused by the expansion of the CAG trinucleotide repeats (TNR) in the N-terminal region of coding sequence of the Huntingtin's (HTT) gene. This results in the addition of a poly-glutamine tract within the Huntingtin protein, resulting in its pathological form. The mechanism by which TRN expansion takes place is not yet fully understood. We have recently shown that DNA polymerase (Pol) β can promote the microhomology-mediated end joining and triplet expansion of a substrate mimicking a double strand break in the TNR region of the HTT gene. Here we show that TNR expansion is dependent on the structure of the DNA substrate, as well as on the two essential Pol β co-factors: flap endonuclease 1 (Fen1) and DNA ligase 1 (Lig1). We found that Fen1 significantly stimulated TNR expansion by Pol β, but not by the related enzyme Pol λ, and subsequent ligation of the DNA products by Lig1. Interestingly, the deletion of N-terminal domains of Pol λ, resulted in an enzyme which displayed properties more similar to Pol β, suggesting a possible evolutionary mechanism. These results may suggest a novel mechanism for somatic TNR expansion in HD.
Collapse
Affiliation(s)
- Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, Pavia I-27100, Italy.
| | - Ulrich Hübscher
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Zürich CH-8057, Switzerland
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, Pavia I-27100, Italy
| |
Collapse
|
23
|
Usdin K, House NCM, Freudenreich CH. Repeat instability during DNA repair: Insights from model systems. Crit Rev Biochem Mol Biol 2015; 50:142-67. [PMID: 25608779 DOI: 10.3109/10409238.2014.999192] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The expansion of repeated sequences is the cause of over 30 inherited genetic diseases, including Huntington disease, myotonic dystrophy (types 1 and 2), fragile X syndrome, many spinocerebellar ataxias, and some cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat expansions are dynamic, and disease inheritance and progression are influenced by the size and the rate of expansion. Thus, an understanding of the various cellular mechanisms that cooperate to control or promote repeat expansions is of interest to human health. In addition, the study of repeat expansion and contraction mechanisms has provided insight into how repair pathways operate in the context of structure-forming DNA, as well as insights into non-canonical roles for repair proteins. Here we review the mechanisms of repeat instability, with a special emphasis on the knowledge gained from the various model systems that have been developed to study this topic. We cover the repair pathways and proteins that operate to maintain genome stability, or in some cases cause instability, and the cross-talk and interactions between them.
Collapse
Affiliation(s)
- Karen Usdin
- Laboratory of Cell and Molecular Biology, NIDDK, NIH , Bethesda, MD , USA
| | | | | |
Collapse
|
24
|
Jackson A, Okely EA, Leach DRF. Expansion of CAG repeats in Escherichia coli is controlled by single-strand DNA exonucleases of both polarities. Genetics 2014; 198:509-17. [PMID: 25081568 PMCID: PMC4196609 DOI: 10.1534/genetics.114.168245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The expansion of CAG·CTG repeat tracts is responsible for several neurodegenerative diseases, including Huntington disease and myotonic dystrophy. Understanding the molecular mechanism of CAG·CTG repeat tract expansion is therefore important if we are to develop medical interventions limiting expansion rates. Escherichia coli provides a simple and tractable model system to understand the fundamental properties of these DNA sequences, with the potential to suggest pathways that might be conserved in humans or to highlight differences in behavior that could signal the existence of human-specific factors affecting repeat array processing. We have addressed the genetics of CAG·CTG repeat expansion in E. coli and shown that these repeat arrays expand via an orientation-independent mechanism that contrasts with the orientation dependence of CAG·CTG repeat tract contraction. The helicase Rep contributes to the orientation dependence of repeat tract contraction and limits repeat tract expansion in both orientations. However, RuvAB-dependent fork reversal, which occurs in a rep mutant, is not responsible for the observed increase in expansions. The frequency of repeat tract expansion is controlled by both the 5'-3' exonuclease RecJ and the 3'-5' exonuclease ExoI, observations that suggest the importance of both 3'and 5' single-strand ends in the pathway of CAG·CTG repeat tract expansion. We discuss the relevance of our results to two competing models of repeat tract expansion.
Collapse
Affiliation(s)
- Adam Jackson
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, United Kingdom
| | - Ewa A Okely
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, United Kingdom
| | - David R F Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, United Kingdom
| |
Collapse
|
25
|
Usdin K, Hayward BE, Kumari D, Lokanga RA, Sciascia N, Zhao XN. Repeat-mediated genetic and epigenetic changes at the FMR1 locus in the Fragile X-related disorders. Front Genet 2014; 5:226. [PMID: 25101111 PMCID: PMC4101883 DOI: 10.3389/fgene.2014.00226] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/29/2014] [Indexed: 01/01/2023] Open
Abstract
The Fragile X-related disorders are a group of genetic conditions that include the neurodegenerative disorder, Fragile X-associated tremor/ataxia syndrome (FXTAS), the fertility disorder, Fragile X-associated primary ovarian insufficiency (FXPOI) and the intellectual disability, Fragile X syndrome (FXS). The pathology in all these diseases is related to the number of CGG/CCG-repeats in the 5′ UTR of the Fragile X mental retardation 1 (FMR1) gene. The repeats are prone to continuous expansion and the increase in repeat number has paradoxical effects on gene expression increasing transcription on mid-sized alleles and decreasing it on longer ones. In some cases the repeats can simultaneously both increase FMR1 mRNA production and decrease the levels of the FMR1 gene product, Fragile X mental retardation 1 protein (FMRP). Since FXTAS and FXPOI result from the deleterious consequences of the expression of elevated levels of FMR1 mRNA and FXS is caused by an FMRP deficiency, the clinical picture is turning out to be more complex than once appreciated. Added complications result from the fact that increasing repeat numbers make the alleles somatically unstable. Thus many individuals have a complex mixture of different sized alleles in different cells. Furthermore, it has become apparent that the eponymous fragile site, once thought to be no more than a useful diagnostic criterion, may have clinical consequences for females who inherit chromosomes that express this site. This review will cover what is currently known about the mechanisms responsible for repeat instability, for the repeat-mediated epigenetic changes that affect expression of the FMR1 gene, and for chromosome fragility. It will also touch on what current and future options are for ameliorating some of these effects.
