1
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Herrick J. DNA Damage, Genome Stability, and Adaptation: A Question of Chance or Necessity? Genes (Basel) 2024; 15:520. [PMID: 38674454 PMCID: PMC11049855 DOI: 10.3390/genes15040520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/14/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
DNA damage causes the mutations that are the principal source of genetic variation. DNA damage detection and repair mechanisms therefore play a determining role in generating the genetic diversity on which natural selection acts. Speciation, it is commonly assumed, occurs at a rate set by the level of standing allelic diversity in a population. The process of speciation is driven by a combination of two evolutionary forces: genetic drift and ecological selection. Genetic drift takes place under the conditions of relaxed selection, and results in a balance between the rates of mutation and the rates of genetic substitution. These two processes, drift and selection, are necessarily mediated by a variety of mechanisms guaranteeing genome stability in any given species. One of the outstanding questions in evolutionary biology concerns the origin of the widely varying phylogenetic distribution of biodiversity across the Tree of Life and how the forces of drift and selection contribute to shaping that distribution. The following examines some of the molecular mechanisms underlying genome stability and the adaptive radiations that are associated with biodiversity and the widely varying species richness and evenness in the different eukaryotic lineages.
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Affiliation(s)
- John Herrick
- Independent Researcher at 3, Rue des Jeûneurs, 75002 Paris, France
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2
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Malzl D, Peycheva M, Rahjouei A, Gnan S, Klein KN, Nazarova M, Schoeberl UE, Gilbert DM, Buonomo SCB, Di Virgilio M, Neumann T, Pavri R. RIF1 regulates early replication timing in murine B cells. Nat Commun 2023; 14:8049. [PMID: 38081811 PMCID: PMC10713614 DOI: 10.1038/s41467-023-43778-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The mammalian DNA replication timing (RT) program is crucial for the proper functioning and integrity of the genome. The best-known mechanism for controlling RT is the suppression of late origins of replication in heterochromatin by RIF1. Here, we report that in antigen-activated, hypermutating murine B lymphocytes, RIF1 binds predominantly to early-replicating active chromatin and promotes early replication, but plays a minor role in regulating replication origin activity, gene expression and genome organization in B cells. Furthermore, we find that RIF1 functions in a complementary and non-epistatic manner with minichromosome maintenance (MCM) proteins to establish early RT signatures genome-wide and, specifically, to ensure the early replication of highly transcribed genes. These findings reveal additional layers of regulation within the B cell RT program, driven by the coordinated activity of RIF1 and MCM proteins.
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Affiliation(s)
- Daniel Malzl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Lazarettgasse 14, Vienna, Austria
| | - Mihaela Peycheva
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Lazarettgasse 14, Vienna, Austria
| | - Ali Rahjouei
- Max-Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Stefano Gnan
- School of Biological Sciences, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Kyle N Klein
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Mariia Nazarova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
| | - Ursula E Schoeberl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Sara C B Buonomo
- School of Biological Sciences, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Michela Di Virgilio
- Max-Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria.
- Quantro Therapeutics, Vienna Biocenter, 1030, Vienna, Austria.
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria.
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3
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Pokusaeva VO, Diez AR, Espinar L, Pérez AT, Filion GJ. Strand asymmetry influences mismatch resolution during a single-strand annealing. Genome Biol 2022; 23:93. [PMID: 35414014 PMCID: PMC9001825 DOI: 10.1186/s13059-022-02665-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/30/2022] [Indexed: 02/08/2023] Open
Abstract
Background Biases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. The molecular mechanisms of those biases are still poorly understood because it is difficult to isolate the contributions of DNA repair from those of DNA damage. Results Here, we develop a genome-wide assay whereby the same DNA lesion is repaired in different genomic contexts. We insert thousands of barcoded transposons carrying a reporter of DNA mismatch repair in the genome of mouse embryonic stem cells. Upon inducing a double-strand break between tandem repeats, a mismatch is generated if the break is repaired through single-strand annealing. The resolution of the mismatch showed a 60–80% bias in favor of the strand with the longest 3′ flap. The location of the lesion in the genome and the type of mismatch had little influence on the bias. Instead, we observe a complete reversal of the bias when the longest 3′ flap is moved to the opposite strand by changing the position of the double-strand break in the reporter. Conclusions These results suggest that the processing of the double-strand break has a major influence on the repair of mismatches during a single-strand annealing. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02665-3.
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Affiliation(s)
- Victoria O Pokusaeva
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Present Address: Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
| | - Aránzazu Rosado Diez
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Present Address: H12O-CNIO Lung Cancer Clinical Research Unit, i + 12 Research Institute, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Lorena Espinar
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Albert Torelló Pérez
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Guillaume J Filion
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,University Pompeu Fabra (UPF), Barcelona, Spain. .,Present Address: Department Biological Sciences, University of Toronto Scarborough, Toronto, Canada.
