201
|
Vasanth S, Eghrari AO, Gapsis BC, Wang J, Haller NF, Stark WJ, Katsanis N, Riazuddin SA, Gottsch JD. Expansion of CTG18.1 Trinucleotide Repeat in TCF4 Is a Potent Driver of Fuchs' Corneal Dystrophy. Invest Ophthalmol Vis Sci 2015. [PMID: 26200491 DOI: 10.1167/iovs.14-16122] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To analyze the expansion of CTG18.1 allele associated with Fuchs' corneal dystrophy (FCD) in our large cohort of late-onset FCD cases. METHODS CTG repeats within the CTG18.1 allele were estimated by short tandem repeat (STR) and triplet primed PCR (TP-PCR) assays in our large cohort of 574 late-onset FCD cases and 354 controls and large multigeneration familial cases. The age versus severity relationships were analyzed in FCD genotypes, namely, nonexpanded (N/N), monoallelic expansion (N/X), and biallelic expansion (X/X) with N ≤ 40 CTG monomers. The threshold for causality conferred by an expansion of CTG18.1 was identified by excluding the population of FCD cases who harbored an allele length equivalent to the maximum CTG monomers observed in the controls. RESULTS The expanded CTG18.1 for (CTG)n>40 showed a strong association (P = 1.56 × 10(-82)) with FCD. Importantly, we delineated the threshold of expansion to 103 CTG repeats above which the allele confers causality in 17.8% of FCD cases. Regression analyses demonstrated a significant correlation between disease severity and age in individuals who harbor either a monoallelic expansion or a biallelic expansion at (CTG) n > 40. These analyses helped predict FCD in two previously unaffected individuals based on their CTG18.1 expansion genotype. CONCLUSIONS A monoallelic expansion of CTG18.1 contributes to increased disease severity and is causal at (CTG)n>103, whereas a biallelic expansion is sufficient to be causal for FCD at (CTG)n>40. This study highlights the largest contributory causal allele for FCD.
Collapse
Affiliation(s)
- Shivakumar Vasanth
- The Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Allen O Eghrari
- The Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Briana C Gapsis
- The Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Jiangxia Wang
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States
| | - Nicolas F Haller
- The Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Walter J Stark
- The Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, United States
| | - S Amer Riazuddin
- The Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - John D Gottsch
- The Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| |
Collapse
|
202
|
Cilli P, Minoprio A, Bossa C, Bignami M, Mazzei F. Formation and Repair of Mismatches Containing Ribonucleotides and Oxidized Bases at Repeated DNA Sequences. J Biol Chem 2015; 290:26259-69. [PMID: 26338705 PMCID: PMC4646274 DOI: 10.1074/jbc.m115.679209] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/02/2015] [Indexed: 11/06/2022] Open
Abstract
The cellular pool of ribonucleotide triphosphates (rNTPs) is higher than that of deoxyribonucleotide triphosphates. To ensure genome stability, DNA polymerases must discriminate against rNTPs and incorporated ribonucleotides must be removed by ribonucleotide excision repair (RER). We investigated DNA polymerase β (POL β) capacity to incorporate ribonucleotides into trinucleotide repeated DNA sequences and the efficiency of base excision repair (BER) and RER enzymes (OGG1, MUTYH, and RNase H2) when presented with an incorrect sugar and an oxidized base. POL β incorporated rAMP and rCMP opposite 7,8-dihydro-8-oxoguanine (8-oxodG) and extended both mispairs. In addition, POL β was able to insert and elongate an oxidized rGMP when paired with dA. We show that RNase H2 always preserves the capacity to remove a single ribonucleotide when paired to an oxidized base or to incise an oxidized ribonucleotide in a DNA duplex. In contrast, BER activity is affected by the presence of a ribonucleotide opposite an 8-oxodG. In particular, MUTYH activity on 8-oxodG:rA mispairs is fully inhibited, although its binding capacity is retained. This results in the reduction of RNase H2 incision capability of this substrate. Thus complex mispairs formed by an oxidized base and a ribonucleotide can compromise BER and RER in repeated sequences.
Collapse
Affiliation(s)
- Piera Cilli
- From the Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma and the Department of Science, University Roma Tre, 00154 Roma, Italy
| | - Anna Minoprio
- From the Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma and
| | - Cecilia Bossa
- From the Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma and
| | - Margherita Bignami
- From the Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma and
| | - Filomena Mazzei
- From the Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma and
| |
Collapse
|
203
|
Gerhardt J. Epigenetic modifications in human fragile X pluripotent stem cells; Implications in fragile X syndrome modeling. Brain Res 2015; 1656:55-62. [PMID: 26475977 DOI: 10.1016/j.brainres.2015.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 08/18/2015] [Accepted: 10/02/2015] [Indexed: 12/18/2022]
Abstract
Patients with fragile X syndrome (FXS) exhibit moderate to severe intellectual disabilities. In addition, one-third of FXS patients show characteristics of autism spectrum disorder. FXS is caused by a trinucleotide repeat expansion, which leads to silencing of the fragile X mental retardation (FMR1) gene. The absence of the FMR1 gene product, FMRP, is the reason for the disease symptoms. It has been suggested that repeat instability and transcription of the FMR1 gene occur during early embryonic development, while after cell differentiation repeats become stable and the FMR1 gene is silent. Epigenetic marks, such as DNA methylation, are associated with gene silencing and repeat stability at the FMR1 locus. However, the mechanisms leading to gene silencing and repeat expansion are still ambiguous, because studies at the human genomic locus were limited until now. The FXS pluripotent stem cells, recently derived from FXS adult cells and FXS blastocysts, are new useful tools to examine these mechanisms at the human endogenous FMR1 locus. This review summarizes the epigenetic features and experimental studies of FXS human embryonic and FXS induced pluripotent stem cells, generated so far. This article is part of a Special Issue entitled SI: Exploiting human neurons.
Collapse
Affiliation(s)
- Jeannine Gerhardt
- Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx 10461, USA.
| |
Collapse
|
204
|
Suh E, Lee EB, Neal D, Wood EM, Toledo JB, Rennert L, Irwin DJ, McMillan CT, Krock B, Elman LB, McCluskey LF, Grossman M, Xie SX, Trojanowski JQ, Van Deerlin VM. Semi-automated quantification of C9orf72 expansion size reveals inverse correlation between hexanucleotide repeat number and disease duration in frontotemporal degeneration. Acta Neuropathol 2015; 130:363-72. [PMID: 26022924 DOI: 10.1007/s00401-015-1445-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 12/11/2022]
Abstract
We investigated whether chromosome 9 open reading frame 72 hexanucleotide repeat expansion (C9orf72 expansion) size in peripheral DNA was associated with clinical differences in frontotemporal degeneration (FTD) and amyotrophic lateral sclerosis (ALS) linked to C9orf72 repeat expansion mutations. A novel quantification workflow was developed to measure C9orf72 expansion size by Southern blot densitometry in a cross-sectional cohort of C9orf72 expansion carriers with FTD (n = 39), ALS (n = 33), both (n = 35), or who are unaffected (n = 21). Multivariate linear regressions were performed to assess whether C9orf72 expansion size from peripheral DNA was associated with clinical phenotype, age of disease onset, disease duration and age at death. Mode values of C9orf72 expansion size were significantly shorter in FTD compared to ALS (p = 0.0001) but were not associated with age at onset in either FTD or ALS. A multivariate regression model correcting for patient's age at DNA collection and disease phenotype revealed that C9orf72 expansion size is significantly associated with shorter disease duration (p = 0.0107) for individuals with FTD, but not with ALS. Despite considerable somatic instability of the C9orf72 expansion, semi-automated expansion size measurements demonstrated an inverse relationship between C9orf72 expansion size and disease duration in patients with FTD. Our finding suggests that C9orf72 repeat size may be a molecular disease modifier in FTD linked to hexanucleotide repeat expansion.
Collapse
Affiliation(s)
- EunRan Suh
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA, 19104-4283, USA,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
205
|
Budworth H, Harris FR, Williams P, Lee DY, Holt A, Pahnke J, Szczesny B, Acevedo-Torres K, Ayala-Peña S, McMurray CT. Suppression of Somatic Expansion Delays the Onset of Pathophysiology in a Mouse Model of Huntington's Disease. PLoS Genet 2015; 11:e1005267. [PMID: 26247199 PMCID: PMC4527696 DOI: 10.1371/journal.pgen.1005267] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 05/07/2015] [Indexed: 11/18/2022] Open
Abstract
Huntington’s Disease (HD) is caused by inheritance of a single disease-length allele harboring an expanded CAG repeat, which continues to expand in somatic tissues with age. The inherited disease allele expresses a toxic protein, and whether further somatic expansion adds to toxicity is unknown. We have created an HD mouse model that resolves the effects of the inherited and somatic expansions. We show here that suppressing somatic expansion substantially delays the onset of disease in littermates that inherit the same disease-length allele. Furthermore, a pharmacological inhibitor, XJB-5-131, inhibits the lengthening of the repeat tracks, and correlates with rescue of motor decline in these animals. The results provide evidence that pharmacological approaches to offset disease progression are possible. Huntington’s Disease (HD) is caused by inheritance of a single disease-length allele harboring an expanded CAG repeat, which continues to expand in somatic tissues with age. There is no correction for the inherited mutation, but if somatic expansion contributes to disease, then a therapeutic approach is possible. The inherited disease allele expresses a toxic protein, and whether further somatic expansion adds to toxicity is unknown. Here we describe a mouse model of Huntington’s disease that allows us to separate out the effects of the inherited gene from the expansion that occurs during life. We find that blocking the continued expansion of the gene causes a delay in onset of symptoms. This result opens the doors to future therapeutics designed to shorten the repeat.