Collapse
Affiliation(s)
- Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Bruce E Hayward
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Rachel A Lokanga
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Nicholas Sciascia
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Xiao-Nan Zhao
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| |
Collapse
|
26
|
Chung L, Onyango D, Guo Z, Jia P, Dai H, Liu S, Zhou M, Lin W, Pang I, Li H, Yuan YC, Huang Q, Zheng L, Lopes J, Nicolas A, Chai W, Raz D, Reckamp KL, Shen B. The FEN1 E359K germline mutation disrupts the FEN1-WRN interaction and FEN1 GEN activity, causing aneuploidy-associated cancers. Oncogene 2014; 34:902-11. [PMID: 24608430 PMCID: PMC4160428 DOI: 10.1038/onc.2014.19] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 11/18/2013] [Accepted: 12/20/2013] [Indexed: 02/02/2023]
Abstract
Polymorphisms and somatic mutations in Flap Endonuclease 1 (FEN1), an essential enzyme involved in DNA replication and repair, can lead to functional deficiencies of the FEN1 protein and a predisposition to cancer. We identified a FEN1 germline mutation which changed residue E359 to K in a patient whose family had a history of breast cancer. We determined that the E359K mutation, which is in the protein-protein domain of FEN1, abolished the interaction of FEN1 with Werner Syndrome protein (WRN), an interaction which is critical for resolving stalled DNA replication forks. Furthermore, although the flap endonuclease activity of FEN1 E359K was unaffected, it failed to resolve bubble structures, which requires the FEN1 gap dependent endonuclease (GEN) activity. To determine the etiological significance of E359K, we established a mouse model containing this mutation. E359K mouse embryonic fibroblasts (MEF) were more sensitive to DNA cross-linking agents that cause replication forks to stall. Cytological analysis suggested that the FEN1-WRN interaction was also required to for telomere stability; mutant cell lines had fragile telomeres, increased numbers of spontaneous chromosomal anomalies and higher frequencies of transformation. Moreover, the incidence of cancer was significantly higher in mice homozygous for FEN1 E359K than in wild-type mice, suggesting that the FEN1 E359K mutation is oncogenic.
Collapse
Affiliation(s)
- L Chung
- Department of Radiation Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - D Onyango
- Department of Radiation Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Z Guo
- 1] Department of Radiation Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA [2] Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - P Jia
- WWAMI Medical Education Program, School of Molecular Biosciences, Washington State University, Spokane, WA, USA
| | - H Dai
- Department of Radiation Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - S Liu
- 1] Department of Radiation Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA [2] College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - M Zhou
- Department of Radiation Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - W Lin
- Department of Radiation Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - I Pang
- Department of Radiation Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - H Li
- Department of Molecular Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Y-C Yuan
- Department of Molecular Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Q Huang
- Department of Pathology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - L Zheng
- Department of Radiation Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - J Lopes
- 1] Section de Recherche, Institut Curie, CNRS UMR3244, Paris, France [2] Muséum National d'Histoire Naturelle, USM 503, INSERM U565, UMR7196, Paris, France
| | - A Nicolas
- Section de Recherche, Institut Curie, CNRS UMR3244, Paris, France
| | - W Chai
- WWAMI Medical Education Program, School of Molecular Biosciences, Washington State University, Spokane, WA, USA
| | - D Raz
- Department of Surgery, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - K L Reckamp
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - B Shen
- Department of Radiation Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| |
Collapse
|
27
|
Xu M, Lai Y, Torner J, Zhang Y, Zhang Z, Liu Y. Base excision repair of oxidative DNA damage coupled with removal of a CAG repeat hairpin attenuates trinucleotide repeat expansion. Nucleic Acids Res 2014; 42:3675-91. [PMID: 24423876 PMCID: PMC3973345 DOI: 10.1093/nar/gkt1372] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Trinucleotide repeat (TNR) expansion is responsible for numerous human neurodegenerative diseases. However, the underlying mechanisms remain unclear. Recent studies have shown that DNA base excision repair (BER) can mediate TNR expansion and deletion by removing base lesions in different locations of a TNR tract, indicating that BER can promote or prevent TNR expansion in a damage location–dependent manner. In this study, we provide the first evidence that the repair of a DNA base lesion located in the loop region of a CAG repeat hairpin can remove the hairpin, attenuating repeat expansion. We found that an 8-oxoguanine located in the loop region of CAG hairpins of varying sizes was removed by OGG1 leaving an abasic site that was subsequently 5′-incised by AP endonuclease 1, introducing a single-strand breakage in the hairpin loop. This converted the hairpin into a double-flap intermediate with a 5′- and 3′-flap that was cleaved by flap endonuclease 1 and a 3′-5′ endonuclease Mus81/Eme1, resulting in complete or partial removal of the CAG hairpin. This further resulted in prevention and attenuation of repeat expansion. Our results demonstrate that TNR expansion can be prevented via BER in hairpin loops that is coupled with the removal of TNR hairpins.
