151
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Kotsantis P, Jones RM, Higgs MR, Petermann E. Cancer therapy and replication stress: forks on the road to perdition. Adv Clin Chem 2015; 69:91-138. [PMID: 25934360 DOI: 10.1016/bs.acc.2014.12.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Deregulated DNA replication occurs in cancer where it contributes to genomic instability. This process is a target of cytotoxic therapies. Chemotherapies exploit high DNA replication in cancer cells by modifying the DNA template or by inhibiting vital enzymatic activities that lead to slowing or stalling replication fork progression. Stalled replication forks can be converted into toxic DNA double-strand breaks resulting in cell death, i.e., replication stress. While likely crucial for many cancer treatments, replication stress is poorly understood due to its complexity. While we still know relatively little about the role of replication stress in cancer therapy, technical advances in recent years have shed new light on the effect that cancer therapeutics have on replication forks and the molecular mechanisms that lead from obstructed fork progression to cell death. This chapter will give an overview of our current understanding of replication stress in the context of cancer therapy.
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Affiliation(s)
- Panagiotis Kotsantis
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Rebecca M Jones
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Martin R Higgs
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Eva Petermann
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.
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152
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Crossovers are associated with mutation and biased gene conversion at recombination hotspots. Proc Natl Acad Sci U S A 2015; 112:2109-14. [PMID: 25646453 DOI: 10.1073/pnas.1416622112] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Meiosis is a potentially important source of germline mutations, as sites of meiotic recombination experience recurrent double-strand breaks (DSBs). However, evidence for a local mutagenic effect of recombination from population sequence data has been equivocal, likely because mutation is only one of several forces shaping sequence variation. By sequencing large numbers of single crossover molecules obtained from human sperm for two recombination hotspots, we find direct evidence that recombination is mutagenic: Crossovers carry more de novo mutations than nonrecombinant DNA molecules analyzed for the same donors and hotspots. The observed mutations were primarily CG to TA transitions, with a higher frequency of transitions at CpG than non-CpGs sites. This enrichment of mutations at CpG sites at hotspots could predominate in methylated regions involving frequent single-stranded DNA processing as part of DSB repair. In addition, our data set provides evidence that GC alleles are preferentially transmitted during crossing over, opposing mutation, and shows that GC-biased gene conversion (gBGC) predominates over mutation in the sequence evolution of hotspots. These findings are consistent with the idea that gBGC could be an adaptation to counteract the mutational load of recombination.
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153
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Kuroda K, Hibi D, Ishii Y, Yokoo Y, Takasu S, Kijima A, Matsushita K, Masumura KI, Kodama Y, Yanai T, Sakai H, Nohmi T, Ogawa K, Umemura T. Role of p53 in the progression from ochratoxin A-induced DNA damage to gene mutations in the kidneys of mice. Toxicol Sci 2015; 144:65-76. [PMID: 25636497 DOI: 10.1093/toxsci/kfu267] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Carcinogenic doses of ochratoxin A (OTA) cause increases of mutant frequencies (MFs) of the red/gam gene (Spi(-)) in the kidneys of p53-deficient gpt delta mice, but not in p53-proficient mice. Here, we investigated the role of p53 in the progression from OTA-induced DNA damage to gene mutations. To this end, p53-proficient and -deficient mice were administered 5 mg/kg OTA for 3 days or 4 weeks by gavage. After 3 days of administration, comet assays were performed and there were no differences in the degrees of OTA-induced DNA damage between p53-proficient and -deficient mice. However, the frequencies of γ-H2AX-positive tubular epithelial cells in p53-deficient mice were significantly higher than those in p53-proficient mice, implying that p53 inhibited the progression from DNA damage to DNA double-strand breaks (DSBs). Evaluation of global gene expression and relevant mRNA/protein expression levels demonstrated that OTA increased the expression of Cdkn1a, which encodes the p21 protein, in p53-proficient mice, but not in p53-deficient mice. Moreover, in p53-deficient mice, mRNA levels of cell cycle progression and DSB repair (homologous recombination repair [HR])-related genes were significantly increased. Thus, G1/S arrest due to activation of the p53/p21 pathway may contribute to the prevention of DSBs in p53-proficient mice. In addition, single base deletions/insertions/substitutions were predominant, possibly due to HR. Overall, these results suggested that OTA induced DSBs at the carcinogenic target site in mice and that p53/p21-mediated cell cycle control prevented an increase in the formation of DSBs, leading to gene mutations.
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Affiliation(s)
- Ken Kuroda
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Daisuke Hibi
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Yuji Ishii
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Yuh Yokoo
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Shinji Takasu
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Aki Kijima
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Kohei Matsushita
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Ken-ichi Masumura
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Yukio Kodama
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Tokuma Yanai
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Hiroki Sakai
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Takehiko Nohmi
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Kumiko Ogawa
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Takashi Umemura
- *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan *Division of Pathology, Division of Genetics and Mutagenesis, Division of Toxicology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193 and Biological Safety Research Center, National Institute of Health Sciences, Tokyo 158-8501, Japan
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154
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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.
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Affiliation(s)
- Karen Usdin
- Laboratory of Cell and Molecular Biology, NIDDK, NIH , Bethesda, MD , USA
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155
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Rattray A, Santoyo G, Shafer B, Strathern JN. Elevated mutation rate during meiosis in Saccharomyces cerevisiae. PLoS Genet 2015; 11:e1004910. [PMID: 25569256 PMCID: PMC4287439 DOI: 10.1371/journal.pgen.1004910] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 11/21/2014] [Indexed: 02/04/2023] Open
Abstract
Mutations accumulate during all stages of growth, but only germ line mutations contribute to evolution. While meiosis contributes to evolution by reassortment of parental alleles, we show here that the process itself is inherently mutagenic. We have previously shown that the DNA synthesis associated with repair of a double-strand break is about 1000-fold less accurate than S-phase synthesis. Since the process of meiosis involves many programmed DSBs, we reasoned that this repair might also be mutagenic. Indeed, in the early 1960's Magni and Von Borstel observed elevated reversion of recessive alleles during meiosis, and found that the revertants were more likely to be associated with a crossover than non-revertants, a process that they called "the meiotic effect." Here we use a forward mutation reporter (CAN1 HIS3) placed at either a meiotic recombination coldspot or hotspot near the MAT locus on Chromosome III. We find that the increased mutation rate at CAN1 (6 to 21 -fold) correlates with the underlying recombination rate at the locus. Importantly, we show that the elevated mutation rate is fully dependent upon Spo11, the protein that introduces the meiosis specific DSBs. To examine associated recombination we selected for random spores with or without a mutation in CAN1. We find that the mutations isolated this way show an increased association with recombination (crossovers, loss of crossover interference and/or increased gene conversion tracts). Polζ appears to contribute about half of the mutations induced during meiosis, but is not the only source of mutations for the meiotic effect. We see no difference in either the spectrum or distribution of mutations between mitosis and meiosis. The correlation of hotspots with elevated mutagenesis provides a mechanism for organisms to control evolution rates in a gene specific manner.
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Affiliation(s)
- Alison Rattray
- Gene Regulation and Chromosome Biology Laboratory, NCI-Frederick, FNLCR, Frederick, Maryland, United States of America
| | - Gustavo Santoyo
- Gene Regulation and Chromosome Biology Laboratory, NCI-Frederick, FNLCR, Frederick, Maryland, United States of America
| | - Brenda Shafer
- Gene Regulation and Chromosome Biology Laboratory, NCI-Frederick, FNLCR, Frederick, Maryland, United States of America
| | - Jeffrey N. Strathern
- Gene Regulation and Chromosome Biology Laboratory, NCI-Frederick, FNLCR, Frederick, Maryland, United States of America
- * E-mail:
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156
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Anand RP, Tsaponina O, Greenwell PW, Lee CS, Du W, Petes TD, Haber JE. Chromosome rearrangements via template switching between diverged repeated sequences. Genes Dev 2014; 28:2394-406. [PMID: 25367035 PMCID: PMC4215184 DOI: 10.1101/gad.250258.114] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Anand et al. examined break-induced replication (BIR) and template switching between highly diverged sequences in S. cerevisiae, induced during repair of a site-specific double-strand break (DSB). Template switches between highly divergent sequences appear to be mechanistically distinct from the initial strand invasions that establish BIR. BIR traversing repeated DNA sequences frequently results in complex translocations analogous to those seen in mammalian cells. These results suggest that template switching among repeated genes is a potent driver of genome instability and evolution. Recent high-resolution genome analyses of cancer and other diseases have revealed the occurrence of microhomology-mediated chromosome rearrangements and copy number changes. Although some of these rearrangements appear to involve nonhomologous end-joining, many must have involved mechanisms requiring new DNA synthesis. Models such as microhomology-mediated break-induced replication (MM-BIR) have been invoked to explain these rearrangements. We examined BIR and template switching between highly diverged sequences in Saccharomyces cerevisiae, induced during repair of a site-specific double-strand break (DSB). Our data show that such template switches are robust mechanisms that give rise to complex rearrangements. Template switches between highly divergent sequences appear to be mechanistically distinct from the initial strand invasions that establish BIR. In particular, such jumps are less constrained by sequence divergence and exhibit a different pattern of microhomology junctions. BIR traversing repeated DNA sequences frequently results in complex translocations analogous to those seen in mammalian cells. These results suggest that template switching among repeated genes is a potent driver of genome instability and evolution.