Collapse
Affiliation(s)
- Helen Budworth
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Faye R. Harris
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Paul Williams
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Do Yup Lee
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul, Korea
| | - Amy Holt
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jens Pahnke
- Department of Neuropathology, University of Oslo, Oslo, Norway
- LIED, University of Lübeck, Lübeck, Germany
| | - Bartosz Szczesny
- Department of Anesthesiology, The University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Karina Acevedo-Torres
- Puerto Rico Center for Inherited Diseases, University of Puerto Rico, San Juan, Puerto Rico
- Department of Pharmacology and Toxicology, University of Puerto Rico, San Juan, Puerto Rico
| | - Sylvette Ayala-Peña
- Puerto Rico Center for Inherited Diseases, University of Puerto Rico, San Juan, Puerto Rico
- Department of Pharmacology and Toxicology, University of Puerto Rico, San Juan, Puerto Rico
| | - Cynthia T. McMurray
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
| |
Collapse
|
206
|
Abstract
Structure-prone DNA repeats are common components of genomic DNA in all kingdoms of life. In humans, these repeats are linked to genomic instabilities that result in various hereditary disorders, including many cancers. It has long been known that DNA repeats are not only highly polymorphic in length but can also cause chromosomal fragility and stimulate gross chromosomal rearrangements, i.e., deletions, duplications, inversions, translocations and more complex shuffles. More recently, it has become clear that inherently unstable DNA repeats dramatically elevate mutation rates in surrounding DNA segments and that these mutations can occur up to ten kilobases away from the repetitive tract, a phenomenon we call repeat-induced mutagenesis (RIM). This review describes experimental data that led to the discovery and characterization of RIM and discusses the molecular mechanisms that could account for this phenomenon.
Collapse
Affiliation(s)
- Kartik A Shah
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
| |
Collapse
|
207
|
Koda H, Brazier JA, Onishi I, Sasaki S. Strong positive cooperativity in binding to the A3T3 repeat by Hoechst 33258 derivatives attaching the quinoline units at the end of a branched linker. Bioorg Med Chem 2015; 23:4583-4590. [DOI: 10.1016/j.bmc.2015.05.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/29/2015] [Accepted: 05/30/2015] [Indexed: 12/15/2022]
|
208
|
Williams GM, Surtees JA. MSH3 Promotes Dynamic Behavior of Trinucleotide Repeat Tracts In Vivo. Genetics 2015; 200:737-54. [PMID: 25969461 PMCID: PMC4512540 DOI: 10.1534/genetics.115.177303] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/04/2015] [Indexed: 11/18/2022] Open
Abstract
Trinucleotide repeat (TNR) expansions are the underlying cause of more than 40 neurodegenerative and neuromuscular diseases, including myotonic dystrophy and Huntington's disease, yet the pathway to expansion remains poorly understood. An important step in expansion is the shift from a stable TNR sequence to an unstable, expanding tract, which is thought to occur once a TNR attains a threshold length. Modeling of human data has indicated that TNR tracts are increasingly likely to expand as they increase in size and to do so in increments that are smaller than the repeat itself, but this has not been tested experimentally. Genetic work has implicated the mismatch repair factor MSH3 in promoting expansions. Using Saccharomyces cerevisiae as a model for CAG and CTG tract dynamics, we examined individual threshold-length TNR tracts in vivo over time in MSH3 and msh3Δ backgrounds. We demonstrate, for the first time, that these TNR tracts are highly dynamic. Furthermore, we establish that once such a tract has expanded by even a few repeat units, it is significantly more likely to expand again. Finally, we show that threshold- length TNR sequences readily accumulate net incremental expansions over time through a series of small expansion and contraction events. Importantly, the tracts were substantially stabilized in the msh3Δ background, with a bias toward contractions, indicating that Msh2-Msh3 plays an important role in shifting the expansion-contraction equilibrium toward expansion in the early stages of TNR tract expansion.
Collapse
Affiliation(s)
- Gregory M Williams
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, New York 14214
| | - Jennifer A Surtees
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, New York 14214 Genetics, Genomics and Bioinformatics Program, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, New York 14214
| |
Collapse
|
209
|
Beaver JM, Lai Y, Xu M, Casin AH, Laverde EE, Liu Y. AP endonuclease 1 prevents trinucleotide repeat expansion via a novel mechanism during base excision repair. Nucleic Acids Res 2015; 43:5948-60. [PMID: 25990721 PMCID: PMC4499148 DOI: 10.1093/nar/gkv530] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/10/2015] [Indexed: 01/28/2023] Open
Abstract
Base excision repair (BER) of an oxidized base within a trinucleotide repeat (TNR) tract can lead to TNR expansions that are associated with over 40 human neurodegenerative diseases. This occurs as a result of DNA secondary structures such as hairpins formed during repair. We have previously shown that BER in a TNR hairpin loop can lead to removal of the hairpin, attenuating or preventing TNR expansions. Here, we further provide the first evidence that AP endonuclease 1 (APE1) prevented TNR expansions via its 3′-5′ exonuclease activity and stimulatory effect on DNA ligation during BER in a hairpin loop. Coordinating with flap endonuclease 1, the APE1 3′-5′ exonuclease activity cleaves the annealed upstream 3′-flap of a double-flap intermediate resulting from 5′-incision of an abasic site in the hairpin loop. Furthermore, APE1 stimulated DNA ligase I to resolve a long double-flap intermediate, thereby promoting hairpin removal and preventing TNR expansions.
Collapse
Affiliation(s)
- Jill M Beaver
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Meng Xu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Astrid H Casin
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Eduardo E Laverde
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA Biomolecular Sciences Institute, School of Integrated Sciences and Humanities, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
210
|
Su XA, Dion V, Gasser SM, Freudenreich CH. Regulation of recombination at yeast nuclear pores controls repair and triplet repeat stability. Genes Dev 2015; 29:1006-17. [PMID: 25940904 PMCID: PMC4441049 DOI: 10.1101/gad.256404.114] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/10/2015] [Indexed: 12/16/2022]
Abstract
Secondary structure-forming DNA sequences such as CAG repeats interfere with replication and repair, provoking fork stalling, chromosome fragility, and recombination. In budding yeast, Su et al. find that expanded CAG repeats are more likely than unexpanded repeats to localize to the nuclear periphery and that the relocation of damage to nuclear pores plays an important role in a naturally occurring repair process. Secondary structure-forming DNA sequences such as CAG repeats interfere with replication and repair, provoking fork stalling, chromosome fragility, and recombination. In budding yeast, we found that expanded CAG repeats are more likely than unexpanded repeats to localize to the nuclear periphery. This positioning is transient, occurs in late S phase, requires replication, and is associated with decreased subnuclear mobility of the locus. In contrast to persistent double-stranded breaks, expanded CAG repeats at the nuclear envelope associate with pores but not with the inner nuclear membrane protein Mps3. Relocation requires Nup84 and the Slx5/8 SUMO-dependent ubiquitin ligase but not Rad51, Mec1, or Tel1. Importantly, the presence of the Nup84 pore subcomplex and Slx5/8 suppresses CAG repeat fragility and instability. Repeat instability in nup84, slx5, or slx8 mutant cells arises through aberrant homologous recombination and is distinct from instability arising from the loss of ligase 4-dependent end-joining. Genetic and physical analysis of Rad52 sumoylation and binding at the CAG tract suggests that Slx5/8 targets sumoylated Rad52 for degradation at the pore to facilitate recovery from acute replication stress by promoting replication fork restart. We thereby confirmed that the relocation of damage to nuclear pores plays an important role in a naturally occurring repair process.
Collapse
Affiliation(s)
- Xiaofeng A Su
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Vincent Dion
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA; Program in Genetics, Tufts University, Medford, Massachusetts 02155, USA;
| |
Collapse
|
211
|
Abstract
Chemical modification and spontaneous loss of nucleotide bases from DNA are estimated to occur at the rate of thousands per human cell per day. DNA base excision repair (BER) is a critical mechanism for repairing such lesions in nuclear and mitochondrial DNA. Defective expression or function of proteins required for BER or proteins that regulate BER have been consistently associated with neurological dysfunction and disease in humans. Recent studies suggest that DNA lesions in the nuclear and mitochondrial compartments and the cellular response to those lesions have a profound effect on cellular energy homeostasis, mitochondrial function and cellular bioenergetics, with especially strong influence on neurological function. Further studies in this area could lead to novel approaches to prevent and treat human neurodegenerative disease.
Collapse
|
212
|
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
|
213
|
Padeken J, Zeller P, Gasser SM. Repeat DNA in genome organization and stability. Curr Opin Genet Dev 2015; 31:12-9. [PMID: 25917896 DOI: 10.1016/j.gde.2015.03.009] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 01/03/2023]
Abstract
Eukaryotic genomes contain millions of copies of repetitive elements (RE). Although the euchromatic parts of most genomes are clearly annotated, the repetitive/heterochromatic parts are poorly defined. It is estimated that between 50 and 70% of the human genome is composed of REs. Despite this, we know surprisingly little about the physiological relevance, molecular regulation and the composition of these regions. This primarily reflects the difficulty that REs pose for PCR-based assays, and their poor map-ability in next generation sequencing experiments. Here we first summarize the nature and classification of REs and then examine how this has been used in the recent years to broaden our understanding of mechanisms that keep the repetitive regions of our genomes silent and stable.