Collapse
Affiliation(s)
- Meng Xu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA, Department of Environmental Health, West China School of Public Health, Sichuan University, Chengdu, Sichuan 610041, P. R. China and Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | | | | | | | | | | |
Collapse
|
28
|
Ayala-Peña S. Role of oxidative DNA damage in mitochondrial dysfunction and Huntington's disease pathogenesis. Free Radic Biol Med 2013; 62:102-110. [PMID: 23602907 PMCID: PMC3722255 DOI: 10.1016/j.freeradbiomed.2013.04.017] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 02/21/2013] [Accepted: 04/12/2013] [Indexed: 12/20/2022]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder with an autosomal dominant expression pattern and typically a late-onset appearance. HD is a movement disorder with a heterogeneous phenotype characterized by involuntary dance-like gait, bioenergetic deficits, motor impairment, and cognitive and psychiatric deficits. Compelling evidence suggests that increased oxidative stress and mitochondrial dysfunction may underlie HD pathogenesis. However, the exact mechanisms underlying mutant huntingtin-induced neurological toxicity remain unclear. The objective of this paper is to review recent literature regarding the role of oxidative DNA damage in mitochondrial dysfunction and HD pathogenesis.
Collapse
Affiliation(s)
- Sylvette Ayala-Peña
- Department of Pharmacology and Toxicology, University of Puerto Rico Medical Sciences Campus, P.O. Box 365067, San Juan, Puerto Rico 00936-5067.
| |
Collapse
|
29
|
Abnormal base excision repair at trinucleotide repeats associated with diseases: a tissue-selective mechanism. Genes (Basel) 2013; 4:375-87. [PMID: 24705210 PMCID: PMC3924826 DOI: 10.3390/genes4030375] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/25/2013] [Accepted: 06/26/2013] [Indexed: 12/03/2022] Open
Abstract
More than fifteen genetic diseases, including Huntington’s disease, myotonic dystrophy 1, fragile X syndrome and Friedreich ataxia, are caused by the aberrant expansion of a trinucleotide repeat. The mutation is unstable and further expands in specific cells or tissues with time, which can accelerate disease progression. DNA damage and base excision repair (BER) are involved in repeat instability and might contribute to the tissue selectivity of the process. In this review, we will discuss the mechanisms of trinucleotide repeat instability, focusing more specifically on the role of BER.
Collapse
|
30
|
Kim JC, Mirkin SM. The balancing act of DNA repeat expansions. Curr Opin Genet Dev 2013; 23:280-8. [PMID: 23725800 DOI: 10.1016/j.gde.2013.04.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 10/26/2022]
Abstract
Expansions of microsatellite DNA repeats contribute to the inheritance of nearly 30 developmental and neurological disorders. Significant progress has been made in elucidating the molecular mechanisms of repeat expansions using various model organisms and mammalian cell culture, and models implicating nearly all DNA transactions such as replication, repair, recombination, and transcription have been proposed. It is likely that different models of repeat expansions are not mutually exclusive and may explain repeat instability for different developmental stages and tissues. This review focuses on the contributions from studies in budding yeast toward unraveling the mechanisms and genetic control of repeat expansions, highlighting similarities and differences of replication models and describing a balancing act hypothesis to account for apparent discrepancies.
Collapse
Affiliation(s)
- Jane C Kim
- Department of Biology, Tufts University, Medford, MA 02155, United States
| | | |
Collapse
|
31
|
Vasquez KM, Wang G. The yin and yang of repair mechanisms in DNA structure-induced genetic instability. Mutat Res 2013; 743-744:118-131. [PMID: 23219604 PMCID: PMC3661696 DOI: 10.1016/j.mrfmmm.2012.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 11/21/2012] [Accepted: 11/24/2012] [Indexed: 01/14/2023]
Abstract
DNA can adopt a variety of secondary structures that deviate from the canonical Watson-Crick B-DNA form. More than 10 types of non-canonical or non-B DNA secondary structures have been characterized, and the sequences that have the capacity to adopt such structures are very abundant in the human genome. Non-B DNA structures have been implicated in many important biological processes and can serve as sources of genetic instability, implicating them in disease and evolution. Non-B DNA conformations interact with a wide variety of proteins involved in replication, transcription, DNA repair, and chromatin architectural regulation. In this review, we will focus on the interactions of DNA repair proteins with non-B DNA and their roles in genetic instability, as the proteins and DNA involved in such interactions may represent plausible targets for selective therapeutic intervention.
Collapse
Affiliation(s)
- Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States.
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
| |
Collapse
|
32
|
Abstract
First discovered as a structure-specific endonuclease that evolved to cut at the base of single-stranded flaps, flap endonuclease (FEN1) is now recognized as a central component of cellular DNA metabolism. Substrate specificity allows FEN1 to process intermediates of Okazaki fragment maturation, long-patch base excision repair, telomere maintenance, and stalled replication fork rescue. For Okazaki fragments, the RNA primer is displaced into a 5' flap and then cleaved off. FEN1 binds to the flap base and then threads the 5' end of the flap through its helical arch and active site to create a configuration for cleavage. The threading requirement prevents this active nuclease from cutting the single-stranded template between Okazaki fragments. FEN1 efficiency and specificity are critical to the maintenance of genome fidelity. Overall, recent advances in our knowledge of FEN1 suggest that it was an ancient protein that has been fine-tuned over eons to coordinate many essential DNA transactions.
Collapse
Affiliation(s)
- Lata Balakrishnan
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA.
| | | |
Collapse
|
33
|
Lee CH, Lee M, Kang HJ, Kim DH, Kang YH, Bae SH, Seo YS. The N-terminal 45-kDa domain of Dna2 endonuclease/helicase targets the enzyme to secondary structure DNA. J Biol Chem 2013; 288:9468-81. [PMID: 23344960 DOI: 10.1074/jbc.m112.418715] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The removal of initiating primers from the 5'-ends of each Okazaki fragment, required for the generation of contiguous daughter strands, can be catalyzed by the combined action of DNA polymerase δ and Fen1. When the flaps generated by displacement of DNA synthesis activity of polymerase δ become long enough to bind replication protein A or form hairpin structures, the helicase/endonuclease enzyme, Dna2, becomes critical because of its ability to remove replication protein A-coated or secondary structure flaps. In this study, we show that the N-terminal 45-kDa domain of Dna2 binds hairpin structures, allowing the enzyme to target secondary structure flap DNA. We found that this activity was essential for the efficient removal of hairpin flaps by the endonuclease activity of Dna2 with the aid of its helicase activity. Thus, the efficient removal of hairpin structure flaps requires the coordinated action of all three functional domains of Dna2. We also found that deletion of the N-terminal 45-kDa domain of Dna2 led to a partial loss of the intra-S-phase checkpoint function and an increased rate of homologous recombination in yeast. We discuss the potential roles of the N-terminal domain of Dna2 in the maintenance of genomic stability.