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Affiliation(s)
- Ranjith P Anand
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, Massachusetts 02254, USA
| | - Olga Tsaponina
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, Massachusetts 02254, USA
| | - Patricia W Greenwell
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Cheng-Sheng Lee
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, Massachusetts 02254, USA
| | - Wei Du
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, Massachusetts 02254, USA
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - James E Haber
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, Massachusetts 02254, USA;
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157
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Extrachromosomal driver mutations in glioblastoma and low-grade glioma. Nat Commun 2014; 5:5690. [PMID: 25471132 PMCID: PMC4338529 DOI: 10.1038/ncomms6690] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 10/29/2014] [Indexed: 01/04/2023] Open
Abstract
Alteration of the number of copies of Double Minutes (DMs) with oncogenic EGFR mutations in response to tyrosine kinase inhibitors (TKIs) is a novel adaptive mechanism of glioblastoma. Here we provide evidence that such mutations in DMs, called here Amplification-Linked Extrachromosomal Mutations (ALEMs), originate extrachromosomally and could therefore be completely eliminated from the cancer cells. By exome sequencing of 7 glioblastoma patients we reveal ALEMs in EGFR, PDGFRA and other genes. These mutations together with DMs are lost by cancer cells in culture. We confirm the extrachromosomal origin of such mutations by showing that wild type and mutated DMs may coexist in the same tumor. Analysis of 4198 tumors suggests the presence of ALEMs across different tumor types with the highest prevalence in glioblastomas and low grade gliomas. The extrachromosomal nature of ALEMs explains the observed drastic changes in the amounts of mutated oncogenes (like EGFR or PDGFRA) in glioblastoma in response to environmental changes.
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158
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Vogt N, Gibaud A, Lemoine F, de la Grange P, Debatisse M, Malfoy B. Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma. Nucleic Acids Res 2014; 42:13194-205. [PMID: 25378339 PMCID: PMC4245956 DOI: 10.1093/nar/gku1101] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 01/18/2023] Open
Abstract
The mechanisms of gene amplification in tumour cells are poorly understood and the relationship between extrachromosomal DNA molecules, named double minutes (dmins), and intrachromosomal homogeneously staining regions (hsr) is not documented at nucleotide resolution. Using fluorescent in situ hybridization and whole genome sequencing, we studied a xenografted human oligodendroglioma where the co-amplification of the EGFR and MYC loci was present in the form of dmins at early passages and of an hsr at later passages. The amplified regions underwent multiple rearrangements and deletions during the formation of the dmins and their transformation into hsr. In both forms of amplification, non-homologous end-joining and microhomology-mediated end-joining rather than replication repair mechanisms prevailed in fusions. Small fragments, some of a few tens of base pairs, were associated in contigs. They came from clusters of breakpoints localized hundreds of kilobases apart in the amplified regions. The characteristics of some pairs of junctions suggest that at least some fragments were not fused randomly but could result from the concomitant repair of neighbouring breakpoints during the interaction of remote DNA sequences. This characterization at nucleotide resolution of the transition between extra- and intrachromosome amplifications highlights a hitherto uncharacterized organization of the amplified regions suggesting the involvement of new mechanisms in their formation.
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Affiliation(s)
- Nicolas Vogt
- Institut Curie, Centre de Recherche, F-75248 Paris, France CNRS, UMR3244, F-75248 Paris, France UPMC, F-75248 Paris, France
| | - Anne Gibaud
- Institut Curie, Centre de Recherche, F-75248 Paris, France CNRS, UMR3244, F-75248 Paris, France UPMC, F-75248 Paris, France
| | | | | | - Michelle Debatisse
- Institut Curie, Centre de Recherche, F-75248 Paris, France CNRS, UMR3244, F-75248 Paris, France UPMC, F-75248 Paris, France
| | - Bernard Malfoy
- Institut Curie, Centre de Recherche, F-75248 Paris, France CNRS, UMR3244, F-75248 Paris, France UPMC, F-75248 Paris, France
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159
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Franchitto A, Pichierri P. Replication fork recovery and regulation of common fragile sites stability. Cell Mol Life Sci 2014; 71:4507-17. [PMID: 25216703 PMCID: PMC11113654 DOI: 10.1007/s00018-014-1718-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
Abstract
The acquisition of genomic instability is a triggering factor in cancer development, and common fragile sites (CFS) are the preferential target of chromosomal instability under conditions of replicative stress in the human genome. Although the mechanisms leading to CFS expression and the cellular factors required to suppress CFS instability remain largely undefined, it is clear that DNA becomes more susceptible to breakage when replication is impaired. The models proposed so far to explain how CFS instability arises imply that replication fork progression along these regions is perturbed due to intrinsic features of fragile sites and events that directly affect DNA replication. The observation that proteins implicated in the safe recovery of stalled forks or in engaging recombination at collapsed forks increase CFS expression when downregulated or mutated suggests that the stabilization and recovery of perturbed replication forks are crucial to guarantee CFS integrity.
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Affiliation(s)
- Annapaola Franchitto
- Section of Molecular Epidemiology, Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy,
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160
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Abstract
A role for somatic mutations in carcinogenesis is well accepted, but the degree to which mutation rates influence cancer initiation and development is under continuous debate. Recently accumulated genomic data have revealed that thousands of tumour samples are riddled by hypermutation, broadening support for the idea that many cancers acquire a mutator phenotype. This major expansion of cancer mutation data sets has provided unprecedented statistical power for the analysis of mutation spectra, which has confirmed several classical sources of mutation in cancer, highlighted new prominent mutation sources (such as apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) enzymes) and empowered the search for cancer drivers. The confluence of cancer mutation genomics and mechanistic insight provides great promise for understanding the basic development of cancer through mutations.
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161
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Koren A, Handsaker RE, Kamitaki N, Karlić R, Ghosh S, Polak P, Eggan K, McCarroll SA. Genetic variation in human DNA replication timing. Cell 2014; 159:1015-1026. [PMID: 25416942 PMCID: PMC4359889 DOI: 10.1016/j.cell.2014.10.025] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 09/02/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022]
Abstract
Genomic DNA replicates in a choreographed temporal order that impacts the distribution of mutations along the genome. We show here that DNA replication timing is shaped by genetic polymorphisms that act in cis upon megabase-scale DNA segments. In genome sequences from proliferating cells, read depth along chromosomes reflected DNA replication activity in those cells. We used this relationship to analyze variation in replication timing among 161 individuals sequenced by the 1000 Genomes Project. Genome-wide association of replication timing with genetic variation identified 16 loci at which inherited alleles associate with replication timing. We call these "replication timing quantitative trait loci" (rtQTLs). rtQTLs involved the differential use of replication origins, exhibited allele-specific effects on replication timing, and associated with gene expression variation at megabase scales. Our results show replication timing to be shaped by genetic polymorphism and identify a means by which inherited polymorphism regulates the mutability of nearby sequences.
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Affiliation(s)
- Amnon Koren
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert E Handsaker
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rosa Karlić
- Bioinformatics Group, Division of Biology, Faculty of Science, Zagreb University, 10000 Zagreb, Croatia
| | - Sulagna Ghosh
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, The Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Paz Polak
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Cancer Center and Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, The Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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162
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Dosage changes of a segment at 17p13.1 lead to intellectual disability and microcephaly as a result of complex genetic interaction of multiple genes. Am J Hum Genet 2014; 95:565-78. [PMID: 25439725 DOI: 10.1016/j.ajhg.2014.10.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/03/2014] [Indexed: 11/24/2022] Open
Abstract
The 17p13.1 microdeletion syndrome is a recently described genomic disorder with a core clinical phenotype of intellectual disability, poor to absent speech, dysmorphic features, and a constellation of more variable clinical features, most prominently microcephaly. We identified five subjects with copy-number variants (CNVs) on 17p13.1 for whom we performed detailed clinical and molecular studies. Breakpoint mapping and retrospective analysis of published cases refined the smallest region of overlap (SRO) for microcephaly to a genomic interval containing nine genes. Dissection of this phenotype in zebrafish embryos revealed a complex genetic architecture: dosage perturbation of four genes (ASGR1, ACADVL, DVL2, and GABARAP) impeded neurodevelopment and decreased dosage of the same loci caused a reduced mitotic index in vitro. Moreover, epistatic analyses in vivo showed that dosage perturbations of discrete gene pairings induce microcephaly. Taken together, these studies support a model in which concomitant dosage perturbation of multiple genes within the CNV drive the microcephaly and possibly other neurodevelopmental phenotypes associated with rearrangements in the 17p13.1 SRO.
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163
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Le Guen T, Ragu S, Guirouilh-Barbat J, Lopez BS. Role of the double-strand break repair pathway in the maintenance of genomic stability. Mol Cell Oncol 2014; 2:e968020. [PMID: 27308383 PMCID: PMC4905226 DOI: 10.4161/23723548.2014.968020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 08/18/2014] [Indexed: 11/19/2022]
Abstract
DNA double-strand breaks (DSBs) are highly lethal lesions that jeopardize genome integrity. However, DSBs are also used to generate diversity during the physiological processes of meiosis or establishment of the immune repertoire. Therefore, DSB repair must be tightly controlled. Two main strategies are used to repair DSBs: homologous recombination (HR) and non-homologous end joining (NHEJ). HR is generally considered to be error-free, whereas NHEJ is considered to be error-prone. However, recent data challenge these assertions. Here, we present the molecular mechanisms involved in HR and NHEJ and the recently described alternative end-joining mechanism, which is exclusively mutagenic. Whereas NHEJ is not intrinsically error-prone but adaptable, HR has the intrinsic ability to modify the DNA sequence. Importantly, in both cases the initial structure of the DNA impacts the outcome. Finally, the consequences and applications of these repair mechanisms are discussed. Both HR and NHEJ are double-edged swords, essential for maintenance of genome stability and diversity but also able to generate genome instability.