Collapse
Affiliation(s)
- Jan Padeken
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Peter Zeller
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
| |
Collapse
|
214
|
Somatic mosaicism: implications for disease and transmission genetics. Trends Genet 2015; 31:382-92. [PMID: 25910407 DOI: 10.1016/j.tig.2015.03.013] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 11/21/2022]
Abstract
Nearly all of the genetic material among cells within an organism is identical. However, single-nucleotide variants (SNVs), small insertions/deletions (indels), copy-number variants (CNVs), and other structural variants (SVs) continually accumulate as cells divide during development. This process results in an organism composed of countless cells, each with its own unique personal genome. Thus, every human is undoubtedly mosaic. Mosaic mutations can go unnoticed, underlie genetic disease or normal human variation, and may be transmitted to the next generation as constitutional variants. We review the influence of the developmental timing of mutations, the mechanisms by which they arise, methods for detecting mosaic variants, and the risk of passing these mutations on to the next generation.
Collapse
|
215
|
Reyes GX, Schmidt TT, Kolodner RD, Hombauer H. New insights into the mechanism of DNA mismatch repair. Chromosoma 2015; 124:443-62. [PMID: 25862369 DOI: 10.1007/s00412-015-0514-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/23/2015] [Accepted: 03/23/2015] [Indexed: 12/20/2022]
Abstract
The genome of all organisms is constantly being challenged by endogenous and exogenous sources of DNA damage. Errors like base:base mismatches or small insertions and deletions, primarily introduced by DNA polymerases during DNA replication are repaired by an evolutionary conserved DNA mismatch repair (MMR) system. The MMR system, together with the DNA replication machinery, promote repair by an excision and resynthesis mechanism during or after DNA replication, increasing replication fidelity by up-to-three orders of magnitude. Consequently, inactivation of MMR genes results in elevated mutation rates that can lead to increased cancer susceptibility in humans. In this review, we summarize our current understanding of MMR with a focus on the different MMR protein complexes, their function and structure. We also discuss how recent findings have provided new insights in the spatio-temporal regulation and mechanism of MMR.
Collapse
Affiliation(s)
- Gloria X Reyes
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Tobias T Schmidt
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Richard D Kolodner
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Moores-UCSD Cancer Center and Institute of Genomic Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093-0669, USA
| | - Hans Hombauer
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.
| |
Collapse
|
216
|
Richard GF. Shortening trinucleotide repeats using highly specific endonucleases: a possible approach to gene therapy? Trends Genet 2015; 31:177-86. [PMID: 25743488 DOI: 10.1016/j.tig.2015.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 12/31/2022]
Abstract
Trinucleotide repeat expansions are involved in more than two dozen neurological and developmental disorders. Conventional therapeutic approaches aimed at regulating the expression level of affected genes, which rely on drugs, oligonucleotides, and/or transgenes, have met with only limited success so far. An alternative approach is to shorten repeats to non-pathological lengths using highly specific nucleases. Here, I review early experiments using meganucleases, zinc-finger nucleases (ZFN), and transcription-activator like effector nucleases (TALENs) to contract trinucleotide repeats, and discuss the possibility of using CRISPR-Cas nucleases to the same end. Although this is a nascent field, I explore the possibility of designing nucleases and effectively delivering them in the context of gene therapy.
Collapse
Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Department Genomes and Genetics, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 3525, 25 Rue du Dr Roux, 75015 Paris, France
| |
Collapse
|
217
|
Muro Y, Sugiura K, Mimori T, Akiyama M. DNA mismatch repair enzymes: Genetic defects and autoimmunity. Clin Chim Acta 2015; 442:102-9. [DOI: 10.1016/j.cca.2015.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/17/2015] [Accepted: 01/17/2015] [Indexed: 12/31/2022]
|
218
|
Neelsen KJ, Lopes M. Replication fork reversal in eukaryotes: from dead end to dynamic response. Nat Rev Mol Cell Biol 2015; 16:207-20. [PMID: 25714681 DOI: 10.1038/nrm3935] [Citation(s) in RCA: 365] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The remodelling of replication forks into four-way junctions following replication perturbation, known as fork reversal, was hypothesized to promote DNA damage tolerance and repair during replication. Albeit conceptually attractive, for a long time fork reversal in vivo was found only in prokaryotes and specific yeast mutants, calling its evolutionary conservation and physiological relevance into question. Based on the recent visualization of replication forks in metazoans, fork reversal has emerged as a global, reversible and regulated process, with intriguing implications for replication completion, chromosome integrity and the DNA damage response. The study of the putative in vivo roles of recently identified eukaryotic factors in fork remodelling promises to shed new light on mechanisms of genome maintenance and to provide novel attractive targets for cancer therapy.
Collapse
Affiliation(s)
- Kai J Neelsen
- 1] Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland. [2] The Novo Nordisk Foundation Center for Protein Research, 2200 Copenhagen, Denmark
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| |
Collapse
|
219
|
Mishra PK, Bunkar N, Raghuram GV, Khare NK, Pathak N, Bhargava A. Epigenetic dimension of oxygen radical injury in spermatogonial epithelial cells. Reprod Toxicol 2015; 52:40-56. [PMID: 25687723 DOI: 10.1016/j.reprotox.2015.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/04/2015] [Accepted: 02/06/2015] [Indexed: 12/17/2022]
Abstract
The present work reports a direct role of mitochondrial oxidative stress induced aberrant chromatin regulation, as a central phenomenon, to perturbed genomic integrity in the testicular milieu. Oxygen-radical injury following N-succinimidyl N-methylcarbamate treatment in mouse spermatogonial epithelial (GC-1 spg) cells induced functional derailment of mitochondrial machinery. Mitophagy resulted in marked inhibition of mitochondrial respiration and reduced mtDNA copy number. Impaired cell cycle progression along with altered H3K9me1, H4K20me3, H3, AcH3 and uH2A histone modifications were observed in the treated cells. Dense heterochromatin foci and aberrant expression of HP1α in nuclei of treated cells implied onset of senescence associated secretory phenotype mediated through nuclear accumulation of NF-κB. Neoplastic nature of daughter clones, emerged from senescent mother phenotypes was confirmed by cytogenetic instability, aberrant let-7a and let-7b miRNA expression and anchorage independent growth. Together, our results provide the first insights of redox-dependent epigenomic imbalance in spermatogonia, a previously unknown molecular paradigm.
Collapse
Affiliation(s)
- Pradyumna K Mishra
- Translational Research Lab, School of Biological Sciences, Dr. H.S. Gour Central University, Sagar, India; Division of Translational Research, Tata Memorial Centre, ACTREC, Navi Mumbai, India.
| | - Neha Bunkar
- Translational Research Lab, School of Biological Sciences, Dr. H.S. Gour Central University, Sagar, India
| | - Gorantla V Raghuram
- Translational Research Lab, School of Biological Sciences, Dr. H.S. Gour Central University, Sagar, India; Division of Translational Research, Tata Memorial Centre, ACTREC, Navi Mumbai, India
| | - Naveen K Khare
- Division of Translational Research, Tata Memorial Centre, ACTREC, Navi Mumbai, India
| | - Neelam Pathak
- Translational Research Lab, School of Biological Sciences, Dr. H.S. Gour Central University, Sagar, India
| | - Arpit Bhargava
- Translational Research Lab, School of Biological Sciences, Dr. H.S. Gour Central University, Sagar, India; Division of Translational Research, Tata Memorial Centre, ACTREC, Navi Mumbai, India
| |
Collapse
|
220
|
Mastushita M, Kitoh H, Subasioglu A, Kurt Colak F, Dundar M, Mishima K, Nishida Y, Ishiguro N. A Glutamine Repeat Variant of the RUNX2 Gene Causes Cleidocranial Dysplasia. Mol Syndromol 2015; 6:50-3. [PMID: 25852448 DOI: 10.1159/000370337] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2014] [Indexed: 11/19/2022] Open
Abstract
Cleidocranial dysplasia (CCD), an autosomal dominant skeletal dysplasia characterized by hypoplastic clavicles and delayed closure of the cranial sutures, is caused by mutations of the runt-related transcription factor 2 (RUNX2) gene. The RUNX2 gene consists of a glutamine and alanine repeat domain (Q/A domain, 23Q/17A), a DNA-binding Runt domain and a proline/serine/threonine-rich domain. We report on a familial case of CCD with a novel mutation within the Q/A domain of the RUNX2 gene, which is an insertion in exon 1 (p.Q71_E72insQQQQ) representing the Q-repeat variant (27Q/17A). Functional analysis of the 27Q variant revealed abolished transactivation capacity of the mutated RUNX2 protein. This is the first case report that demonstrated a glutamine repeat variant of the RUNX2 gene causes CCD.