Collapse
Affiliation(s)
- Chul-Hwan Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | | | | | | | | | | | | |
Collapse
|
34
|
Xu M, Gabison J, Liu Y. Trinucleotide repeat deletion via a unique hairpin bypass by DNA polymerase β and alternate flap cleavage by flap endonuclease 1. Nucleic Acids Res 2012; 41:1684-97. [PMID: 23258707 PMCID: PMC3561997 DOI: 10.1093/nar/gks1306] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Trinucleotide repeat (TNR) expansions and deletions are associated with human neurodegenerative diseases and prostate cancer. Recent studies have pointed to a linkage between oxidative DNA damage, base excision repair (BER) and TNR expansion, which is demonstrated by the observation that DNA polymerase β (pol β) gap-filling synthesis acts in concert with alternate flap cleavage by flap endonuclease 1 (FEN1) to mediate CAG repeat expansions. In this study, we provide the first evidence that the repair of a DNA base lesion can also contribute to CAG repeat deletions that were initiated by the formation of hairpins on both the template and the damaged strand of a continuous run of (CAG)20 or (CAG)25 repeats. Most important, we found that pol β not only bypassed one part of the large template hairpin but also managed to pass through almost the entire length of small hairpin. The unique hairpin bypass of pol β resulted in large and small deletions in coordination with FEN1 alternate flap cleavage. Our results provide new insight into the role of BER in modulating genome stability that is associated with human diseases.
Collapse
Affiliation(s)
- Meng Xu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | | | | |
Collapse
|
35
|
Goula AV, Pearson CE, Della Maria J, Trottier Y, Tomkinson AE, Wilson DM, Merienne K. The nucleotide sequence, DNA damage location, and protein stoichiometry influence the base excision repair outcome at CAG/CTG repeats. Biochemistry 2012; 51:3919-32. [PMID: 22497302 PMCID: PMC3357312 DOI: 10.1021/bi300410d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Expansion of CAG/CTG repeats is the underlying cause of >14 genetic disorders, including Huntington's disease (HD) and myotonic dystrophy. The mutational process is ongoing, with increases in repeat size enhancing the toxicity of the expansion in specific tissues. In many repeat diseases, the repeats exhibit high instability in the striatum, whereas instability is minimal in the cerebellum. We provide molecular insights into how base excision repair (BER) protein stoichiometry may contribute to the tissue-selective instability of CAG/CTG repeats by using specific repair assays. Oligonucleotide substrates with an abasic site were mixed with either reconstituted BER protein stoichiometries mimicking the levels present in HD mouse striatum or cerebellum, or with protein extracts prepared from HD mouse striatum or cerebellum. In both cases, the repair efficiency at CAG/CTG repeats and at control DNA sequences was markedly reduced under the striatal conditions, likely because of the lower level of APE1, FEN1, and LIG1. Damage located toward the 5' end of the repeat tract was poorly repaired, with the accumulation of incompletely processed intermediates as compared to an AP lesion in the center or at the 3' end of the repeats or within control sequences. Moreover, repair of lesions at the 5' end of CAG or CTG repeats involved multinucleotide synthesis, particularly at the cerebellar stoichiometry, suggesting that long-patch BER processes lesions at sequences susceptible to hairpin formation. Our results show that the BER stoichiometry, nucleotide sequence, and DNA damage position modulate repair outcome and suggest that a suboptimal long-patch BER activity promotes CAG/CTG repeat instability.
Collapse
Affiliation(s)
- Agathi-Vasiliki Goula
- Department of Neurogenetics and Translational Medicine, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR 7104-CNRS/INSERM/UdS, Illkirch, France
| | - Christopher E. Pearson
- Genetics and Genome Biology, The Hospital for Sick Children, TMDT Building 101 College St., 15th Floor, Room 15-312 East Tower, Toronto, ON, M5G 1L7
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Julie Della Maria
- Department of Radiation Oncology and the Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Yvon Trottier
- Department of Neurogenetics and Translational Medicine, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR 7104-CNRS/INSERM/UdS, Illkirch, France
| | - Alan E. Tomkinson
- Department of Radiation Oncology and the Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David M. Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging (NIA)/ National Institutes of Health (NIH), Baltimore, Maryland, United States of America
| | - Karine Merienne
- Department of Neurogenetics and Translational Medicine, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR 7104-CNRS/INSERM/UdS, Illkirch, France
| |
Collapse
|
36
|
Völker J, Gindikin V, Klump HH, Plum GE, Breslauer KJ. Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states. J Am Chem Soc 2012; 134:6033-44. [PMID: 22397401 PMCID: PMC3318849 DOI: 10.1021/ja3010896] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Indexed: 11/30/2022]
Abstract
DNA repeat domains can form ensembles of canonical and noncanonical states, including stable and metastable DNA secondary structures. Such sequence-induced structural diversity creates complex conformational landscapes for DNA processing pathways, including those triplet expansion events that accompany replication, recombination, and/or repair. Here we demonstrate further levels of conformational complexity within repeat domains. Specifically, we show that bulge loop structures within an extended repeat domain can form dynamic ensembles containing a distribution of loop positions, thereby yielding families of positional loop isomers, which we designate as "rollamers". Our fluorescence, absorbance, and calorimetric data are consistent with loop migration/translocation between sites within the repeat domain ("rollamerization"). We demonstrate that such "rollameric" migration of bulge loops within repeat sequences can invade and disrupt previously formed base-paired domains via an isoenthalpic, entropy-driven process. We further demonstrate that destabilizing abasic lesions alter the loop distributions so as to favor "rollamers" with the lesion positioned at the duplex/loop junction, sites where the flexibility of the abasic "universal hinge" relaxes unfavorable interactions and/or facilitates topological accommodation. Another strategic siting of an abasic site induces directed loop migration toward denaturing domains, a phenomenon that merges destabilizing domains. In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature. These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery. We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA expansion.