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Affiliation(s)
- Tangui Le Guen
- Université Paris Sud; CNRS UMR 8200; Institut de Cancérologie Gustave-Roussy; Team labeled "Ligue 2014" ; Villejuif, France
| | - Sandrine Ragu
- Université Paris Sud; CNRS UMR 8200; Institut de Cancérologie Gustave-Roussy; Team labeled "Ligue 2014" ; Villejuif, France
| | - Josée Guirouilh-Barbat
- Université Paris Sud; CNRS UMR 8200; Institut de Cancérologie Gustave-Roussy; Team labeled "Ligue 2014" ; Villejuif, France
| | - Bernard S Lopez
- Université Paris Sud; CNRS UMR 8200; Institut de Cancérologie Gustave-Roussy; Team labeled "Ligue 2014" ; Villejuif, France
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164
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Prado F. Homologous recombination maintenance of genome integrity during DNA damage tolerance. Mol Cell Oncol 2014; 1:e957039. [PMID: 27308329 PMCID: PMC4905194 DOI: 10.4161/23723548.2014.957039] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 01/01/2023]
Abstract
The DNA strand exchange protein Rad51 provides a safe mechanism for the repair of DNA breaks using the information of a homologous DNA template. Homologous recombination (HR) also plays a key role in the response to DNA damage that impairs the advance of the replication forks by providing mechanisms to circumvent the lesion and fill in the tracks of single-stranded DNA that are generated during the process of lesion bypass. These activities postpone repair of the blocking lesion to ensure that DNA replication is completed in a timely manner. Experimental evidence generated over the last few years indicates that HR participates in this DNA damage tolerance response together with additional error-free (template switch) and error-prone (translesion synthesis) mechanisms through intricate connections, which are presented here. The choice between repair and tolerance, and the mechanism of tolerance, is critical to avoid increased mutagenesis and/or genome rearrangements, which are both hallmarks of cancer.
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Affiliation(s)
- Félix Prado
- Departamento de Biología Molecular; Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) ; Consejo Superior de Investigaciones Científicas (CSIC) ; Seville, Spain
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165
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Vasianovich Y, Harrington LA, Makovets S. Break-induced replication requires DNA damage-induced phosphorylation of Pif1 and leads to telomere lengthening. PLoS Genet 2014; 10:e1004679. [PMID: 25329304 PMCID: PMC4199488 DOI: 10.1371/journal.pgen.1004679] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/18/2014] [Indexed: 11/18/2022] Open
Abstract
Broken replication forks result in DNA breaks that are normally repaired via homologous recombination or break induced replication (BIR). Mild insufficiency in the replicative ligase Cdc9 in budding yeast Saccharomyces cerevisiae resulted in a population of cells with persistent DNA damage, most likely due to broken replication forks, constitutive activation of the DNA damage checkpoint and longer telomeres. This telomere lengthening required functional telomerase, the core DNA damage signaling cascade Mec1-Rad9-Rad53, and the components of the BIR repair pathway - Rad51, Rad52, Pol32, and Pif1. The Mec1-Rad53 induced phosphorylation of Pif1, previously found necessary for inhibition of telomerase at double strand breaks, was also important for the role of Pif1 in BIR and telomere elongation in cdc9-1 cells. Two other mutants with impaired DNA replication, cdc44-5 and rrm3Δ, were similar to cdc9-1: their long telomere phenotype was dependent on the Pif1 phosphorylation locus. We propose a model whereby the passage of BIR forks through telomeres promotes telomerase activity and leads to telomere lengthening.
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Affiliation(s)
- Yulia Vasianovich
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Lea A. Harrington
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, Montréal, Québec, Canada
| | - Svetlana Makovets
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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166
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Waters CE, Saldivar JC, Hosseini SA, Huebner K. The FHIT gene product: tumor suppressor and genome "caretaker". Cell Mol Life Sci 2014; 71:4577-87. [PMID: 25283145 DOI: 10.1007/s00018-014-1722-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 01/13/2023]
Abstract
The FHIT gene at FRA3B is one of the earliest and most frequently altered genes in the majority of human cancers. It was recently discovered that the FHIT gene is not the most fragile locus in epithelial cells, the cell of origin for most Fhit-negative cancers, eroding support for past claims that deletions at this locus are simply passenger events that are carried along in expanding cancer clones, due to extreme vulnerability to DNA damage rather than to loss of FHIT function. Indeed, recent reports have reconfirmed FHIT as a tumor suppressor gene with roles in apoptosis and prevention of the epithelial-mesenchymal transition. Other recent works have identified a novel role for the FHIT gene product, Fhit, as a genome "caretaker." Loss of this caretaker function leads to nucleotide imbalance, spontaneous replication stress, and DNA breaks. Because Fhit loss-induced DNA damage is "checkpoint blind," cells accumulate further DNA damage during subsequent cell cycles, accruing global genome instability that could facilitate oncogenic mutation acquisition and expedite clonal expansion. Loss of Fhit activity therefore induces a mutator phenotype. Evidence for FHIT as a mutator gene is discussed in light of these recent investigations of Fhit loss and subsequent genome instability.
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Affiliation(s)
- Catherine E Waters
- Biomedical Sciences Graduate Program, Ohio State University Wexner Medical Center, Columbus, OH, USA
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167
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Liu T, Huang J. Quality control of homologous recombination. Cell Mol Life Sci 2014; 71:3779-97. [PMID: 24858417 PMCID: PMC11114062 DOI: 10.1007/s00018-014-1649-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/09/2014] [Indexed: 12/21/2022]
Abstract
Exogenous and endogenous genotoxic agents, such as ionizing radiation and numerous chemical agents, cause DNA double-strand breaks (DSBs), which are highly toxic and lead to genomic instability or tumorigenesis if not repaired accurately and efficiently. Cells have over evolutionary time developed certain repair mechanisms in response to DSBs to maintain genomic integrity. Major DSB repair mechanisms include non-homologous end joining and homologous recombination (HR). Using sister homologues as templates, HR is a high-fidelity repair pathway that can rejoin DSBs without introducing mutations. However, HR execution without appropriate guarding may lead to more severe gross genome rearrangements. Here we review current knowledge regarding the factors and mechanisms required for accomplishment of accurate HR.
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Affiliation(s)
- Ting Liu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
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168
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Mehta A, Haber JE. Sources of DNA double-strand breaks and models of recombinational DNA repair. Cold Spring Harb Perspect Biol 2014; 6:a016428. [PMID: 25104768 PMCID: PMC4142968 DOI: 10.1101/cshperspect.a016428] [Citation(s) in RCA: 491] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA is subject to many endogenous and exogenous insults that impair DNA replication and proper chromosome segregation. DNA double-strand breaks (DSBs) are one of the most toxic of these lesions and must be repaired to preserve chromosomal integrity. Eukaryotes are equipped with several different, but related, repair mechanisms involving homologous recombination, including single-strand annealing, gene conversion, and break-induced replication. In this review, we highlight the chief sources of DSBs and crucial requirements for each of these repair processes, as well as the methods to identify and study intermediate steps in DSB repair by homologous recombination.
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Affiliation(s)
- Anuja Mehta
- Rosenstiel Basic Medical Sciences Research Center, MS029 Rosenstiel Center, Brandeis University, Waltham, Massachusetts 02454-9110
| | - James E Haber
- Rosenstiel Basic Medical Sciences Research Center, MS029 Rosenstiel Center, Brandeis University, Waltham, Massachusetts 02454-9110
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169
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Mawer JSP, Leach DRF. Branch migration prevents DNA loss during double-strand break repair. PLoS Genet 2014; 10:e1004485. [PMID: 25102287 PMCID: PMC4125073 DOI: 10.1371/journal.pgen.1004485] [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: 02/01/2014] [Accepted: 05/18/2014] [Indexed: 11/19/2022] Open
Abstract
The repair of DNA double-strand breaks must be accurate to avoid genomic rearrangements that can lead to cell death and disease. This can be accomplished by promoting homologous recombination between correctly aligned sister chromosomes. Here, using a unique system for generating a site-specific DNA double-strand break in one copy of two replicating Escherichia coli sister chromosomes, we analyse the intermediates of sister-sister double-strand break repair. Using two-dimensional agarose gel electrophoresis, we show that when double-strand breaks are formed in the absence of RuvAB, 4-way DNA (Holliday) junctions are accumulated in a RecG-dependent manner, arguing against the long-standing view that the redundancy of RuvAB and RecG is in the resolution of Holliday junctions. Using pulsed-field gel electrophoresis, we explain the redundancy by showing that branch migration catalysed by RuvAB and RecG is required for stabilising the intermediates of repair as, when branch migration cannot take place, repair is aborted and DNA is lost at the break locus. We demonstrate that in the repair of correctly aligned sister chromosomes, an unstable early intermediate is stabilised by branch migration. This reliance on branch migration may have evolved to help promote recombination between correctly aligned sister chromosomes to prevent genomic rearrangements. Genetic recombination is critically important for the repair of DNA double-strand breaks and is the only repair mechanism available to the bacterium Escherichia coli. Repair requires that the appropriate location on an unbroken sister chromosome is recognised as a repair template, and this can be accomplished by a system that detects the presence of extensive DNA sequence identity. We show here that the two known branch migration activities of the cell, RuvAB and RecG, provide alternative mechanisms for stabilising early recombination intermediates. In their absence, broken DNA is extensively degraded at the site of the break consistent with abortion of recombination. It has previously been proposed that RuvABC and RecG can substitute for each other in the resolution of four-way Holliday junctions, whereas we show that they play a synergistic role in the formations of these junctions. Our results demonstrate that branch migration provides a mechanism capable of stabilising recombination intermediates when extensive DNA sequence homology is available, a reaction that may contribute to ensuring that repair occurs at an appropriate location on a sister chromosome.