Collapse
Affiliation(s)
- Masaki Mastushita
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroshi Kitoh
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Asli Subasioglu
- Department of Medical Genetics, Izmir Katip Celebi University Ataturk Training and Research Hospital, Izmir, Turkey
| | - Fatma Kurt Colak
- Department of Medical Genetics, Erciyes University, Kayseri, Turkey
| | - Munis Dundar
- Department of Medical Genetics, Erciyes University, Kayseri, Turkey
| | - Kenichi Mishima
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshihiro Nishida
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Naoki Ishiguro
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|
221
|
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
|
222
|
Abstract
DNA mismatch repair is a conserved antimutagenic pathway that maintains genomic stability through rectification of DNA replication errors and attenuation of chromosomal rearrangements. Paradoxically, mutagenic action of mismatch repair has been implicated as a cause of triplet repeat expansions that cause neurological diseases such as Huntington disease and myotonic dystrophy. This mutagenic process requires the mismatch recognition factor MutSβ and the MutLα (and/or possibly MutLγ) endonuclease, and is thought to be triggered by the transient formation of unusual DNA structures within the expanded triplet repeat element. This review summarizes the current knowledge of DNA mismatch repair involvement in triplet repeat expansion, which encompasses in vitro biochemical findings, cellular studies, and various in vivo transgenic animal model experiments. We present current mechanistic hypotheses regarding mismatch repair protein function in mediating triplet repeat expansions and discuss potential therapeutic approaches targeting the mismatch repair pathway.
Collapse
Affiliation(s)
- Ravi R Iyer
- Teva Branded Pharmaceutical Products R&D, Inc., West Chester, Pennsylvania 19380;
| | | | | | | |
Collapse
|
223
|
Somatic mosaicism in the human genome. Genes (Basel) 2014; 5:1064-94. [PMID: 25513881 PMCID: PMC4276927 DOI: 10.3390/genes5041064] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/26/2014] [Accepted: 11/28/2014] [Indexed: 12/17/2022] Open
Abstract
Somatic mosaicism refers to the occurrence of two genetically distinct populations of cells within an individual, derived from a postzygotic mutation. In contrast to inherited mutations, somatic mosaic mutations may affect only a portion of the body and are not transmitted to progeny. These mutations affect varying genomic sizes ranging from single nucleotides to entire chromosomes and have been implicated in disease, most prominently cancer. The phenotypic consequences of somatic mosaicism are dependent upon many factors including the developmental time at which the mutation occurs, the areas of the body that are affected, and the pathophysiological effect(s) of the mutation. The advent of second-generation sequencing technologies has augmented existing array-based and cytogenetic approaches for the identification of somatic mutations. We outline the strengths and weaknesses of these techniques and highlight recent insights into the role of somatic mosaicism in causing cancer, neurodegenerative, monogenic, and complex disease.
Collapse
|
224
|
Yadav P, Harcy V, Argueso JL, Dominska M, Jinks-Robertson S, Kim N. Topoisomerase I plays a critical role in suppressing genome instability at a highly transcribed G-quadruplex-forming sequence. PLoS Genet 2014; 10:e1004839. [PMID: 25473964 PMCID: PMC4256205 DOI: 10.1371/journal.pgen.1004839] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/20/2014] [Indexed: 11/18/2022] Open
Abstract
G-quadruplex or G4 DNA is a non-B secondary DNA structure that comprises a stacked array of guanine-quartets. Cellular processes such as transcription and replication can be hindered by unresolved DNA secondary structures potentially endangering genome maintenance. As G4-forming sequences are highly frequent throughout eukaryotic genomes, it is important to define what factors contribute to a G4 motif becoming a hotspot of genome instability. Using a genetic assay in Saccharomyces cerevisiae, we previously demonstrated that a potential G4-forming sequence derived from a guanine-run containing immunoglobulin switch Mu (Sμ) region becomes highly unstable when actively transcribed. Here we describe assays designed to survey spontaneous genome rearrangements initiated at the Sμ sequence in the context of large genomic areas. We demonstrate that, in the absence of Top1, a G4 DNA-forming sequence becomes a strong hotspot of gross chromosomal rearrangements and loss of heterozygosity associated with mitotic recombination within the ∼20 kb or ∼100 kb regions of yeast chromosome V or III, respectively. Transcription confers a critical strand bias since genome rearrangements at the G4-forming Sμ are elevated only when the guanine-runs are located on the non-transcribed strand. The direction of replication and transcription, when in a head-on orientation, further contribute to the elevated genome instability at a potential G4 DNA-forming sequence. The implications of our identification of Top1 as a critical factor in suppression of instability associated with potential G4 DNA-forming sequences are discussed. Genome instability is not evenly distributed, but rather is highly elevated at certain genomic loci containing DNA sequences that can fold into non-canonical secondary structures. The four-stranded G-quadruplex or G4 DNA is one such DNA structure capable of instigating transcription and/or replication obstruction and subsequent genome instability. In this study, we used a reporter system to quantitatively measure the level of genome instability occurring at a G4 DNA motif integrated into the yeast genome. We showed that the disruption of Topoisomerase I function significantly elevated various types of genome instability at the highly transcribed G4 motif generating loss of heterozygosity and copy number alterations (deletions and duplications), both of which are frequently observed in cancer genomes.
Collapse
Affiliation(s)
- Puja Yadav
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Victoria Harcy
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|
225
|
Kamat N, Khidhir MA, Hussain S, Alashari MM, Rannug U. Chemotherapy induced microsatellite instability and loss of heterozygosity in chromosomes 2, 5, 10, and 17 in solid tumor patients. Cancer Cell Int 2014; 14:118. [PMID: 25493073 PMCID: PMC4260186 DOI: 10.1186/s12935-014-0118-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 10/27/2014] [Indexed: 01/05/2023] Open
Abstract
Background The inevitable side effects of the currently used chemotherapy are associated with serious syndromes. Genotoxic effects and consequent genetic instability may play an important role in these syndromes. The aim of the study was to evaluate chemotherapy-related microsatellite instability (MSI), loss of heterozygosity (LOH), and loss of mismatch repair (MMR) expression in solid tumor patients. Methods Samples were collected from 117 de novo patients with solid tumors of different origins. Specimens, taken pre- and post-treatment, were screened for MSI and LOH in 10 microsatellite sequences in blood, and expression of five MMR proteins were analyzed in cancer tissues using immunohistochemistry. Statistical analysis included the use of; Fisher’s exact test, Chi Square, and an inter-rater reliability test using Cohen’s kappa coefficient. Results Microsatellite analysis showed that 66.7% of the patients had MSI, including 23.1% high-positive MSI and 43.6% low-positive MSI. A large portion (41%) of the patients exhibited LOH in addition to MSI. MSI and LOH were detected in seven loci in which incidence rates ranged from 3.8% positive for Bat-26 to 34.6% positive for Tp53-Alu. Immunohistochemistry revealed that human mutL homolog 1 (hMLH1) expression was deficient in 29.1% of the patients, whereas 18.8%, 23.9%, 13.4%, and 9.7% were deficient for human mutS homolog 2 (hMSH2), P53, human mutS homolog 6 (hMSH6) and human post-meiotic segregation increased 2 (hPMS2), respectively. There was a significant correlation between MSI and LOH incidence in Tp53-Alu, Mfd41, and APC with low or deficient expression of hMLH1, hMSH2, and P53. A significant association between MSI and LOH, and incidence of secondary tumors was also evident. Conclusions The negative correlation between MMR expression, MSI, and LOH and increased resistance to anti-cancer drugs and development of secondary cancers demonstrates a useful aid in early detection of potential chemotherapy-related side-effects. The diagnostic value demonstrated in our earlier study on breast cancer patients was confirmed for other solid tumors. Electronic supplementary material The online version of this article (doi:10.1186/s12935-014-0118-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Nasir Kamat
- Department of Molecular Biosciences, the Wenner-Gren Institute (MBW), Stockholm University, SE-106 91 Stockholm, Sweden
| | - Mohammed A Khidhir
- Department of Genetics Research, Management of Natural Conservations, AlAin City, UAE
| | - Sabir Hussain
- Department of Oncology and Hematology, Tawam Hospital, AlAin City, UAE
| | - Mouied M Alashari
- Department of Pathology, University of Utah, Salt Lake City, Utah 84112 USA
| | - Ulf Rannug
- Department of Molecular Biosciences, the Wenner-Gren Institute (MBW), Stockholm University, SE-106 91 Stockholm, Sweden
| |
Collapse
|
226
|
Xu M, Lai Y, Jiang Z, Terzidis MA, Masi A, Chatgilialoglu C, Liu Y. A 5', 8-cyclo-2'-deoxypurine lesion induces trinucleotide repeat deletion via a unique lesion bypass by DNA polymerase β. Nucleic Acids Res 2014; 42:13749-63. [PMID: 25428354 PMCID: PMC4267656 DOI: 10.1093/nar/gku1239] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
5',8-cyclo-2'-deoxypurines (cdPus) are common forms of oxidized DNA lesions resulting from endogenous and environmental oxidative stress such as ionizing radiation. The lesions can only be repaired by nucleotide excision repair with a low efficiency. This results in their accumulation in the genome that leads to stalling of the replication DNA polymerases and poor lesion bypass by translesion DNA polymerases. Trinucleotide repeats (TNRs) consist of tandem repeats of Gs and As and therefore are hotspots of cdPus. In this study, we provided the first evidence that both (5'R)- and (5'S)-5',8-cyclo-2'-deoxyadenosine (cdA) in a CAG repeat tract caused CTG repeat deletion exclusively during DNA lagging strand maturation and base excision repair. We found that a cdA induced the formation of a CAG loop in the template strand, which was skipped over by DNA polymerase β (pol β) lesion bypass synthesis. This subsequently resulted in the formation of a long flap that was efficiently cleaved by flap endonuclease 1, thereby leading to repeat deletion. Our study indicates that accumulation of cdPus in the human genome can lead to TNR instability via a unique lesion bypass by pol β.