Collapse
Affiliation(s)
- Jens Völker
- Department
of Chemistry and
Chemical Biology, Rutgers, The State University of New
Jersey, 610 Taylor Road, Piscataway, New Jersey 08854,
United States
| | - Vera Gindikin
- Department
of Chemistry and
Chemical Biology, Rutgers, The State University of New
Jersey, 610 Taylor Road, Piscataway, New Jersey 08854,
United States
| | - Horst H. Klump
- Department
of Molecular and
Cell Biology, University of Cape Town,
Private Bag, Rondebosch 7800, South Africa
| | - G. Eric Plum
- IBET Inc., 1507 Chambers
Road, Suite 301, Columbus, Ohio 43212, United States
| | - Kenneth J. Breslauer
- Department
of Chemistry and
Chemical Biology, Rutgers, The State University of New
Jersey, 610 Taylor Road, Piscataway, New Jersey 08854,
United States
- The Cancer Institute
of New Jersey, New Brunswick, New Jersey 08901, United
States
| |
Collapse
|
37
|
Liu G, Leffak M. Instability of (CTG)n•(CAG)n trinucleotide repeats and DNA synthesis. Cell Biosci 2012; 2:7. [PMID: 22369689 PMCID: PMC3310812 DOI: 10.1186/2045-3701-2-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 02/27/2012] [Indexed: 12/21/2022] Open
Abstract
Expansion of (CTG)n•(CAG)n trinucleotide repeat (TNR) microsatellite sequences is the cause of more than a dozen human neurodegenerative diseases. (CTG)n and (CAG)n repeats form imperfectly base paired hairpins that tend to expand in vivo in a length-dependent manner. Yeast, mouse and human models confirm that (CTG)n•(CAG)n instability increases with repeat number, and implicate both DNA replication and DNA damage response mechanisms in (CTG)n•(CAG)n TNR expansion and contraction. Mutation and knockdown models that abrogate the expression of individual genes might also mask more subtle, cumulative effects of multiple additional pathways on (CTG)n•(CAG)n instability in whole animals. The identification of second site genetic modifiers may help to explain the variability of (CTG)n•(CAG)n TNR instability patterns between tissues and individuals, and offer opportunities for prognosis and treatment.
Collapse
Affiliation(s)
- Guoqi Liu
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA.
| | | |
Collapse
|
38
|
Liu Y, Wilson SH. DNA base excision repair: a mechanism of trinucleotide repeat expansion. Trends Biochem Sci 2012; 37:162-72. [PMID: 22285516 DOI: 10.1016/j.tibs.2011.12.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 12/15/2011] [Accepted: 12/23/2011] [Indexed: 12/16/2022]
Abstract
The expansion of trinucleotide repeat (TNR) sequences in human DNA is considered to be a key factor in the pathogenesis of more than 40 neurodegenerative diseases. TNR expansion occurs during DNA replication and also, as suggested by recent studies, during the repair of DNA lesions produced by oxidative stress. In particular, the oxidized guanine base 8-oxoguanine within sequences containing CAG repeats may induce formation of pro-expansion intermediates through strand slippage during DNA base excision repair (BER). In this article, we describe how oxidized DNA lesions are repaired by BER and discuss the importance of the coordinated activities of the key repair enzymes, such as DNA polymerase β, flap endonuclease 1 (FEN1) and DNA ligase, in preventing strand slippage and TNR expansion.
Collapse
Affiliation(s)
- Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | | |
Collapse
|
39
|
|
40
|
Abstract
Fragile X syndrome (FXS) is characterized by moderate to severe intellectual disability, which is accompanied by macroorchidism and distinct facial morphology. FXS is caused by the expansion of the CGG trinucleotide repeat in the 5' untranslated region of the fragile X mental retardation 1 (FMR1) gene. The syndrome has been studied in ethnically diverse populations around the world and has been extensively characterized in several populations. Similar to other trinucleotide expansion disorders, the gene-specific instability of FMR1 is not accompanied by genomic instability. Currently we do not have a comprehensive understanding of the molecular underpinnings of gene-specific instability associated with tandem repeats. Molecular evidence from in vitro experiments and animal models supports several pathways for gene-specific trinucleotide repeat expansion. However, whether the mechanisms reported from other systems contribute to trinucleotide repeat expansion in humans is not clear. To understand how repeat instability in humans could occur, the CGG repeat expansion is explored through molecular analysis and population studies which characterized CGG repeat alleles of FMR1. Finally, the review discusses the relevance of these studies in understanding the mechanism of trinucleotide repeat expansion in FXS.