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Affiliation(s)
- Julia S. P. Mawer
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, Edinburgh, United Kingdom
| | - David R. F. Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, Edinburgh, United Kingdom
- * E-mail:
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170
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Tsaponina O, Haber JE. Frequent Interchromosomal Template Switches during Gene Conversion in S. cerevisiae. Mol Cell 2014; 55:615-25. [PMID: 25066232 DOI: 10.1016/j.molcel.2014.06.025] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/15/2014] [Accepted: 06/12/2014] [Indexed: 11/26/2022]
Abstract
Although repair of double-strand breaks (DSBs) by gene conversion is the most accurate way to repair such lesions, in budding yeast there is a 1,000-fold increase in accompanying mutations, including interchromosomal template switches (ICTS) involving highly mismatched (homeologous) ectopic sequences. Although such events are rare and appear at a rate of 2 × 10(-7) when template jumps occur between 71% identical sequences, they are surprisingly frequent (0.3% of all repair events) when the second template is identical to the first, revealing the remarkable instability of repair DNA synthesis. With homeologous donors, ICTS uses microhomologies as small as 2 bp. Cells lacking mismatch repair proteins Msh6 and Mlh1 form chimeric recombinants with two distinct patches of microhomology, implying that these proteins are crucial for strand discrimination of heteroduplex DNA formed during ICTS. We identify the chromatin remodeler Rdh54 as the first protein required for template switching that does not affect simple gene conversion.
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Affiliation(s)
- Olga Tsaponina
- Department of Biology, Brandeis University, Waltham, MA 02454-9110, USA; Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA
| | - James E Haber
- Department of Biology, Brandeis University, Waltham, MA 02454-9110, USA; Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA.
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171
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Meier B, Cooke SL, Weiss J, Bailly AP, Alexandrov LB, Marshall J, Raine K, Maddison M, Anderson E, Stratton MR, Gartner A, Campbell PJ. C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency. Genome Res 2014; 24:1624-36. [PMID: 25030888 PMCID: PMC4199376 DOI: 10.1101/gr.175547.114] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Mutation is associated with developmental and hereditary disorders, aging, and cancer. While we understand some mutational processes operative in human disease, most remain mysterious. We used Caenorhabditis elegans whole-genome sequencing to model mutational signatures, analyzing 183 worm populations across 17 DNA repair-deficient backgrounds propagated for 20 generations or exposed to carcinogens. The baseline mutation rate in C. elegans was approximately one per genome per generation, not overtly altered across several DNA repair deficiencies over 20 generations. Telomere erosion led to complex chromosomal rearrangements initiated by breakage–fusion–bridge cycles and completed by simultaneously acquired, localized clusters of breakpoints. Aflatoxin B1 induced substitutions of guanines in a GpC context, as observed in aflatoxin-induced liver cancers. Mutational burden increased with impaired nucleotide excision repair. Cisplatin and mechlorethamine, DNA crosslinking agents, caused dose- and genotype-dependent signatures among indels, substitutions, and rearrangements. Strikingly, both agents induced clustered rearrangements resembling “chromoanasynthesis,” a replication-based mutational signature seen in constitutional genomic disorders, suggesting that interstrand crosslinks may play a pathogenic role in such events. Cisplatin mutagenicity was most pronounced in xpf-1 mutants, suggesting that this gene critically protects cells against platinum chemotherapy. Thus, experimental model systems combined with genome sequencing can recapture and mechanistically explain mutational signatures associated with human disease.
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Affiliation(s)
- Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Susanna L Cooke
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Joerg Weiss
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Aymeric P Bailly
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom; CRBM/CNRS UMR5237, University of Montpellier, Montpellier 34293, France
| | - Ludmil B Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - John Marshall
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Mark Maddison
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Elizabeth Anderson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom;
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom; Department of Haematology, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
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172
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Abstract
Genetic instabilities, including mutations and chromosomal rearrangements, lead to cancer and other diseases in humans and play an important role in evolution. A frequent cause of genetic instabilities is double-strand DNA breaks (DSBs), which may arise from a wide range of exogeneous and endogeneous cellular factors. Although the repair of DSBs is required, some repair pathways are dangerous because they may destabilize the genome. One such pathway, break-induced replication (BIR), is the mechanism for repairing DSBs that possesses only one repairable end. This situation commonly arises as a result of eroded telomeres or collapsed replication forks. Although BIR plays a positive role in repairing DSBs, it can alternatively be a dangerous source of several types of genetic instabilities, including loss of heterozygosity, telomere maintenance in the absence of telomerase, and non-reciprocal translocations. Also, mutation rates in BIR are about 1000 times higher as compared to normal DNA replication. In addition, micro-homology-mediated BIR (MMBIR), which is a mechanism related to BIR, can generate copy-number variations (CNVs) as well as various complex chromosomal rearrangements. Overall, activation of BIR may contribute to genomic destabilization resulting in substantial biological consequences including those affecting human health.
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Affiliation(s)
| | | | - Anna Malkova
- Author to whom correspondence should be addressed; ; Tel.: +1-317-278-5717; Fax: +1-317-274-2946
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173
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Guirouilh-Barbat J, Lambert S, Bertrand P, Lopez BS. Is homologous recombination really an error-free process? Front Genet 2014; 5:175. [PMID: 24966870 PMCID: PMC4052342 DOI: 10.3389/fgene.2014.00175] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/23/2014] [Indexed: 11/13/2022] Open
Abstract
Homologous recombination (HR) is an evolutionarily conserved process that plays a pivotal role in the equilibrium between genetic stability and diversity. HR is commonly considered to be error-free, but several studies have shown that HR can be error-prone. Here, we discuss the actual accuracy of HR. First, we present the product of genetic exchanges (gene conversion, GC, and crossing over, CO) and the mechanisms of HR during double strand break repair and replication restart. We discuss the intrinsic capacities of HR to generate genome rearrangements by GC or CO, either during DSB repair or replication restart. During this process, abortive HR intermediates generate genetic instability and cell toxicity. In addition to genome rearrangements, HR also primes error-prone DNA synthesis and favors mutagenesis on single stranded DNA, a key DNA intermediate during the HR process. The fact that cells have developed several mechanisms protecting against HR excess emphasize its potential risks. Consistent with this duality, several pro-oncogenic situations have been consistently associated with either decreased or increased HR levels. Nevertheless, this versatility also has advantages that we outline here. We conclude that HR is a double-edged sword, which on one hand controls the equilibrium between genome stability and diversity but, on the other hand, can jeopardize the maintenance of genomic integrity. Therefore, whether non-homologous end joining (which, in contrast with HR, is not intrinsically mutagenic) or HR is the more mutagenic process is a question that should be re-evaluated. Both processes can be "Dr. Jekyll" in maintaining genome stability/variability and "Mr. Hyde" in jeopardizing genome integrity.
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Affiliation(s)
- Josée Guirouilh-Barbat
- CNRS, UMR 8200, Institut de Cancérologie Gustave Roussy, Équipe Labélisée, Université Paris-Sud, «LIGUE 2014» Villejuif, France
| | | | - Pascale Bertrand
- CEA DSV, UMR 967 CEA-INSERM-Université Paris Diderot-Université Paris Sud, Institut de Radiobiologie Cellulaire et Moléculaire Fontenay-aux-Roses, France
| | - Bernard S Lopez
- CNRS, UMR 8200, Institut de Cancérologie Gustave Roussy, Équipe Labélisée, Université Paris-Sud, «LIGUE 2014» Villejuif, France
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174
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Henninger EE, Pursell ZF. DNA polymerase ε and its roles in genome stability. IUBMB Life 2014; 66:339-51. [PMID: 24861832 DOI: 10.1002/iub.1276] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 05/02/2014] [Indexed: 12/14/2022]
Abstract
DNA Polymerase Epsilon (Pol ε) is one of three DNA Polymerases (along with Pol δ and Pol α) required for nuclear DNA replication in eukaryotes. Pol ε is comprised of four subunits, the largest of which is encoded by the POLE gene and contains the catalytic polymerase and exonuclease activities. The 3'-5' exonuclease proofreading activity is able to correct DNA synthesis errors and helps protect against genome instability. Recent cancer genome sequencing efforts have shown that 3% of colorectal and 7% of endometrial cancers contain mutations within the exonuclease domain of POLE and are associated with significantly elevated levels of single nucleotide substitutions (15-500 per Mb) and microsatellite stability. POLE mutations have also been found in other tumor types, though at lower frequency, suggesting roles in tumorigenesis more broadly in different tissue types. In addition to its proofreading activity, Pol ε contributes to genome stability through multiple mechanisms that are discussed in this review.
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Affiliation(s)
- Erin E Henninger
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
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175
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Magdalou I, Lopez BS, Pasero P, Lambert SAE. The causes of replication stress and their consequences on genome stability and cell fate. Semin Cell Dev Biol 2014; 30:154-64. [PMID: 24818779 DOI: 10.1016/j.semcdb.2014.04.035] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 04/29/2014] [Indexed: 01/28/2023]
Abstract
Alterations of the dynamics of DNA replication cause genome instability. These alterations known as "replication stress" have emerged as a major source of genomic instability in pre-neoplasic lesions, contributing to cancer development. The concept of replication stress covers a wide variety of events that distort the temporal and spatial DNA replication program. These events have endogenous or exogenous origins and impact globally or locally on the dynamics of DNA replication. They may arise within a short window of time (acute stress) or during each S phase (chronic stress). Here, we review the known situations in which the dynamics of DNA replication is distorted. We have united them in four main categories: (i) inadequate firing of replication origins (deficiency or excess), (ii) obstacles to fork progression, (iii) conflicts between replication and transcription and (iv) DNA replication under inappropriate metabolic conditions (unbalanced DNA replication). Because the DNA replication program is a process tightly regulated by many factors, replication stress often appears as a cascade of events. A local stress may prevent the completion of DNA replication at a single locus and subsequently compromise chromosome segregation in mitosis and therefore have a global effect on genome integrity. Finally, we discuss how replication stress drives genome instability and to what extent it is relevant to cancer biology.