Collapse
Affiliation(s)
- Meng Xu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA
| | - Zhongliang Jiang
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA
| | - Michael A Terzidis
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Annalisa Masi
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy Institute of Nanoscience and Nanotechnology, N.C.S.R. 'Demokritos', 15341 Agia, Paraskevi, Athens, Greece
| | - Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA Biomolecular Sciences Institute, School of Integrated Sciences and Humanities, Florida International University, 11200 SW, 8th Street, Miami, FL 33199, USA
| |
Collapse
|
227
|
Shah KA, McGinty RJ, Egorova VI, Mirkin SM. Coupling transcriptional state to large-scale repeat expansions in yeast. Cell Rep 2014; 9:1594-1602. [PMID: 25464841 DOI: 10.1016/j.celrep.2014.10.048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 09/07/2014] [Accepted: 10/19/2014] [Indexed: 11/15/2022] Open
Abstract
Expansions of simple DNA repeats cause numerous hereditary disorders in humans. Replication, repair, and transcription are implicated in the expansion process, but their relative contributions are yet to be distinguished. To separate the roles of replication and transcription in the expansion of Friedreich's ataxia (GAA)n repeats, we designed two yeast genetic systems that utilize a galactose-inducible GAL1 promoter but contain these repeats in either the transcribed or nontranscribed region of a selectable cassette. We found that large-scale repeat expansions can occur in the lack of transcription. Induction of transcription strongly elevated the rate of expansions in both systems, indicating that active transcriptional state rather than transcription through the repeat per se affects this process. Furthermore, replication defects increased the rate of repeat expansions irrespective of transcriptional state. We present a model in which transcriptional state, linked to the nucleosomal density of a region, acts as a modulator of large-scale repeat expansions.
Collapse
Affiliation(s)
- Kartik A Shah
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Ryan J McGinty
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Vera I Egorova
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
| |
Collapse
|
228
|
Yrigollen CM, Sweha S, Durbin-Johnson B, Zhou L, Berry-Kravis E, Fernandez-Carvajal I, Faradz SMH, Amiri K, Shaheen H, Polli R, Murillo-Bonilla L, Silva Arevalo GDJ, Cogram P, Murgia A, Tassone F. Distribution of AGG interruption patterns within nine world populations. Intractable Rare Dis Res 2014; 3:153-61. [PMID: 25606365 PMCID: PMC4298645 DOI: 10.5582/irdr.2014.01028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 11/28/2014] [Indexed: 01/04/2023] Open
Abstract
The CGG trinucleotide repeat within the FMR1 gene is associated with multiple clinical disorders, including fragile X-associated tremor/ataxia syndrome, fragile X-associated primary ovarian insufficiency, and fragile X syndrome. Differences in the distribution and prevalence of CGG repeat length and of AGG interruption patterns have been reported among different populations and ethnicities. In this study we characterized the AGG interruption patterns within 3,065 normal CGG repeat alleles from nine world populations including Australia, Chile, United Arab Emirates, Guatemala, Indonesia, Italy, Mexico, Spain, and United States. Additionally, we compared these populations with those previously reported, and summarized the similarities and differences. We observed significant differences in AGG interruption patterns. Frequencies of longer alleles, longer uninterrupted CGG repeat segments and alleles with greater than 2 AGG interruptions varied between cohorts. The prevalence of fragile X syndrome and FMR1 associated disorders in various populations is thought to be affected by the total length of the CGG repeat and may also be influenced by the AGG distribution pattern. Thus, the results of this study may be important in considering the risk of fragile X-related conditions in various populations.
Collapse
Affiliation(s)
- Carolyn M. Yrigollen
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Davis, CA, USA
| | - Stefan Sweha
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Davis, CA, USA
| | - Blythe Durbin-Johnson
- Department of Public Health Sciences, University of California Davis, School of Medicine, Davis, CA, USA
| | - Lili Zhou
- Department of Pediatrics, Neurological Sciences, Biochemistry, Rush University Medical Center, Chicago, IL, USA
| | - Elizabeth Berry-Kravis
- Department of Pediatrics, Neurological Sciences, Biochemistry, Rush University Medical Center, Chicago, IL, USA
| | - Isabel Fernandez-Carvajal
- Laboratorio de Enfermedades genéticas y cribado neonatal, Departamento de Genetica Molecular de la Enfermedad, Instituto de Biologìa y Genética Molecular Universidad de Valladolid-CSIC, Valladolid, Spain
| | - Sultana MH Faradz
- Center for Biomedical Research, Diponegoro University, Semarang, Central Java, Indonesia
| | - Khaled Amiri
- Department of Biology, College of Science, United Arab University, United Arab Emirates
| | - Huda Shaheen
- Department of Biology, College of Science, United Arab University, United Arab Emirates
| | - Roberta Polli
- Laboratory of Molecular Genetics of Neurodevelopment, Department of Women's and Children's Health, University of Padova, Italy
| | | | - Gabriel de Jesus Silva Arevalo
- Genetic and Neurometabolic Clinic, Obras Sociales Santo Hermano Pedro, Antigua Guatemala. Center by Biomedical Research, Medicine school San Carlos University, Guatemala Central America
| | - Patricia Cogram
- Biomedicine Division, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Alessandra Murgia
- Laboratory of Molecular Genetics of Neurodevelopment, Department of Women's and Children's Health, University of Padova, Italy
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Davis, CA, USA
- M.I.N.D. Institute, University of California Davis Medical Center, Davis, CA, USA
- Address correspondence to: Dr. Flora Tassone, Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, 2700 Stockton Blvd, Suite 2102, Sacramento, CA 95817, USA; M.I.N.D. Institute, University of California Davis Medical Center, 2805 50th Street Sacramento, CA 95817, USA. E-mail:
| |
Collapse
|
229
|
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
|
230
|
Trinucleotide expansion in disease: why is there a length threshold? Curr Opin Genet Dev 2014; 26:131-40. [PMID: 25282113 DOI: 10.1016/j.gde.2014.07.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 11/24/2022]
Abstract
Trinucleotide repeats (TNRs) expansion disorders are severe neurodegenerative and neuromuscular disorders that arise from inheriting a long tract (30-50 copies) of a trinucleotide unit within or near an expressed gene (Figure 1a). The mutation is referred to as 'trinucleotide expansion' since the number of triplet units in a mutated gene is greater than the number found in the normal gene. Expansion becomes obvious once the number of repeating units passes a critical threshold length, but what happens at the threshold to render the repeating tract unstable? Here we discuss DNA-dependent and RNA-dependent models by which a particular DNA length permits a rapid transition to an unstable state.
Collapse
|
231
|
Moily NS, Kota LN, Anjanappa RM, Venugopal S, Vaidyanathan R, Pal P, Purushottam M, Jain S, Kandasamy M. Trinucleotide repeats and haplotypes at the huntingtin locus in an Indian sample overlaps with European haplogroup a. PLOS CURRENTS 2014; 6:ecurrents.hd.a3ad1a381ab1eed117675145318c9a80. [PMID: 25642374 PMCID: PMC4205232 DOI: 10.1371/currents.hd.a3ad1a381ab1eed117675145318c9a80] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Huntington's disease (HD), an autosomal dominant neurodegenerative syndrome, has a world-wide distribution. An estimated 2.5-10/100,000 people of European ancestry are affected with HD, while the Asian populations have lower prevalence (0.6-3.8/100,000). The epidemiology of HD is not well described in India, and the distribution of the pathogenic CAG expansion, and the associated haplotype, in this population needs to be better understood. This study demonstrates a distribution of CAG repeats, at the HTT locus, comparable to the European population in both normal and HD affected chromosomes. Further, we provide an evidence for similarity of the HD halpotype in Indian sample to the European HD haplogroup.
Collapse
Affiliation(s)
- Nagaraj S Moily
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; The University of Melbourne, Melbourne,Australia
| | - Lakshmi Narayanan Kota
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Ram Murthy Anjanappa
- Human Molecular Genetics, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Sowmya Venugopal
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Radhika Vaidyanathan
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Pramod Pal
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Meera Purushottam
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Sanjeev Jain
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Mahesh Kandasamy
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| |
Collapse
|
232
|
House NCM, Yang JH, Walsh SC, Moy JM, Freudenreich CH. NuA4 initiates dynamic histone H4 acetylation to promote high-fidelity sister chromatid recombination at postreplication gaps. Mol Cell 2014; 55:818-828. [PMID: 25132173 PMCID: PMC4169719 DOI: 10.1016/j.molcel.2014.07.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 04/16/2014] [Accepted: 07/10/2014] [Indexed: 11/24/2022]
Abstract
CAG/CTG trinucleotide repeats are unstable, fragile sequences that strongly position nucleosomes, but little is known about chromatin modifications required to prevent genomic instability at these or other structure-forming sequences. We discovered that regulated histone H4 acetylation is required to maintain CAG repeat stability and promote gap-induced sister chromatid recombination. CAG expansions in the absence of H4 HATs NuA4 and Hat1 and HDACs Sir2, Hos2, and Hst1 depended on Rad52, Rad57, and Rad5 and were therefore arising through homology-mediated postreplication repair (PRR) events. H4K12 and H4K16 acetylation were required to prevent Rad5-dependent CAG repeat expansions, and H4K16 acetylation was enriched at CAG repeats during S phase. Genetic experiments placed the RSC chromatin remodeler in the same PRR pathway, and Rsc2 recruitment was coincident with H4K16 acetylation. Here we have utilized a repetitive DNA sequence that induces endogenous DNA damage to identify histone modifications that regulate recombination efficiency and fidelity during postreplication gap repair.