Collapse
Affiliation(s)
- Emmanuel Peprah
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institute of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
41
|
Jeppesen DK, Bohr VA, Stevnsner T. DNA repair deficiency in neurodegeneration. Prog Neurobiol 2011; 94:166-200. [PMID: 21550379 DOI: 10.1016/j.pneurobio.2011.04.013] [Citation(s) in RCA: 243] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 04/18/2011] [Accepted: 04/22/2011] [Indexed: 01/17/2023]
Abstract
Deficiency in repair of nuclear and mitochondrial DNA damage has been linked to several neurodegenerative disorders. Many recent experimental results indicate that the post-mitotic neurons are particularly prone to accumulation of unrepaired DNA lesions potentially leading to progressive neurodegeneration. Nucleotide excision repair is the cellular pathway responsible for removing helix-distorting DNA damage and deficiency in such repair is found in a number of diseases with neurodegenerative phenotypes, including Xeroderma Pigmentosum and Cockayne syndrome. The main pathway for repairing oxidative base lesions is base excision repair, and such repair is crucial for neurons given their high rates of oxygen metabolism. Mismatch repair corrects base mispairs generated during replication and evidence indicates that oxidative DNA damage can cause this pathway to expand trinucleotide repeats, thereby causing Huntington's disease. Single-strand breaks are common DNA lesions and are associated with the neurodegenerative diseases, ataxia-oculomotor apraxia-1 and spinocerebellar ataxia with axonal neuropathy-1. DNA double-strand breaks are toxic lesions and two main pathways exist for their repair: homologous recombination and non-homologous end-joining. Ataxia telangiectasia and related disorders with defects in these pathways illustrate that such defects can lead to early childhood neurodegeneration. Aging is a risk factor for neurodegeneration and accumulation of oxidative mitochondrial DNA damage may be linked with the age-associated neurodegenerative disorders Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. Mutation in the WRN protein leads to the premature aging disease Werner syndrome, a disorder that features neurodegeneration. In this article we review the evidence linking deficiencies in the DNA repair pathways with neurodegeneration.
Collapse
Affiliation(s)
- Dennis Kjølhede Jeppesen
- Danish Centre for Molecular Gerontology and Danish Aging Research Center, University of Aarhus, Department of Molecular Biology, Aarhus, Denmark
| | | | | |
Collapse
|
42
|
Continuous and periodic expansion of CAG repeats in Huntington's disease R6/1 mice. PLoS Genet 2010; 6:e1001242. [PMID: 21170307 PMCID: PMC3000365 DOI: 10.1371/journal.pgen.1001242] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Accepted: 11/05/2010] [Indexed: 11/19/2022] Open
Abstract
Huntington's disease (HD) is one of several neurodegenerative disorders caused by expansion of CAG repeats in a coding gene. Somatic CAG expansion rates in HD vary between organs, and the greatest instability is observed in the brain, correlating with neuropathology. The fundamental mechanisms of somatic CAG repeat instability are poorly understood, but locally formed secondary DNA structures generated during replication and/or repair are believed to underlie triplet repeat expansion. Recent studies in HD mice have demonstrated that mismatch repair (MMR) and base excision repair (BER) proteins are expansion inducing components in brain tissues. This study was designed to simultaneously investigate the rates and modes of expansion in different tissues of HD R6/1 mice in order to further understand the expansion mechanisms in vivo. We demonstrate continuous small expansions in most somatic tissues (exemplified by tail), which bear the signature of many short, probably single-repeat expansions and contractions occurring over time. In contrast, striatum and cortex display a dramatic—and apparently irreversible—periodic expansion. Expansion profiles displaying this kind of periodicity in the expansion process have not previously been reported. These in vivo findings imply that mechanistically distinct expansion processes occur in different tissues. Huntington's disease (HD) is a genetically determined neurodegenerative disorder identified by the presence of a mutation for a long series of CAG repeats (>36 repeats) in the Huntingtin (HTT) gene. Longer repeat sequences cause disease onset at a younger age. The mutation encodes an expanded glutamine tract within the huntingtin protein. This enlarged polyglutamine fragment in the protein leads to the formation of the huntingtin aggregates that are observed in HD brains. The stretch of CAG repeats expands with age in affected brain areas, increasing the length of the polyglutamine tract, and is believed to amplify the effect of the disease. Several HD mouse models display phenotypes relevant to the human disease. We have investigated the rate and modes of expansion in striatum, cortex, and tail in transgenic R6/1 mice. Tail was included as a stable tissue, however we observed a small continuous expansion of CAG repeats in tail tissues. In brain tissues, we identified a periodic expansion process consisting of predominantly seven repeat steps. Our findings point towards a very controlled molecular mechanism as the cause of expansion in the most severely affected tissues, which may provide useful targets that can be used to inhibit disease development.
Collapse
|
43
|
Abstract
Trinucleotide expansion underlies several human diseases. Expansion occurs during multiple stages of human development in different cell types, and is sensitive to the gender of the parent who transmits the repeats. Repair and replication models for expansions have been described, but we do not know whether the pathway involved is the same under all conditions and for all repeat tract lengths, which differ among diseases. Currently, researchers rely on bacteria, yeast and mice to study expansion, but these models differ substantially from humans. We need now to connect the dots among human genetics, pathway biochemistry and the appropriate model systems to understand the mechanism of expansion as it occurs in human disease.
Collapse
|
44
|
Zheng L, Jia J, Finger LD, Guo Z, Zer C, Shen B. Functional regulation of FEN1 nuclease and its link to cancer. Nucleic Acids Res 2010; 39:781-94. [PMID: 20929870 PMCID: PMC3035468 DOI: 10.1093/nar/gkq884] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Flap endonuclease-1 (FEN1) is a member of the Rad2 structure-specific nuclease family. FEN1 possesses FEN, 5′-exonuclease and gap-endonuclease activities. The multiple nuclease activities of FEN1 allow it to participate in numerous DNA metabolic pathways, including Okazaki fragment maturation, stalled replication fork rescue, telomere maintenance, long-patch base excision repair and apoptotic DNA fragmentation. Here, we summarize the distinct roles of the different nuclease activities of FEN1 in these pathways. Recent biochemical and genetic studies indicate that FEN1 interacts with more than 30 proteins and undergoes post-translational modifications. We discuss how FEN1 is regulated via these mechanisms. Moreover, FEN1 interacts with five distinct groups of DNA metabolic proteins, allowing the nuclease to be recruited to a specific DNA metabolic complex, such as the DNA replication machinery for RNA primer removal or the DNA degradosome for apoptotic DNA fragmentation. Some FEN1 interaction partners also stimulate FEN1 nuclease activities to further ensure efficient action in processing of different DNA structures. Post-translational modifications, on the other hand, may be critical to regulate protein–protein interactions and cellular localizations of FEN1. Lastly, we also review the biological significance of FEN1 as a tumor suppressor, with an emphasis on studies of human mutations and mouse models.