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Affiliation(s)
- Indiana Magdalou
- Université Paris Sud, CNRS, UMR 8200 and Institut de Cancérologie Gustave Roussy, équipe labélisée «LIGUE 2014», Villejuif, France
| | - Bernard S Lopez
- Université Paris Sud, CNRS, UMR 8200 and Institut de Cancérologie Gustave Roussy, équipe labélisée «LIGUE 2014», Villejuif, France
| | - Philippe Pasero
- Institute of Human Genetics, CNRS UPR 1142, équipe labélisée LIGUE contre le Cancer, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Sarah A E Lambert
- Institut Curie, centre de recherche, CNRS UMR338, Bat 110, centre universitaire, 91405 Orsay, France.
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176
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Affiliation(s)
- Bénédicte Michel
- Centre de Génétique Moléculaire; CNRS; Gif sur Yvette France
- Université Paris-Sud; Orsay France
| | - Rolf Bernander
- Department of Molecular Biosciences; The Wenner-Gren Institute; Stockholm University; Stockholm Sweden
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177
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Vasan S, Deem A, Ramakrishnan S, Argueso JL, Malkova A. Cascades of genetic instability resulting from compromised break-induced replication. PLoS Genet 2014; 10:e1004119. [PMID: 24586181 PMCID: PMC3937135 DOI: 10.1371/journal.pgen.1004119] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 12/02/2013] [Indexed: 11/18/2022] Open
Abstract
Break-induced replication (BIR) is a mechanism to repair double-strand breaks (DSBs) that possess only a single end that can find homology in the genome. This situation can result from the collapse of replication forks or telomere erosion. BIR frequently produces various genetic instabilities including mutations, loss of heterozygosity, deletions, duplications, and template switching that can result in copy-number variations (CNVs). An important type of genomic rearrangement specifically linked to BIR is half-crossovers (HCs), which result from fusions between parts of recombining chromosomes. Because HC formation produces a fused molecule as well as a broken chromosome fragment, these events could be highly destabilizing. Here we demonstrate that HC formation results from the interruption of BIR caused by a damaged template, defective replisome or premature onset of mitosis. Additionally, we document that checkpoint failure promotes channeling of BIR into half-crossover-initiated instability cascades (HCC) that resemble cycles of non-reciprocal translocations (NRTs) previously described in human tumors. We postulate that HCs represent a potent source of genetic destabilization with significant consequences that mimic those observed in human diseases, including cancer.
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Affiliation(s)
- Soumini Vasan
- Department of Biology, School of Science, IUPUI, Indianapolis, Indiana, United States of America
| | - Angela Deem
- Department of Biology, School of Science, IUPUI, Indianapolis, Indiana, United States of America
| | - Sreejith Ramakrishnan
- Department of Biology, School of Science, IUPUI, Indianapolis, Indiana, United States of America
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences Colorado State University, Fort Collins, Colorado, United States of America
| | - Anna Malkova
- Department of Biology, School of Science, IUPUI, Indianapolis, Indiana, United States of America
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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178
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Prado F. Genetic instability is prevented by Mrc1-dependent spatio-temporal separation of replicative and repair activities of homologous recombination: homologous recombination tolerates replicative stress by Mrc1-regulated replication and repair activities operating at S and G2 in distinct subnuclear compartments. Bioessays 2014; 36:451-62. [PMID: 24615940 PMCID: PMC4312893 DOI: 10.1002/bies.201300161] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Homologous recombination (HR) is required to protect and restart stressed replication forks. Paradoxically, the Mrc1 branch of the S phase checkpoints, which is activated by replicative stress, prevents HR repair at breaks and arrested forks. Indeed, the mechanisms underlying HR can threaten genome integrity if not properly regulated. Thus, understanding how cells avoid genetic instability associated with replicative stress, a hallmark of cancer, is still a challenge. Here I discuss recent results that support a model by which HR responds to replication stress through replicative and repair activities that operate at different stages of the cell cycle (S and G2, respectively) and in distinct subnuclear structures. Remarkably, the replication checkpoint appears to control this scenario by inhibiting the assembly of HR repair centers at stressed forks during S phase, thereby avoiding genetic instability.
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Affiliation(s)
- Félix Prado
- Departamento de Biología Molecular, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
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179
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Template switching during break-induced replication is promoted by the Mph1 helicase in Saccharomyces cerevisiae. Genetics 2014; 196:1017-28. [PMID: 24496010 PMCID: PMC3982708 DOI: 10.1534/genetics.114.162297] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Chromosomal double-strand breaks (DSBs) that have only one end with homology to a donor duplex undergo repair by strand invasion followed by replication to the chromosome terminus (break-induced replication, BIR). Using a transformation-based assay system, it was previously shown that BIR could occur by several rounds of strand invasion, DNA synthesis, and dissociation. Here we describe a modification of the transformation-based assay to facilitate detection of switching between donor templates during BIR by genetic selection in diploid yeast. In addition to the expected recovery of template switch products, we found a high frequency of recombination between chromosome homologs during BIR, suggesting transfer of the DSB from the transforming linear DNA to the donor chromosome, initiating secondary recombination events. The frequency of BIR increased in the mph1Δ mutant, but the percentage of template switch events was significantly decreased, revealing an important role for Mph1 in promoting BIR-associated template switching. In addition, we show that the Mus81, Rad1, and Yen1 structure-selective nucleases act redundantly to facilitate BIR.
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180
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Chung WH. To peep into Pif1 helicase: multifaceted all the way from genome stability to repair-associated DNA synthesis. J Microbiol 2014; 52:89-98. [PMID: 24500472 DOI: 10.1007/s12275-014-3524-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 10/29/2013] [Indexed: 01/05/2023]
Abstract
Pif1 DNA helicase is the prototypical member of a 5' to 3' helicase superfamily conserved from bacteria to humans. In Saccharomyces cerevisiae, Pif1 and its homologue Rrm3, localize in both mitochondria and nucleus playing multiple roles in the maintenance of genomic homeostasis. They display relatively weak processivities in vitro, but have largely non-overlapping functions on common genomic loci such as mitochondrial DNA, telomeric ends, and many replication forks especially at hard-to-replicate regions including ribosomal DNA and G-quadruplex structures. Recently, emerging evidence shows that Pif1, but not Rrm3, has a significant new role in repair-associated DNA synthesis with Polδ during homologous recombination stimulating D-loop migration for conservative DNA replication. Comparative genetic and biochemical studies on the structure and function of Pif1 family helicases across different biological systems are further needed to elucidate both diversity and specificity of their mechanisms of action that contribute to genome stability.
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Affiliation(s)
- Woo-Hyun Chung
- College of Pharmacy, Duksung Women's University, Seoul, 132-714, Republic of Korea,
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181
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Abstract
In addition to environmental factors and intrinsic variations in base substitution rates, specific genome-destabilizing mutations can shape the mutational trajectory of genomes. How specific alleles influence the nature and position of accumulated mutations in a genomic context is largely unknown. Understanding the impact of genome-destabilizing alleles is particularly relevant to cancer genomes where biased mutational signatures are identifiable. We first created a more complete picture of cellular pathways that impact mutation rate using a primary screen to identify essential Saccharomyces cerevisiae gene mutations that cause mutator phenotypes. Drawing primarily on new alleles identified in this resource, we measure the impact of diverse mutator alleles on mutation patterns directly by whole-genome sequencing of 68 mutation-accumulation strains derived from wild-type and 11 parental mutator genotypes. The accumulated mutations differ across mutator strains, displaying base-substitution biases, allele-specific mutation hotspots, and break-associated mutation clustering. For example, in mutants of POLα and the Cdc13–Stn1–Ten1 complex, we find a distinct subtelomeric bias for mutations that we show is independent of the target sequence. Together our data suggest that specific genome-instability mutations are sufficient to drive discrete mutational signatures, some of which share properties with mutation patterns seen in tumors. Thus, in a population of cells, genome-instability mutations could influence clonal evolution by establishing discrete mutational trajectories for genomes.
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182
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Abstract
Recombination-dependent DNA replication, often called break-induced replication (BIR), was initially invoked to explain recombination events in bacteriophage but it has recently been recognized as a fundamentally important mechanism to repair double-strand chromosome breaks in eukaryotes. This mechanism appears to be critically important in the restarting of stalled and broken replication forks and in maintaining the integrity of eroded telomeres. Although BIR helps preserve genome integrity during replication, it also promotes genome instability by the production of loss of heterozygosity and the formation of nonreciprocal translocations, as well as in the generation of complex chromosomal rearrangements.