Collapse
Affiliation(s)
| | - Jiahui H Yang
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Stephen C Walsh
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Jonathan M Moy
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, MA 02155, USA; Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA.
| |
Collapse
|
233
|
Simard O, Grégoire MC, Arguin M, Brazeau MA, Leduc F, Marois I, Richter MV, Boissonneault G. Instability of trinucleotidic repeats during chromatin remodeling in spermatids. Hum Mutat 2014; 35:1280-4. [PMID: 25136821 DOI: 10.1002/humu.22637] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 08/07/2014] [Indexed: 11/08/2022]
Abstract
Transient DNA breaks and evidence of DNA damage response have recently been reported during the chromatin remodeling process in haploid spermatids, creating a potential window of enhanced genetic instability. We used flow cytometry to achieve separation of differentiating spermatids into four highly purified populations using transgenic mice harboring 160 CAG repeats within exon 1 of the human Huntington disease gene (HTT). Trinucleotic repeat expansion was found to occur immediately following the chromatin remodeling steps, confirming the genetic instability of the process and pointing to the origin of paternal anticipation observed in some trinucleotidic repeats diseases.
Collapse
Affiliation(s)
- Olivier Simard
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | | | | | | | | | | | | | | |
Collapse
|
234
|
House NCM, Koch MR, Freudenreich CH. Chromatin modifications and DNA repair: beyond double-strand breaks. Front Genet 2014; 5:296. [PMID: 25250043 PMCID: PMC4155812 DOI: 10.3389/fgene.2014.00296] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 08/08/2014] [Indexed: 12/28/2022] Open
Abstract
DNA repair must take place in the context of chromatin, and chromatin modifications and DNA repair are intimately linked. The study of double-strand break repair has revealed numerous histone modifications that occur after induction of a DSB, and modification of the repair factors themselves can also occur. In some cases the function of the modification is at least partially understood, but in many cases it is not yet clear. Although DSB repair is a crucial activity for cell survival, DSBs account for only a small percentage of the DNA lesions that occur over the lifetime of a cell. Repair of single-strand gaps, nicks, stalled forks, alternative DNA structures, and base lesions must also occur in a chromatin context. There is increasing evidence that these repair pathways are also regulated by histone modifications and chromatin remodeling. In this review, we will summarize the current state of knowledge of chromatin modifications that occur during non-DSB repair, highlighting similarities and differences to DSB repair as well as remaining questions.
Collapse
Affiliation(s)
| | - Melissa R Koch
- Department of Biology, Tufts University Medford, MA, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University Medford, MA, USA ; Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University Boston, MA, USA
| |
Collapse
|
235
|
Bak ST, Sakellariou D, Pena-Diaz J. The dual nature of mismatch repair as antimutator and mutator: for better or for worse. Front Genet 2014; 5:287. [PMID: 25191341 PMCID: PMC4139959 DOI: 10.3389/fgene.2014.00287] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/04/2014] [Indexed: 01/19/2023] Open
Abstract
DNA is constantly under attack by a number of both exogenous and endogenous agents that challenge its integrity. Among the mechanisms that have evolved to counteract this deleterious action, mismatch repair (MMR) has specialized in removing DNA biosynthetic errors that occur when replicating the genome. Malfunction or inactivation of this system results in an increase in spontaneous mutability and a strong predisposition to tumor development. Besides this key corrective role, MMR proteins are involved in other pathways of DNA metabolism such as mitotic and meiotic recombination and processing of oxidative damage. Surprisingly, MMR is also required for certain mutagenic processes. The mutagenic MMR has beneficial consequences contributing to the generation of a vast repertoire of antibodies through class switch recombination and somatic hypermutation processes. However, this non-canonical mutagenic MMR also has detrimental effects; it promotes repeat expansions associated with neuromuscular and neurodegenerative diseases and may contribute to cancer/disease-related aberrant mutations and translocations. The reaction responsible for replication error correction has been the most thoroughly studied and it is the subject to numerous reviews. This review describes briefly the biochemistry of MMR and focuses primarily on the non-canonical MMR activities described in mammals as well as emerging research implicating interplay of MMR and chromatin.
Collapse
Affiliation(s)
- Sara Thornby Bak
- Department of Neuroscience and Pharmacology and Center for Healthy Aging, University of Copenhagen Copenhagen, Denmark
| | - Despoina Sakellariou
- Department of Neuroscience and Pharmacology and Center for Healthy Aging, University of Copenhagen Copenhagen, Denmark
| | - Javier Pena-Diaz
- Department of Neuroscience and Pharmacology and Center for Healthy Aging, University of Copenhagen Copenhagen, Denmark
| |
Collapse
|
236
|
Pan L, Penney J, Tsai LH. Chromatin regulation of DNA damage repair and genome integrity in the central nervous system. J Mol Biol 2014; 426:3376-88. [PMID: 25128619 DOI: 10.1016/j.jmb.2014.08.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/04/2014] [Accepted: 08/05/2014] [Indexed: 12/17/2022]
Abstract
With the continued extension of lifespan, aging and age-related diseases have become a major medical challenge to our society. Aging is accompanied by changes in multiple systems. Among these, the aging process in the central nervous system is critically important but very poorly understood. Neurons, as post-mitotic cells, are devoid of replicative associated aging processes, such as senescence and telomere shortening. However, because of the inability to self-replenish, neurons have to withstand challenge from numerous stressors over their lifetime. Many of these stressors can lead to damage of the neurons' DNA. When the accumulation of DNA damage exceeds a neuron's capacity for repair, or when there are deficiencies in DNA repair machinery, genome instability can manifest. The increased mutation load associated with genome instability can lead to neuronal dysfunction and ultimately to neuron degeneration. In this review, we first briefly introduce the sources and types of DNA damage and the relevant repair pathways in the nervous system (summarized in Fig. 1). We then discuss the chromatin regulation of these processes and summarize our understanding of the contribution of genomic instability to neurodegenerative diseases.
Collapse
Affiliation(s)
- Ling Pan
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jay Penney
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
237
|
Yrigollen CM, Martorell L, Durbin-Johnson B, Naudo M, Genoves J, Murgia A, Polli R, Zhou L, Barbouth D, Rupchock A, Finucane B, Latham GJ, Hadd A, Berry-Kravis E, Tassone F. AGG interruptions and maternal age affect FMR1 CGG repeat allele stability during transmission. J Neurodev Disord 2014; 6:24. [PMID: 25110527 PMCID: PMC4126815 DOI: 10.1186/1866-1955-6-24] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/17/2014] [Indexed: 01/25/2023] Open
Abstract
Background The presence of AGG interruptions in the CGG repeat locus of the fragile X mental retardation 1 (FMR1) gene decreases the instability of the allele during transmission from parent to child, and decreases the risk of expansion of a premutation allele to a full mutation allele (the predominant cause of fragile X syndrome) during maternal transmission. Methods To strengthen recent findings on the utility of AGG interruptions in predicting instability or expansion to a full mutation of FMR1 CGG repeat alleles, we assessed the outcomes of 108 intermediate (also named gray zone) and 710 premutation alleles that were transmitted from parent to child, and collected from four international clinical sites. We have used the results to revise our initial model that predicted the risk of a maternal premutation allele expanding to a full mutation during transmission and to test the effect of AGG interruptions on the magnitude of expanded allele instability of intermediate or premutation alleles that did not expand to a full mutation. Results Consistent with previous studies, the number of AGG triplets that interrupts the CGG repeat locus was found to influence the risk of allele instability, including expansion to a full mutation. The total length of the CGG repeat allele remains the best predictor of instability or expansion to a full mutation, but the number of AGG interruptions and, to a much lesser degree, maternal age are also factors when considering the risk of transmission of the premutation allele to a full mutation. Conclusions Our findings demonstrate that a model with total CGG length, number of AGG interruptions, and maternal age is recommended for calculating the risk of expansion to a full mutation during maternal transmission. Taken together, the results of this study provide relevant information for the genetic counseling of female premutation carriers, and improve the current predictive models which calculate risk of expansion to a full mutation using only total CGG repeat length.