Collapse
Affiliation(s)
- Li Zheng
- Institute of Cell Biology and Genetics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | | | | | | | | | | |
Collapse
|
45
|
Kang YH, Lee CH, Seo YS. Dna2 on the road to Okazaki fragment processing and genome stability in eukaryotes. Crit Rev Biochem Mol Biol 2010; 45:71-96. [PMID: 20131965 DOI: 10.3109/10409230903578593] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA replication is a primary mechanism for maintaining genome integrity, but it serves this purpose best by cooperating with other proteins involved in DNA repair and recombination. Unlike leading strand synthesis, lagging strand synthesis has a greater risk of faulty replication for several reasons: First, a significant part of DNA is synthesized by polymerase alpha, which lacks a proofreading function. Second, a great number of Okazaki fragments are synthesized, processed and ligated per cell division. Third, the principal mechanism of Okazaki fragment processing is via generation of flaps, which have the potential to form a variety of structures in their sequence context. Finally, many proteins for the lagging strand interact with factors involved in repair and recombination. Thus, lagging strand DNA synthesis could be the best example of a converging place of both replication and repair proteins. To achieve the risky task with extraordinary fidelity, Okazaki fragment processing may depend on multiple layers of redundant, but connected pathways. An essential Dna2 endonuclease/helicase plays a pivotal role in processing common structural intermediates that occur during diverse DNA metabolisms (e.g. lagging strand synthesis and telomere maintenance). Many roles of Dna2 suggest that the preemptive removal of long or structured flaps ultimately contributes to genome maintenance in eukaryotes. In this review, we describe the function of Dna2 in Okazaki fragment processing, and discuss its role in the maintenance of genome integrity with an emphasis on its functional interactions with other factors required for genome maintenance.
Collapse
Affiliation(s)
- Young-Hoon Kang
- Center for DNA Replication and Genome Instability, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | | | | |
Collapse
|
46
|
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: 312] [Impact Index Per Article: 22.3] [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
|
47
|
Goula AV, Berquist BR, Wilson DM, Wheeler VC, Trottier Y, Merienne K. Stoichiometry of base excision repair proteins correlates with increased somatic CAG instability in striatum over cerebellum in Huntington's disease transgenic mice. PLoS Genet 2009; 5:e1000749. [PMID: 19997493 PMCID: PMC2778875 DOI: 10.1371/journal.pgen.1000749] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 11/02/2009] [Indexed: 11/18/2022] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by expansion of an unstable CAG repeat in the coding sequence of the Huntingtin (HTT) gene. Instability affects both germline and somatic cells. Somatic instability increases with age and is tissue-specific. In particular, the CAG repeat sequence in the striatum, the brain region that preferentially degenerates in HD, is highly unstable, whereas it is rather stable in the disease-spared cerebellum. The mechanisms underlying the age-dependence and tissue-specificity of somatic CAG instability remain obscure. Recent studies have suggested that DNA oxidation and OGG1, a glycosylase involved in the repair of 8-oxoguanine lesions, contribute to this process. We show that in HD mice oxidative DNA damage abnormally accumulates at CAG repeats in a length-dependent, but age- and tissue-independent manner, indicating that oxidative DNA damage alone is not sufficient to trigger somatic instability. Protein levels and activities of major base excision repair (BER) enzymes were compared between striatum and cerebellum of HD mice. Strikingly, 5′-flap endonuclease activity was much lower in the striatum than in the cerebellum of HD mice. Accordingly, Flap Endonuclease-1 (FEN1), the main enzyme responsible for 5′-flap endonuclease activity, and the BER cofactor HMGB1, both of which participate in long-patch BER (LP–BER), were also significantly lower in the striatum compared to the cerebellum. Finally, chromatin immunoprecipitation experiments revealed that POLβ was specifically enriched at CAG expansions in the striatum, but not in the cerebellum of HD mice. These in vivo data fit a model in which POLβ strand displacement activity during LP–BER promotes the formation of stable 5′-flap structures at CAG repeats representing pre-expanded intermediate structures, which are not efficiently removed when FEN1 activity is constitutively low. We propose that the stoichiometry of BER enzymes is one critical factor underlying the tissue selectivity of somatic CAG expansion. Huntington's disease (HD) is a neurodegenerative disorder that belongs to a family of genetic diseases caused by abnormal expansion of CAG/CTG repetitive sequences. The instability of trinucleotide repeat expansions in germline and somatic cells has deleterious clinical consequences in HD. For instance, transmission of longer repeats to offspring results in an earlier onset of disease, where extensive somatic expansion in the striatum, the brain region primarily affected in HD, is proposed to accelerate disease pathology. Thus, understanding the mechanisms of trinucleotide repeat instability is a major interest. We have examined the role of oxidative DNA damage and base excision repair (BER) in somatic instability, which is tissue-selective and age-dependent. We show that oxidative DNA lesions abnormally accumulate at CAG expansions in a length-dependent, yet age- and tissue-independent manners, likely due to the secondary structures formed by CAG repeats that limit access of enzymes initiating BER. In addition, our data indicate that repair by BER enzymes of some of the accessible lesions results in somatic expansion when the ratio of FEN1 to POLβ is low, as found to occur in the striatum. Our results support BER enzyme stoichiometry as a contributor to the tissue selectivity of somatic CAG expansion in HD.