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Affiliation(s)
- Ranjith P Anand
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02254-9110
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183
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Rass U. Resolving branched DNA intermediates with structure-specific nucleases during replication in eukaryotes. Chromosoma 2013; 122:499-515. [PMID: 24008669 PMCID: PMC3827899 DOI: 10.1007/s00412-013-0431-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 08/03/2013] [Accepted: 08/08/2013] [Indexed: 11/29/2022]
Abstract
Genome duplication requires that replication forks track the entire length of every chromosome. When complications occur, homologous recombination-mediated repair supports replication fork movement and recovery. This leads to physical connections between the nascent sister chromatids in the form of Holliday junctions and other branched DNA intermediates. A key role in the removal of these recombination intermediates falls to structure-specific nucleases such as the Holliday junction resolvase RuvC in Escherichia coli. RuvC is also known to cut branched DNA intermediates that originate directly from blocked replication forks, targeting them for origin-independent replication restart. In eukaryotes, multiple structure-specific nucleases, including Mus81-Mms4/MUS81-EME1, Yen1/GEN1, and Slx1-Slx4/SLX1-SLX4 (FANCP) have been implicated in the resolution of branched DNA intermediates. It is becoming increasingly clear that, as a group, they reflect the dual function of RuvC in cleaving recombination intermediates and failing replication forks to assist the DNA replication process.
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Affiliation(s)
- Ulrich Rass
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland,
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184
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Carr AM, Lambert S. Replication stress-induced genome instability: the dark side of replication maintenance by homologous recombination. J Mol Biol 2013; 425:4733-44. [PMID: 23643490 DOI: 10.1016/j.jmb.2013.04.023] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 03/30/2013] [Accepted: 04/22/2013] [Indexed: 12/17/2022]
Abstract
Homologous recombination (HR) is an evolutionary-conserved mechanism involved in a subtle balance between genome stability and diversity. HR is a faithful DNA repair pathway and has been largely characterized in the context of double-strand break (DSB) repair. Recently, multiple functions for the HR machinery have been identified at arrested forks. These are evident across different organisms and include replication fork-stabilization and fork-restart functions. Interestingly, a DSB appears not to be a prerequisite for HR-mediated replication maintenance. HR has the ability to rebuild a replisome at inactivated forks, but perhaps surprisingly, the resulting replisome is liable to intrastrand and interstrand switches leading to replication errors. Here, we review our current understanding of the replication maintenance function of HR. The error proneness of these pathways leads us to suggest that the origin of replication-associated genome instability should be re-evaluated.
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Affiliation(s)
- Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
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185
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Kim N, Cho JE, Li YC, Jinks-Robertson S. RNA∶DNA hybrids initiate quasi-palindrome-associated mutations in highly transcribed yeast DNA. PLoS Genet 2013; 9:e1003924. [PMID: 24244191 PMCID: PMC3820800 DOI: 10.1371/journal.pgen.1003924] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/05/2013] [Indexed: 11/18/2022] Open
Abstract
RNase H enzymes promote genetic stability by degrading aberrant RNA∶DNA hybrids and by removing ribonucleotide monophosphates (rNMPs) that are present in duplex DNA. Here, we report that loss of RNase H2 in yeast is associated with mutations that extend identity between the arms of imperfect inverted repeats (quasi-palindromes or QPs), a mutation type generally attributed to a template switch during DNA synthesis. QP events were detected using frameshift-reversion assays and were only observed under conditions of high transcription. In striking contrast to transcription-associated short deletions that also are detected by these assays, QP events do not require Top1 activity. QP mutation rates are strongly affected by the direction of DNA replication and, in contrast to their elevation in the absence of RNase H2, are reduced when RNase H1 is additionally eliminated. Finally, transcription-associated QP events are limited by components of the nucleotide excision repair pathway and are promoted by translesion synthesis DNA polymerases. We suggest that QP mutations reflect either a transcription-associated perturbation of Okazaki-fragment processing, or the use of a nascent transcript to resume replication following a transcription-replication conflict. Mutation rates are correlated with the level of gene expression in budding yeast, demonstrating a link between transcription and stability of the underlying DNA template. In the current work, we describe a novel type of transcription-associated mutation that converts imperfect inverted repeats (quasi-palindromes or QPs) to perfect inverted repeats. Using appropriate mutation reporters, we demonstrate that QP mutations are strongly affected by the direction of DNA replication and have distinctive genetic requirements. Most notably, rates of transcription-associated QP events are regulated by the RNase H class of enzymes, which are specialized to process the RNA component of RNA∶DNA hybrids. The source of the RNA∶DNA hybrids that initiate QP mutations is unclear, but could reflect transcripts that remain stably base-paired with the DNA template, or aberrant processing of the RNA primers normally used to initiate DNA synthesis. These studies further expand the diverse ways that transcription affects the mutation landscape, and establish a novel way that RNA∶DNA hybrids can contribute to genetic instability. The high conservation of basic DNA-related metabolic processes suggests that results in yeast will be broadly applicable in higher eukaryotes.
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Affiliation(s)
- Nayun Kim
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jang-Eun Cho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Yue C. Li
- 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
- * E-mail:
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186
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Aze A, Zhou JC, Costa A, Costanzo V. DNA replication and homologous recombination factors: acting together to maintain genome stability. Chromosoma 2013; 122:401-13. [PMID: 23584157 DOI: 10.1007/s00412-013-0411-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/27/2013] [Accepted: 03/27/2013] [Indexed: 10/27/2022]
Abstract
Genome duplication requires the coordinated action of multiple proteins to ensure a fast replication with high fidelity. These factors form a complex called the Replisome, which is assembled onto the DNA duplex to promote its unwinding and to catalyze the polymerization of two new strands. Key constituents of the Replisome are the Cdc45-Mcm2-7-GINS helicase and the And1-Claspin-Tipin-Tim1 complex, which coordinate DNA unwinding with polymerase alpha-, delta-, and epsilon- dependent DNA polymerization. These factors encounter numerous obstacles, such as endogenous DNA lesions leading to template breakage and complex structures arising from intrinsic features of specific DNA sequences. To overcome these roadblocks, homologous recombination DNA repair factors, such as Rad51 and the Mre11-Rad50-Nbs1 complex, are required to ensure complete and faithful replication. Consistent with this notion, many of the genes involved in this process result in lethal phenotypes when inactivated in organisms with complex and large genomes. Here, we summarize the architectural and functional properties of the Replisome and propose a unified view of DNA replication and repair processes.
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Affiliation(s)
- Antoine Aze
- Clare Hall Laboratories, London Research Institute, South Mimms, Herts, EN63LD, UK
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187
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Replicative mechanisms for CNV formation are error prone. Nat Genet 2013; 45:1319-26. [PMID: 24056715 PMCID: PMC3821386 DOI: 10.1038/ng.2768] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 08/27/2013] [Indexed: 01/20/2023]
Abstract
We investigated 67 breakpoint junctions of gene copy number gains (CNVs) in 31 unrelated subjects. We observed a strikingly high frequency of small deletions and insertions (29%) apparently originating from polymerase-slippage events, in addition to frameshifts and point mutations in homonucleotide runs (13%), at or flanking the breakpoint junctions of complex CNVs. These simple nucleotide variants (SNV) were generated concomitantly with the de novo complex genomic rearrangement (CGR) event. Our findings implicate a low fidelity error-prone DNA polymerase in synthesis associated with DNA repair mechanisms that leads to a local increase in point mutation burden associated with human CGR.
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188
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Migrating bubble during break-induced replication drives conservative DNA synthesis. Nature 2013; 502:389-92. [PMID: 24025772 PMCID: PMC3804423 DOI: 10.1038/nature12584] [Citation(s) in RCA: 258] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 08/20/2013] [Indexed: 11/08/2022]
Abstract
The repair of chromosomal double strand breaks (DSBs) is crucial for the maintenance of genomic integrity. However, the repair of DSBs can also destabilize the genome by causing mutations and chromosomal rearrangements, the driving forces for carcinogenesis and hereditary diseases. Break-induced replication (BIR) is one of the DSB repair pathways that is highly prone to genetic instability. BIR proceeds by invasion of one broken end into a homologous DNA sequence followed by replication that can copy hundreds of kilobases of DNA from a donor molecule all the way through its telomere. The resulting repaired chromosome comes at a great cost to the cell, as BIR promotes mutagenesis, loss of heterozygosity, translocations, and copy number variations, all hallmarks of carcinogenesis. BIR uses most known replication proteins to copy large portions of DNA, similar to S-phase replication. It has therefore been suggested that BIR proceeds by semiconservative replication; however, the model of a bona fide, stable replication fork contradicts the known instabilities associated with BIR such as a 1,000-fold increase in mutation rate compared to normal replication. Here we demonstrate that in budding yeast the mechanism of replication during BIR is significantly different from S-phase replication, as it proceeds via an unusual bubble-like replication fork that results in conservative inheritance of the new genetic material. We provide evidence that this atypical mode of DNA replication, dependent on Pif1 helicase, is responsible for the marked increase in BIR-associated mutations. We propose that the BIR mode of synthesis presents a powerful mechanism that can initiate bursts of genetic instability in eukaryotes, including humans.