Collapse
Affiliation(s)
- Carolyn M Yrigollen
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, 2700 Stockton Blvd., Suite 2102, Sacramento, CA 95817, USA
| | - Loreto Martorell
- Molecular Genetics Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Blythe Durbin-Johnson
- Department of Public Health Sciences, University of California, Davis, Davis, CA, USA
| | - Montserrat Naudo
- Molecular Genetics Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Jordi Genoves
- Molecular Genetics Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Alessandra Murgia
- Laboratory of Molecular Genetics of Neurodevelopment, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Roberta Polli
- Laboratory of Molecular Genetics of Neurodevelopment, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Lili Zhou
- Department of Pediatrics, Neurological Sciences, and Biochemistry, Rush University Medical Center, Chicago, IL, USA
| | - Deborah Barbouth
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Abigail Rupchock
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Brenda Finucane
- Geisinger Autism and Developmental Medicine Institute, Lewisburg, PA, USA
| | | | | | - Elizabeth Berry-Kravis
- Department of Pediatrics, Neurological Sciences, and Biochemistry, Rush University Medical Center, Chicago, IL, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, 2700 Stockton Blvd., Suite 2102, Sacramento, CA 95817, USA ; MIND Institute, University of California, Davis, School of Medicine, Davis, CA, USA
| |
Collapse
|
238
|
Nucleases in homologous recombination as targets for cancer therapy. FEBS Lett 2014; 588:2446-56. [DOI: 10.1016/j.febslet.2014.06.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/02/2014] [Accepted: 06/02/2014] [Indexed: 11/21/2022]
|
239
|
Heterochromatin controls γH2A localization in Neurospora crassa. EUKARYOTIC CELL 2014; 13:990-1000. [PMID: 24879124 DOI: 10.1128/ec.00117-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In response to genotoxic stress, ATR and ATM kinases phosphorylate H2A in fungi and H2AX in animals on a C-terminal serine. The resulting modified histone, called γH2A, recruits chromatin-binding proteins that stabilize stalled replication forks or promote DNA double-strand-break repair. To identify genomic loci that might be prone to replication fork stalling or DNA breakage in Neurospora crassa, we performed chromatin immunoprecipitation (ChIP) of γH2A followed by next-generation sequencing (ChIP-seq). γH2A-containing nucleosomes are enriched in Neurospora heterochromatin domains. These domains are comprised of A·T-rich repetitive DNA sequences associated with histone H3 methylated at lysine-9 (H3K9me), the H3K9me-binding protein heterochromatin protein 1 (HP1), and DNA cytosine methylation. H3K9 methylation, catalyzed by DIM-5, is required for normal γH2A localization. In contrast, γH2A is not required for H3K9 methylation or DNA methylation. Normal γH2A localization also depends on HP1 and a histone deacetylase, HDA-1, but is independent of the DNA methyltransferase DIM-2. γH2A is globally induced in dim-5 mutants under normal growth conditions, suggesting that the DNA damage response is activated in these mutants in the absence of exogenous DNA damage. Together, these data suggest that heterochromatin formation is essential for normal DNA replication or repair.
Collapse
|
240
|
Gomes-Pereira M, Hilley JD, Morales F, Adam B, James HE, Monckton DG. Disease-associated CAG·CTG triplet repeats expand rapidly in non-dividing mouse cells, but cell cycle arrest is insufficient to drive expansion. Nucleic Acids Res 2014; 42:7047-56. [PMID: 24860168 PMCID: PMC4066746 DOI: 10.1093/nar/gku285] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Genetically unstable expanded CAG·CTG trinucleotide repeats are causal in a number of human disorders, including Huntington disease and myotonic dystrophy type 1. It is still widely assumed that DNA polymerase slippage during replication plays an important role in the accumulation of expansions. Nevertheless, somatic mosaicism correlates poorly with the proliferative capacity of the tissue and rates of cell turnover, suggesting that expansions can occur in the absence of replication. We monitored CAG·CTG repeat instability in transgenic mouse cells arrested by chemical or genetic manipulation of the cell cycle and generated unequivocal evidence for the continuous accumulation of repeat expansions in non-dividing cells. Importantly, the rates of expansion in non-dividing cells were at least as high as those of proliferating cells. These data are consistent with a major role for cell division-independent expansion in generating somatic mosaicism in vivo. Although expansions can accrue in non-dividing cells, we also show that cell cycle arrest is not sufficient to drive instability, implicating other factors as the key regulators of tissue-specific instability. Our data reveal that de novo expansion events are not limited to S-phase and further support a cell division-independent mutational pathway.
Collapse
Affiliation(s)
- Mário Gomes-Pereira
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK Inserm UMR 1163, Laboratory of CTG Repeat Instability and Myotonic Dystrophy Type 1, 75015 Paris, France Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
| | - James D Hilley
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Fernando Morales
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK Instituto de Investigaciones en Salud y Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica
| | - Berit Adam
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Helen E James
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| |
Collapse
|
241
|
Dion V. Tissue specificity in DNA repair: lessons from trinucleotide repeat instability. Trends Genet 2014; 30:220-9. [PMID: 24842550 DOI: 10.1016/j.tig.2014.04.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/14/2014] [Accepted: 04/16/2014] [Indexed: 12/13/2022]
Abstract
DNA must constantly be repaired to maintain genome stability. Although it is clear that DNA repair reactions depend on cell type and developmental stage, we know surprisingly little about the mechanisms that underlie this tissue specificity. This is due, in part, to the lack of adequate study systems. This review discusses recent progress toward understanding the mechanism leading to varying rates of instability at expanded trinucleotide repeats (TNRs) in different tissues. Although they are not DNA lesions, TNRs are hotspots for genome instability because normal DNA repair activities cause changes in repeat length. The rates of expansions and contractions are readily detectable and depend on cell identity, making TNR instability a particularly convenient model system. A better understanding of this type of genome instability will provide a foundation for studying tissue-specific DNA repair more generally, which has implications in cancer and other diseases caused by mutations in the caretakers of the genome.
Collapse
Affiliation(s)
- Vincent Dion
- University of Lausanne, Center for Integrative Genomics, Bâtiment Génopode, 1015 Lausanne, Switzerland.
| |
Collapse
|
242
|
Metsu S, Rooms L, Rainger J, Taylor MS, Bengani H, Wilson DI, Chilamakuri CSR, Morrison H, Vandeweyer G, Reyniers E, Douglas E, Thompson G, Haan E, Gecz J, FitzPatrick DR, Kooy RF. FRA2A is a CGG repeat expansion associated with silencing of AFF3. PLoS Genet 2014; 10:e1004242. [PMID: 24763282 PMCID: PMC3998887 DOI: 10.1371/journal.pgen.1004242] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 02/02/2014] [Indexed: 11/19/2022] Open
Abstract
Folate-sensitive fragile sites (FSFS) are a rare cytogenetically visible subset of dynamic mutations. Of the eight molecularly characterized FSFS, four are associated with intellectual disability (ID). Cytogenetic expression results from CGG tri-nucleotide-repeat expansion mutation associated with local CpG hypermethylation and transcriptional silencing. The best studied is the FRAXA site in the FMR1 gene, where large expansions cause fragile X syndrome, the most common inherited ID syndrome. Here we studied three families with FRA2A expression at 2q11 associated with a wide spectrum of neurodevelopmental phenotypes. We identified a polymorphic CGG repeat in a conserved, brain-active alternative promoter of the AFF3 gene, an autosomal homolog of the X-linked AFF2/FMR2 gene: Expansion of the AFF2 CGG repeat causes FRAXE ID. We found that FRA2A-expressing individuals have mosaic expansions of the AFF3 CGG repeat in the range of several hundred repeat units. Moreover, bisulfite sequencing and pyrosequencing both suggest AFF3 promoter hypermethylation. cSNP-analysis demonstrates monoallelic expression of the AFF3 gene in FRA2A carriers thus predicting that FRA2A expression results in functional haploinsufficiency for AFF3 at least in a subset of tissues. By whole-mount in situ hybridization the mouse AFF3 ortholog shows strong regional expression in the developing brain, somites and limb buds in 9.5–12.5dpc mouse embryos. Our data suggest that there may be an association between FRA2A and a delay in the acquisition of motor and language skills in the families studied here. However, additional cases are required to firmly establish a causal relationship. Some human genetic diseases are caused by dynamic mutations, or expansions of a short repeated sequence in the genome that can be unstably passed on from generation to generation. A subset of these dynamic mutations known as fragile sites can be seen as a break or gap on the chromosome when cells are cultured under specific conditions. To date eight folate-sensitive fragile sites (FSFS) have been characterized, and all are due to CGG-repeat expansions within the 5′ UTR or promoter region of the respective gene. When the repeat expands in size, it becomes hypermethylated and the adjacent gene or genes are transcriptionally silenced. For at least four of the eight known fragile sites this silencing of the associated gene(s) lead to intellectual disability syndromes such as fragile X. In this work we describe molecular characterization of an autosomal FSFS called FRA2A on chromosome 2. As the molecular cause of FRA2A, we identify an expansion of a CGG repeat which subsequently results in silencing of the neighbouring gene AFF3. This gene is one of the four autosomal paralogss of the AFF2/FMR2 gene which, when mutated, is the cause of the FRAXE syndrome. We find that FRA2A expression is associated with highly variable developmental anomalies in the three FRA2A families studied.