Collapse
Affiliation(s)
- Agathi-Vassiliki Goula
- Department of Neurobiology and Genetics, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR 7104-CNRS/INSERM/UdS, Illkirch, France
| | - Brian R. Berquist
- Laboratory of Molecular Gerontology, National Institute on Aging (NIA)/National Institutes of Health (NIH), Baltimore, Maryland, United States of America
| | - David M. Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging (NIA)/National Institutes of Health (NIH), Baltimore, Maryland, United States of America
| | - Vanessa C. Wheeler
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachussetts, United States of America
| | - Yvon Trottier
- Department of Neurobiology and Genetics, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR 7104-CNRS/INSERM/UdS, Illkirch, France
- * E-mail: (KM); (YT)
| | - Karine Merienne
- Department of Neurobiology and Genetics, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR 7104-CNRS/INSERM/UdS, Illkirch, France
- * E-mail: (KM); (YT)
| |
Collapse
|
48
|
Double-strand break repair pathways protect against CAG/CTG repeat expansions, contractions and repeat-mediated chromosomal fragility in Saccharomyces cerevisiae. Genetics 2009; 184:65-77. [PMID: 19901069 DOI: 10.1534/genetics.109.111039] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trinucleotide repeats can form secondary structures, whose inappropriate repair or replication can lead to repeat expansions. There are multiple loci within the human genome where expansion of trinucleotide repeats leads to disease. Although it is known that expanded repeats accumulate double-strand breaks (DSBs), it is not known which DSB repair pathways act on such lesions and whether inaccurate DSB repair pathways contribute to repeat expansions. Using Saccharomyces cerevisiae, we found that CAG/CTG tracts of 70 or 155 repeats exhibited significantly elevated levels of breakage and expansions in strains lacking MRE11, implicating the Mre11/Rad50/Xrs2 complex in repairing lesions at structure-forming repeats. About two-thirds of the expansions that occurred in the absence of MRE11 were dependent on RAD52, implicating aberrant homologous recombination as a mechanism for generating expansions. Expansions were also elevated in a sae2 deletion background and these were not dependent on RAD52, supporting an additional role for Mre11 in facilitating Sae2-dependent hairpin processing at the repeat. Mre11 nuclease activity and Tel1-dependent checkpoint functions were largely dispensable for repeat maintenance. In addition, we found that intact homologous recombination and nonhomologous end-joining pathways of DSB repair are needed to prevent repeat fragility and that both pathways also protect against repeat instability. We conclude that failure of principal DSB repair pathways to repair breaks that occur within the repeats can result in the accumulation of atypical intermediates, whose aberrant resolution will then lead to CAG expansions, contractions, and repeat-mediated chromosomal fragility.
Collapse
|
49
|
Liu Y, Prasad R, Beard WA, Hou EW, Horton JK, McMurray CT, Wilson SH. Coordination between polymerase beta and FEN1 can modulate CAG repeat expansion. J Biol Chem 2009; 284:28352-28366. [PMID: 19674974 DOI: 10.1074/jbc.m109.050286] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The oxidized DNA base 8-oxoguanine (8-oxoG) is implicated in neuronal CAG repeat expansion associated with Huntington disease, yet it is unclear how such a DNA base lesion and its repair might cause the expansion. Here, we discovered size-limited expansion of CAG repeats during repair of 8-oxoG in a wild-type mouse cell extract. This expansion was deficient in extracts from cells lacking pol beta and HMGB1. We demonstrate that expansion is mediated through pol beta multinucleotide gap-filling DNA synthesis during long-patch base excision repair. Unexpectedly, FEN1 promotes expansion by facilitating ligation of hairpins formed by strand slippage. This alternate role of FEN1 and the polymerase beta (pol beta) multinucleotide gap-filling synthesis is the result of uncoupling of the usual coordination between pol beta and FEN1. HMGB1 probably promotes expansion by stimulating APE1 and FEN1 in forming single strand breaks and ligatable nicks, respectively. This is the first report illustrating that disruption of pol beta and FEN1 coordination during long-patch BER results in CAG repeat expansion.
Collapse
Affiliation(s)
- Yuan Liu
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Rajendra Prasad
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - William A Beard
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Esther W Hou
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Julie K Horton
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Cynthia T McMurray
- Department of Pharmacology and Experimental Therapeutics, Mayo Clinic and Foundation, Rochester, Minnesota 55905
| | - Samuel H Wilson
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709.
| |
Collapse
|
50
|
Incision-dependent and error-free repair of (CAG)(n)/(CTG)(n) hairpins in human cell extracts. Nat Struct Mol Biol 2009; 16:869-75. [PMID: 19597480 PMCID: PMC5039229 DOI: 10.1038/nsmb.1638] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Accepted: 05/28/2009] [Indexed: 12/27/2022]
Abstract
Expansion of CAG/CTG trinucleotide repeats is associated with certain familial neurological disorders, including Huntington's disease. Increasing evidence suggests that formation of a stable DNA hairpin within CAG/CTG repeats during DNA metabolism contributes to their expansion. However, the molecular mechanism(s) by which cells remove CAG/CTG hairpins remain unknown. Here, we demonstrate that human cell extracts can catalyze error-free repair of CAG/CTG hairpins in a nick-directed manner. The repair system specifically targets CAG/CTG tracts for incisions in the nicked DNA strand, followed by DNA resynthesis using the continuous strand as a template, thereby ensuring CAG/CTG stability. PCNA is required for the incision step of the hairpin removal, which utilizes distinct endonuclease activities for individual CAG/CTG hairpins depending on their strand locations and/or secondary structures. The implication of these data for understanding the etiology of neurological diseases and trinucleotide repeat instability is discussed.
Collapse
|