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189
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Shor E, Fox CA, Broach JR. The yeast environmental stress response regulates mutagenesis induced by proteotoxic stress. PLoS Genet 2013; 9:e1003680. [PMID: 23935537 PMCID: PMC3731204 DOI: 10.1371/journal.pgen.1003680] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/13/2013] [Indexed: 12/26/2022] Open
Abstract
Conditions of chronic stress are associated with genetic instability in many organisms, but the roles of stress responses in mutagenesis have so far been elucidated only in bacteria. Here, we present data demonstrating that the environmental stress response (ESR) in yeast functions in mutagenesis induced by proteotoxic stress. We show that the drug canavanine causes proteotoxic stress, activates the ESR, and induces mutagenesis at several loci in an ESR-dependent manner. Canavanine-induced mutagenesis also involves translesion DNA polymerases Rev1 and Polζ and non-homologous end joining factor Ku. Furthermore, under conditions of chronic sub-lethal canavanine stress, deletions of Rev1, Polζ, and Ku-encoding genes exhibit genetic interactions with ESR mutants indicative of ESR regulating these mutagenic DNA repair processes. Analyses of mutagenesis induced by several different stresses showed that the ESR specifically modulates mutagenesis induced by proteotoxic stress. Together, these results document the first known example of an involvement of a eukaryotic stress response pathway in mutagenesis and have important implications for mechanisms of evolution, carcinogenesis, and emergence of drug-resistant pathogens and chemotherapy-resistant tumors. Cellular capability to mutate its DNA plays an important role in evolution and impinges on medical issues, including acquisition of mutator phenotypes by cancer cells and emergence of drug-resistant pathogens. Whether and how the environment affects rates of mutation has been studied predominantly in the context of environmental agents that damage DNA (e.g. UV and γ-rays). However, it has been observed that conditions of chronic non-DNA-damaging stress (e.g. starvation or heat shock) also increase mutagenesis. It has been shown that in bacteria, activation of the general stress response activates a pro-mutagenic pathway and thus promotes mutagenesis during periods of stress. However, in eukaryotes, so far there has been no evidence of a stress response regulating mutagenesis. In this manuscript we demonstrate that in budding yeast, a model eukaryote, the general environmental stress response (ESR) regulates mutagenesis induced by proteotoxic stress (accumulation of unfolded proteins) at several loci. We also identify two pro-mutagenic DNA metabolic pathways that contribute to this mutagenesis and present genetic data showing that the ESR regulates these pathways. Together, these data advance our understanding of how cellular sensing and responding to environmental cues affect cellular capability for mutagenesis.
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Affiliation(s)
- Erika Shor
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - James R. Broach
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, United States of America
- * E-mail:
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190
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Break-induced replication: functions and molecular mechanism. Curr Opin Genet Dev 2013; 23:271-9. [PMID: 23790415 DOI: 10.1016/j.gde.2013.05.007] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 05/21/2013] [Accepted: 05/22/2013] [Indexed: 02/08/2023]
Abstract
Break-induced replication (BIR) is the pathway of homologous recombination (HR) conserved from phages to eukaryotes that serves to repair DNA breaks that have only one end. BIR contributes to the repair of broken replication forks and allows telomere lengthening in the absence of telomerase. Nonallelic BIR may lead to translocations and other chromosomal rearrangements. In addition, BIR initiated at sites of microhomology can generate copy number variations (CNVs) and complex chromosomal changes. The level of mutagenesis associated with DNA synthesis in BIR is significantly higher than during normal replication. These features make BIR a likely pathway to promote bursts of genetic changes that fuel cancer progression and evolution.
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191
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Saini N, Zhang Y, Nishida Y, Sheng Z, Choudhury S, Mieczkowski P, Lobachev KS. Fragile DNA motifs trigger mutagenesis at distant chromosomal loci in saccharomyces cerevisiae. PLoS Genet 2013; 9:e1003551. [PMID: 23785298 PMCID: PMC3681665 DOI: 10.1371/journal.pgen.1003551] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 04/23/2013] [Indexed: 11/19/2022] Open
Abstract
DNA sequences capable of adopting non-canonical secondary structures have been associated with gross-chromosomal rearrangements in humans and model organisms. Previously, we have shown that long inverted repeats that form hairpin and cruciform structures and triplex-forming GAA/TTC repeats induce the formation of double-strand breaks which trigger genome instability in yeast. In this study, we demonstrate that breakage at both inverted repeats and GAA/TTC repeats is augmented by defects in DNA replication. Increased fragility is associated with increased mutation levels in the reporter genes located as far as 8 kb from both sides of the repeats. The increase in mutations was dependent on the presence of inverted or GAA/TTC repeats and activity of the translesion polymerase Polζ. Mutagenesis induced by inverted repeats also required Sae2 which opens hairpin-capped breaks and initiates end resection. The amount of breakage at the repeats is an important determinant of mutations as a perfect palindromic sequence with inherently increased fragility was also found to elevate mutation rates even in replication-proficient strains. We hypothesize that the underlying mechanism for mutagenesis induced by fragile motifs involves the formation of long single-stranded regions in the broken chromosome, invasion of the undamaged sister chromatid for repair, and faulty DNA synthesis employing Polζ. These data demonstrate that repeat-mediated breaks pose a dual threat to eukaryotic genome integrity by inducing chromosomal aberrations as well as mutations in flanking genes.
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Affiliation(s)
- Natalie Saini
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America,
| | - Yu Zhang
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America,
| | - Yuri Nishida
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America,
| | - Ziwei Sheng
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America,
| | - Shilpa Choudhury
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America,
| | - Piotr Mieczkowski
- Department of Genetics, School of Medicine, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kirill S. Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America,
- * E-mail:
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192
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Abstract
Mutations stimulate evolutionary change and lead to birth defects and cancer in humans as well as to antibiotic resistance in bacteria. According to the classic view, most mutations arise in dividing cells and result from uncorrected errors of S-phase DNA replication, which is highly accurate because of the involvement of selective DNA polymerases and efficient error-correcting mechanisms. In contrast, studies in bacteria and yeast reveal that DNA synthesis associated with repair of double-strand chromosomal breaks (DSBs) by homologous recombination is highly inaccurate, thus making DSBs and their repair an important source of mutations. Different error-prone mechanisms appear to operate in different repair scenarios. In the filling in of single-stranded DNA regions, error-prone translesion DNA polymerases appear to produce most errors. In contrast, in gene conversion gap repair and in break-induced replication, errors are independent of translesion polymerases, and many mutations have the signatures of template switching during DNA repair synthesis. DNA repair also appears to create complex copy-number variants. Overall, homologous recombination, which is traditionally considered a safe pathway of DSB repair, is an important source of mutagenesis that may contribute to human disease and evolution.
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Affiliation(s)
- Anna Malkova
- Department of Biology, School of Science, IUPUI, Indianapolis, Indiana 46202-5132, USA.
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193
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Gaillard H, Herrera-Moyano E, Aguilera A. Transcription-associated genome instability. Chem Rev 2013; 113:8638-61. [PMID: 23597121 DOI: 10.1021/cr400017y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hélène Gaillard
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla , Av. Américo Vespucio s/n, 41092 Seville, Spain
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194
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Lambert S, Carr AM. Replication stress and genome rearrangements: lessons from yeast models. Curr Opin Genet Dev 2013; 23:132-9. [PMID: 23267817 DOI: 10.1016/j.gde.2012.11.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 11/10/2012] [Accepted: 11/16/2012] [Indexed: 10/27/2022]
Abstract
Replication failures induced by replication fork barriers (RFBs) or global replication stress generate many of the chromosome rearrangement (CR) observed in human genomic disorders and cancer. RFBs have multiple causes and cells protect themselves from the consequences of RFBs using three general strategies: preventing expression of RFB activity, stabilising the arrested replisome and, in the case of replisome failure, shielding the fork DNA to allow rebuilding of the replisome. Yeast models provide powerful tools to understand the cellular response to RFBs, delineate pathways that suppress genome instability and define mechanisms by which CRs occur when these fail. Recent progress has identified key features underlying RFBs activity and is beginning to uncover the DNA dynamics that bring about genome instability.
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195
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Mizuno K, Miyabe I, Schalbetter S, Carr AM, Murray JM. Recombination-restarted replication makes inverted chromosome fusions at inverted repeats. Nature 2013; 493:246-9. [PMID: 23178809 PMCID: PMC3605775 DOI: 10.1038/nature11676] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 10/15/2012] [Indexed: 01/24/2023]
Abstract
Impediments to DNA replication are known to induce gross chromosomal rearrangements (GCRs) and copy-number variations (CNVs). GCRs and CNVs underlie human genomic disorders and are a feature of cancer. During cancer development, environmental factors and oncogene-driven proliferation promote replication stress. Resulting GCRs and CNVs are proposed to contribute to cancer development and therapy resistance. When stress arrests replication, the replisome remains associated with the fork DNA (stalled fork) and is protected by the inter-S-phase checkpoint. Stalled forks efficiently resume when the stress is relieved. However, if the polymerases dissociate from the fork (fork collapse) or the fork structure breaks (broken fork), replication restart can proceed either by homologous recombination or microhomology-primed re-initiation. Here we ascertain the consequences of replication with a fork restarted by homologous recombination in fission yeast. We identify a new mechanism of chromosomal rearrangement through the observation that recombination-restarted forks have a considerably high propensity to execute a U-turn at small inverted repeats (up to 1 in 40 replication events). We propose that the error-prone nature of restarted forks contributes to the generation of GCRs and gene amplification in cancer, and to non-recurrent CNVs in genomic disorders.