Collapse
Affiliation(s)
- Sofie Metsu
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Liesbeth Rooms
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Jacqueline Rainger
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Martin S. Taylor
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Hemant Bengani
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - David I. Wilson
- University of Southampton, Centre for Human Development, Stem Cells and Regeneration, Human Genetics, Southampton, United Kingdom
| | | | - Harris Morrison
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Edwin Reyniers
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Geoffrey Thompson
- Department of Paediatrics, The University of Adelaide, Adelaide, South Australia, Australia
- Department of Paediatrics and Child Health, Flinders University, Adelaide, South Australia, Australia
| | - Eric Haan
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- South Australian Clinical Genetic Service, SA Pathology (at Women's and Children's Hospital), Adelaide, South Australia, Australia
| | - Jozef Gecz
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Department of Paediatrics, The University of Adelaide, Adelaide, South Australia, Australia
| | - David R. FitzPatrick
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (DRF); (RFK)
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
- * E-mail: (DRF); (RFK)
| |
Collapse
|
243
|
Richard GF, Viterbo D, Khanna V, Mosbach V, Castelain L, Dujon B. Highly specific contractions of a single CAG/CTG trinucleotide repeat by TALEN in yeast. PLoS One 2014; 9:e95611. [PMID: 24748175 PMCID: PMC3991675 DOI: 10.1371/journal.pone.0095611] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 03/28/2014] [Indexed: 12/22/2022] Open
Abstract
Trinucleotide repeat expansions are responsible for more than two dozens severe neurological disorders in humans. A double-strand break between two short CAG/CTG trinucleotide repeats was formerly shown to induce a high frequency of repeat contractions in yeast. Here, using a dedicated TALEN, we show that induction of a double-strand break into a CAG/CTG trinucleotide repeat in heterozygous yeast diploid cells results in gene conversion of the repeat tract with near 100% efficacy, deleting the repeat tract. Induction of the same TALEN in homozygous yeast diploids leads to contractions of both repeats to a final length of 3–13 triplets, with 100% efficacy in cells that survived the double-strand breaks. Whole-genome sequencing of surviving yeast cells shows that the TALEN does not increase mutation rate. No other CAG/CTG repeat of the yeast genome showed any length alteration or mutation. No large genomic rearrangement such as aneuploidy, segmental duplication or translocation was detected. It is the first demonstration that induction of a TALEN in an eukaryotic cell leads to shortening of trinucleotide repeat tracts to lengths below pathological thresholds in humans, with 100% efficacy and very high specificity.
Collapse
Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, IFD, Paris, France
- CNRS, UMR3525, Paris, France
- * E-mail:
| | - David Viterbo
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, IFD, Paris, France
- CNRS, UMR3525, Paris, France
| | - Varun Khanna
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, IFD, Paris, France
- CNRS, UMR3525, Paris, France
| | - Valentine Mosbach
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, IFD, Paris, France
- CNRS, UMR3525, Paris, France
| | - Lauriane Castelain
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, IFD, Paris, France
- CNRS, UMR3525, Paris, France
| | - Bernard Dujon
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, IFD, Paris, France
- CNRS, UMR3525, Paris, France
| |
Collapse
|
244
|
Frizzell A, Nguyen JHG, Petalcorin MIR, Turner KD, Boulton SJ, Freudenreich CH, Lahue RS. RTEL1 inhibits trinucleotide repeat expansions and fragility. Cell Rep 2014; 6:827-35. [PMID: 24561255 PMCID: PMC5783307 DOI: 10.1016/j.celrep.2014.01.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 12/20/2013] [Accepted: 01/24/2014] [Indexed: 02/06/2023] Open
Abstract
Human RTEL1 is an essential, multifunctional helicase that maintains telomeres, regulates homologous recombination, and helps prevent bone marrow failure. Here, we show that RTEL1 also blocks trinucleotide repeat expansions, the causal mutation for 17 neurological diseases. Increased expansion frequencies of (CTG⋅CAG) repeats occurred in human cells following knockdown of RTEL1, but not the alternative helicase Fbh1, and purified RTEL1 efficiently unwound triplet repeat hairpins in vitro. The expansion-blocking activity of RTEL1 also required Rad18 and HLTF, homologs of yeast Rad18 and Rad5. These findings are reminiscent of budding yeast Srs2, which inhibits expansions, unwinds hairpins, and prevents triplet-repeat-induced chromosome fragility. Accordingly, we found expansions and fragility were suppressed in yeast srs2 mutants expressing RTEL1, but not Fbh1. We propose that RTEL1 serves as a human analog of Srs2 to inhibit (CTG⋅CAG) repeat expansions and fragility, likely by unwinding problematic hairpins.
Collapse
Affiliation(s)
- Aisling Frizzell
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Newcastle Road, Galway, Ireland
| | | | - Mark I R Petalcorin
- DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms EN6 3LD, UK
| | - Katherine D Turner
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Newcastle Road, Galway, Ireland; NCBES Galway Neuroscience Centre, National University of Ireland Galway, Newcastle Road, Galway, Ireland
| | - Simon J Boulton
- DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms EN6 3LD, UK
| | | | - Robert S Lahue
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Newcastle Road, Galway, Ireland; NCBES Galway Neuroscience Centre, National University of Ireland Galway, Newcastle Road, Galway, Ireland.
| |
Collapse
|
245
|
Abstract
Replication stress is a complex phenomenon that has serious implications for genome stability, cell survival and human disease. Generation of aberrant replication fork structures containing single-stranded DNA activates the replication stress response, primarily mediated by the kinase ATR (ATM- and Rad3-related). Along with its downstream effectors, ATR stabilizes and helps to restart stalled replication forks, avoiding the generation of DNA damage and genome instability. Understanding this response may be key to diagnosing and treating human diseases caused by defective responses to replication stress.
Collapse
Affiliation(s)
- Michelle K Zeman
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| |
Collapse
|
246
|
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
|
247
|
Kiechle FL, Arcenas RC, Rogers LC. Establishing benchmarks and metrics for disruptive technologies, inappropriate and obsolete tests in the clinical laboratory. Clin Chim Acta 2014; 427:131-6. [PMID: 23732401 PMCID: PMC7124233 DOI: 10.1016/j.cca.2013.05.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/24/2013] [Accepted: 05/25/2013] [Indexed: 12/31/2022]
Abstract
Benchmarks and metrics related to laboratory test utilization are based on evidence-based medical literature that may suffer from a positive publication bias. Guidelines are only as good as the data reviewed to create them. Disruptive technologies require time for appropriate use to be established before utilization review will be meaningful. Metrics include monitoring the use of obsolete tests and the inappropriate use of lab tests. Test utilization by clients in a hospital outreach program can be used to monitor the impact of new clients on lab workload. A multi-disciplinary laboratory utilization committee is the most effective tool for modifying bad habits, and reviewing and approving new tests for the lab formulary or by sending them out to a reference lab.
Collapse
Affiliation(s)
- Frederick L Kiechle
- Memorial Healthcare System, Pathology Consultants of South Broward, LLP, Department of Pathology, 3501 Johnson Street, Hollywood, FL 33021, USA.
| | | | | |
Collapse
|
248
|
Völker J, Plum GE, Gindikin V, Klump HH, Breslauer KJ. Impact of bulge loop size on DNA triplet repeat domains: Implications for DNA repair and expansion. Biopolymers 2014; 101:1-12. [PMID: 23494673 PMCID: PMC3920904 DOI: 10.1002/bip.22236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 03/05/2013] [Indexed: 11/12/2022]
Abstract
Repetitive DNA sequences exhibit complex structural and energy landscapes, populated by metastable, noncanonical states, that favor expansion and deletion events correlated with disease phenotypes. To probe the origins of such genotype-phenotype linkages, we report the impact of sequence and repeat number on properties of (CNG) repeat bulge loops. We find the stability of duplexes with a repeat bulge loop is controlled by two opposing effects; a loop junction-dependent destabilization of the underlying double helix, and a self-structure dependent stabilization of the repeat bulge loop. For small bulge loops, destabilization of the underlying double helix overwhelms any favorable contribution from loop self-structure. As bulge loop size increases, the stabilizing loop structure contribution dominates. The role of sequence on repeat loop stability can be understood in terms of its impact on the opposing influences of junction formation and loop structure. The nature of the bulge loop affects the thermodynamics of these two contributions differently, resulting in unique differences in repeat size-dependent minima in the overall enthalpy, entropy, and free energy changes. Our results define factors that control repeat bulge loop formation; knowledge required to understand how this helix imperfection is linked to DNA expansion, deletion, and disease phenotypes.
Collapse
Affiliation(s)
- Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers, The
State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
| | - G. Eric Plum
- IBET, Inc., 1507 Chambers Road, Suite 301, Columbus, OH
43212
| | - Vera Gindikin
- Department of Chemistry and Chemical Biology, Rutgers, The
State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
| | - Horst H. Klump
- Department of Molecular and Cell Biology,
University of Cape Town, Private Bag, Rondebosch 7800, South Africa
| | - Kenneth J. Breslauer
- Department of Chemistry and Chemical Biology, Rutgers, The
State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
- The Cancer Institute of New Jersey, New Brunswick,
NJ 08901
| |
Collapse
|
249
|
Abstract
Replication stress is a complex phenomenon that has serious implications for genome stability, cell survival and human disease. Generation of aberrant replication fork structures containing single-stranded DNA activates the replication stress response, primarily mediated by the kinase ATR (ATM- and Rad3-related). Along with its downstream effectors, ATR stabilizes and helps to restart stalled replication forks, avoiding the generation of DNA damage and genome instability. Understanding this response may be key to diagnosing and treating human diseases caused by defective responses to replication stress.
Collapse
Affiliation(s)
- Michelle K Zeman
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| |
Collapse
|
250
|
Concannon C, Lahue RS. Nucleotide excision repair and the 26S proteasome function together to promote trinucleotide repeat expansions. DNA Repair (Amst) 2014; 13:42-9. [DOI: 10.1016/j.dnarep.2013.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 11/26/2013] [Accepted: 11/30/2013] [Indexed: 10/25/2022]
|