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Affiliation(s)
- Ken’Ichi Mizuno
- Genome Damage and Stability Centre, University of Sussex, Brighton, East Sussex, BN1 9RQ, United Kingdom
| | - Izumi Miyabe
- Genome Damage and Stability Centre, University of Sussex, Brighton, East Sussex, BN1 9RQ, United Kingdom
| | - Stephanie Schalbetter
- Genome Damage and Stability Centre, University of Sussex, Brighton, East Sussex, BN1 9RQ, United Kingdom
| | - Antony M. Carr
- Genome Damage and Stability Centre, University of Sussex, Brighton, East Sussex, BN1 9RQ, United Kingdom
| | - Johanne M. Murray
- Genome Damage and Stability Centre, University of Sussex, Brighton, East Sussex, BN1 9RQ, United Kingdom
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196
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Costes A, Lambert SAE. Homologous recombination as a replication fork escort: fork-protection and recovery. Biomolecules 2012; 3:39-71. [PMID: 24970156 PMCID: PMC4030885 DOI: 10.3390/biom3010039] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/11/2012] [Accepted: 12/11/2012] [Indexed: 01/03/2023] Open
Abstract
Homologous recombination is a universal mechanism that allows DNA repair and ensures the efficiency of DNA replication. The substrate initiating the process of homologous recombination is a single-stranded DNA that promotes a strand exchange reaction resulting in a genetic exchange that promotes genetic diversity and DNA repair. The molecular mechanisms by which homologous recombination repairs a double-strand break have been extensively studied and are now well characterized. However, the mechanisms by which homologous recombination contribute to DNA replication in eukaryotes remains poorly understood. Studies in bacteria have identified multiple roles for the machinery of homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving the homologous recombination machinery to support the robustness of DNA replication. In addition to its role in fork-recovery and in rebuilding a functional replication fork apparatus, homologous recombination may also act as a fork-protection mechanism. We discuss that some of the fork-escort functions of homologous recombination might be achieved by loading of the recombination machinery at inactivated forks without a need for a strand exchange step; as well as the consequence of such a model for the stability of eukaryotic genomes.
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Affiliation(s)
- Audrey Costes
- Institut Curie, Centre de Recherche, CNRS, UMR3348, Centre Universitaire, Bat110, 91405, Orsay, France.
| | - Sarah A E Lambert
- Institut Curie, Centre de Recherche, CNRS, UMR3348, Centre Universitaire, Bat110, 91405, Orsay, France.
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197
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Waisertreiger ISR, Liston VG, Menezes MR, Kim HM, Lobachev KS, Stepchenkova EI, Tahirov TH, Rogozin IB, Pavlov YI. Modulation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:699-724. [PMID: 23055184 PMCID: PMC3893020 DOI: 10.1002/em.21735] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/13/2012] [Accepted: 08/15/2012] [Indexed: 06/01/2023]
Abstract
The rate of mutations in eukaryotes depends on a plethora of factors and is not immediately derived from the fidelity of DNA polymerases (Pols). Replication of chromosomes containing the anti-parallel strands of duplex DNA occurs through the copying of leading and lagging strand templates by a trio of Pols α, δ and ϵ, with the assistance of Pol ζ and Y-family Pols at difficult DNA template structures or sites of DNA damage. The parameters of the synthesis at a given location are dictated by the quality and quantity of nucleotides in the pools, replication fork architecture, transcription status, regulation of Pol switches, and structure of chromatin. The result of these transactions is a subject of survey and editing by DNA repair.
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Affiliation(s)
- Irina S.-R. Waisertreiger
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Victoria G. Liston
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Miriam R. Menezes
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Hyun-Min Kim
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Kirill S. Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Elena I. Stepchenkova
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Saint Petersburg Branch of Vavilov Institute of General Genetics, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
| | - Tahir H. Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Igor B. Rogozin
- National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, U.S.A
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | - Youri. I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
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198
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Saldivar JC, Miuma S, Bene J, Hosseini SA, Shibata H, Sun J, Wheeler LJ, Mathews CK, Huebner K. Initiation of genome instability and preneoplastic processes through loss of Fhit expression. PLoS Genet 2012; 8:e1003077. [PMID: 23209436 PMCID: PMC3510054 DOI: 10.1371/journal.pgen.1003077] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 09/25/2012] [Indexed: 12/27/2022] Open
Abstract
Genomic instability drives tumorigenesis, but how it is initiated in sporadic neoplasias is unknown. In early preneoplasias, alterations at chromosome fragile sites arise due to DNA replication stress. A frequent, perhaps earliest, genetic alteration in preneoplasias is deletion within the fragile FRA3B/FHIT locus, leading to loss of Fhit protein expression. Because common chromosome fragile sites are exquisitely sensitive to replication stress, it has been proposed that their clonal alterations in cancer cells are due to stress sensitivity rather than to a selective advantage imparted by loss of expression of fragile gene products. Here, we show in normal, transformed, and cancer-derived cell lines that Fhit-depletion causes replication stress-induced DNA double-strand breaks. Using DNA combing, we observed a defect in replication fork progression in Fhit-deficient cells that stemmed primarily from fork stalling and collapse. The likely mechanism for the role of Fhit in replication fork progression is through regulation of Thymidine kinase 1 expression and thymidine triphosphate pool levels; notably, restoration of nucleotide balance rescued DNA replication defects and suppressed DNA breakage in Fhit-deficient cells. Depletion of Fhit did not activate the DNA damage response nor cause cell cycle arrest, allowing continued cell proliferation and ongoing chromosomal instability. This finding was in accord with in vivo studies, as Fhit knockout mouse tissue showed no evidence of cell cycle arrest or senescence yet exhibited numerous somatic DNA copy number aberrations at replication stress-sensitive loci. Furthermore, cells established from Fhit knockout tissue showed rapid immortalization and selection of DNA deletions and amplifications, including amplification of the Mdm2 gene, suggesting that Fhit loss-induced genome instability facilitates transformation. We propose that loss of Fhit expression in precancerous lesions is the first step in the initiation of genomic instability, linking alterations at common fragile sites to the origin of genome instability. Normal cells have robust mechanisms to maintain the proper sequence of their DNA; in cancer cells these mechanisms are compromised, resulting in complex changes in the DNA of tumors. How this genome instability begins has not been defined, except in cases of familial cancers, which often have mutations in genes called “caretaker” genes, necessary to preserve DNA stability. We have defined a mechanism for genome instability in non-familial tumors that occur sporadically in the population. Certain fragile regions of our DNA are more difficult to duplicate during cell division and are prone to breakage. A fragile region, FRA3B, lies within the FHIT gene, and deletions within FRA3B are common in precancer cells, causing loss of Fhit protein expression. We find that loss of Fhit protein causes defective DNA replication, leading to further DNA breaks. Cells that continue DNA replication in the absence of Fhit develop numerous chromosomal aberrations. Importantly, cells established from tissues of mice that are missing Fhit undergo selection for increasing DNA alterations that can promote immortality, a cancer cell hallmark. Thus, loss of Fhit expression in precancer cells is the first step in the initiation of genomic instability and facilitates cancer development.
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Affiliation(s)
- Joshua C Saldivar
- Biomedical Sciences Graduate Program, Ohio State University, Columbus, Ohio, United States of America
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199
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Tang W, Dominska M, Gawel M, Greenwell PW, Petes TD. Genomic deletions and point mutations induced in Saccharomyces cerevisiae by the trinucleotide repeats (GAA·TTC) associated with Friedreich's ataxia. DNA Repair (Amst) 2012. [PMID: 23182423 DOI: 10.1016/j.dnarep.2012.10.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Expansion of certain trinucleotide repeats causes several types of human diseases, and such tracts are associated with the formation of deletions and other types of genetic rearrangements in Escherichia coli, yeast, and mammalian cells. Below, we show that long (230 repeats) tracts of the trinucleotide associated with Friedreich's ataxia (GAA·TTC) stimulate both large (>50 bp) deletions and point mutations in a reporter gene located more than 1 kb from the repetitive tract. Sequence analysis of deletion breakpoints indicates that the deletions reflect non-homologous end joining of double-stranded DNA breaks (DSBs) initiated in the tract. The tract-induced point mutations appear to reflect a different mechanism involving single-strand annealing of DNA molecules generated by DSBs within the tract, followed by filling-in of single-stranded gaps by the error-prone DNA polymerase zeta.
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Affiliation(s)
- Wei Tang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
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200
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Microhomology directs diverse DNA break repair pathways and chromosomal translocations. PLoS Genet 2012; 8:e1003026. [PMID: 23144625 PMCID: PMC3493447 DOI: 10.1371/journal.pgen.1003026] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/24/2012] [Indexed: 11/23/2022] Open
Abstract
Chromosomal structural change triggers carcinogenesis and the formation of other genetic diseases. The breakpoint junctions of these rearrangements often contain small overlapping sequences called “microhomology,” yet the genetic pathway(s) responsible have yet to be defined. We report a simple genetic system to detect microhomology-mediated repair (MHMR) events after a DNA double-strand break (DSB) in budding yeast cells. MHMR using >15 bp operates as a single-strand annealing variant, requiring the non-essential DNA polymerase subunit Pol32. MHMR is inhibited by sequence mismatches, but independent of extensive DNA synthesis like break-induced replication. However, MHMR using less than 14 bp is genetically distinct from that using longer microhomology and far less efficient for the repair of distant DSBs. MHMR catalyzes chromosomal translocation almost as efficiently as intra-chromosomal repair. The results suggest that the intrinsic annealing propensity between microhomology sequences efficiently leads to chromosomal rearrangements. Cancer results from an accumulation of mutations that transform a normal cell into one that proliferates uncontrollably. DNA double-strand breaks (DSBs) can lead to genetic mutations and chromosome rearrangements, underscoring the importance of functional DNA DSB repair pathways in the maintenance of chromosome integrity and tumor suppression. Ample evidence suggests that cells possess multiple DSB repair mechanisms with distinct mutational potentials, and one or more of these pathways is likely responsible for the formation of chromosomal translocations. Importantly, at the junctions of many rearrangements, small (2–20 bp in length) overlapping sequences from each of the original sequences, termed “microhomology,” are found, and they may provide a clue as to how these rearrangements form. Here, we describe our genetic investigation into how flanking microhomology influences the type and frequency of DSB repair. We also show that microhomology-mediated repair (MHMR) efficiently induces chromosomal translocations. This research provides a basic understanding of the mechanisms that utilize microhomology for mutagenic repair.
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