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4
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Foss EJ, Sripathy S, Gatbonton-Schwager T, Kwak H, Thiesen AH, Lao U, Bedalov A. Chromosomal Mcm2-7 distribution and the genome replication program in species from yeast to humans. PLoS Genet 2021; 17:e1009714. [PMID: 34473702 PMCID: PMC8443269 DOI: 10.1371/journal.pgen.1009714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 09/15/2021] [Accepted: 07/13/2021] [Indexed: 01/24/2023] Open
Abstract
The spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome at the onset of S-phase, and by differences in the timing of activation of these complexes during S phase. To determine the degree to which distribution of pre-RC loading alone could account for chromosomal replication patterns, we mapped the binding sites of the Mcm2-7 helicase complex (MCM) in budding yeast, fission yeast, mouse and humans. We observed similar individual MCM double-hexamer (DH) footprints across the species, but notable differences in their distribution: Footprints in budding yeast were more sharply focused compared to the other three organisms, consistent with the relative sequence specificity of replication origins in S. cerevisiae. Nonetheless, with some clear exceptions, most notably the inactive X-chromosome, much of the fluctuation in replication timing along the chromosomes in all four organisms reflected uneven chromosomal distribution of pre-replication complexes. Gene-rich regions of the genome tend to replicate earlier in S phase than do repetitive and other non-genic regions. This may be an evolutionary consequence of the fact that replication later in S phase is associated with higher frequencies of mutation and genome rearrangement. Replication timing along the chromosome is determined by 1) events prior to S-phase that specify the locations where DNA replication can be initiated, referred to as origin licensing; and 2) the timing of activation of these licensed origins during S-phase, referred to as origin firing. To determine the relative importance of these two mechanisms, here we identify both the binding sites and the abundance of a key component of the origin licensing machinery in budding yeast, fission yeast, mice, and humans, namely the replicative helicase complex. We discovered that, with a few notable exceptions, which include the inactive X chromosome in mammals, the program of replication timing can be largely explained simply on the basis of origin licensing. Our results support a model for replication timing that emphasizes stochastic firing of origins that have been licensed before S phase begins.
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Affiliation(s)
- Eric J. Foss
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Smitha Sripathy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Tonibelle Gatbonton-Schwager
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Hyunchang Kwak
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Adam H. Thiesen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Uyen Lao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Antonio Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Medicine, Department of Biochemistry, University of Washington, Seattle Washington, United States of America
- * E-mail:
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5
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Replication Stress, Genomic Instability, and Replication Timing: A Complex Relationship. Int J Mol Sci 2021; 22:ijms22094764. [PMID: 33946274 PMCID: PMC8125245 DOI: 10.3390/ijms22094764] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022] Open
Abstract
The replication-timing program constitutes a key element of the organization and coordination of numerous nuclear processes in eukaryotes. This program is established at a crucial moment in the cell cycle and occurs simultaneously with the organization of the genome, thus indicating the vital significance of this process. With recent technological achievements of high-throughput approaches, a very strong link has been confirmed between replication timing, transcriptional activity, the epigenetic and mutational landscape, and the 3D organization of the genome. There is also a clear relationship between replication stress, replication timing, and genomic instability, but the extent to which they are mutually linked to each other is unclear. Recent evidence has shown that replication timing is affected in cancer cells, although the cause and consequence of this effect remain unknown. However, in-depth studies remain to be performed to characterize the molecular mechanisms of replication-timing regulation and clearly identify different cis- and trans-acting factors. The results of these studies will potentially facilitate the discovery of new therapeutic pathways, particularly for personalized medicine, or new biomarkers. This review focuses on the complex relationship between replication timing, replication stress, and genomic instability.
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6
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Němečková A, Koláčková V, Vrána J, Doležel J, Hřibová E. DNA replication and chromosome positioning throughout the interphase in three-dimensional space of plant nuclei. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6262-6272. [PMID: 32805034 DOI: 10.1093/jxb/eraa370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/31/2020] [Indexed: 05/23/2023]
Abstract
Despite much recent progress, our understanding of the principles of plant genome organization and its dynamics in three-dimensional space of interphase nuclei remains surprisingly limited. Notably, it is not clear how these processes could be affected by the size of a plant's nuclear genome. In this study, DNA replication timing and interphase chromosome positioning were analyzed in seven Poaceae species that differ in their genome size. To provide a comprehensive picture, a suite of advanced, complementary methods was used: labeling of newly replicated DNA by ethynyl-2'-deoxyuridine, isolation of nuclei at particular cell cycle phases by flow cytometric sorting, three-dimensional immunofluorescence in situ hybridization, and confocal microscopy. Our results revealed conserved dynamics of DNA replication in all species, and a similar replication timing order for telomeres and centromeres, as well as for euchromatin and heterochromatin regions, irrespective of genome size. Moreover, stable chromosome positioning was observed while transitioning through different stages of interphase. These findings expand upon earlier studies in suggesting that a more complex interplay exists between genome size, organization of repetitive DNA sequences along chromosomes, and higher order chromatin structure and its maintenance in interphase, albeit controlled by currently unknown factors.
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Affiliation(s)
- Alžběta Němečková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Veronika Koláčková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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7
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Hulke ML, Siefert JC, Sansam CL, Koren A. Germline Structural Variations Are Preferential Sites of DNA Replication Timing Plasticity during Development. Genome Biol Evol 2019; 11:1663-1678. [PMID: 31076752 PMCID: PMC6582765 DOI: 10.1093/gbe/evz098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2019] [Indexed: 02/06/2023] Open
Abstract
The DNA replication timing program is modulated throughout development and is also one of the main factors influencing the distribution of mutation rates across the genome. However, the relationship between the mutagenic influence of replication timing and its developmental plasticity remains unexplored. Here, we studied the distribution of copy number variations (CNVs) and single nucleotide polymorphisms across the zebrafish genome in relation to changes in DNA replication timing during embryonic development in this model vertebrate species. We show that CNV sites exhibit strong replication timing plasticity during development, replicating significantly early during early development but significantly late during more advanced developmental stages. Reciprocally, genomic regions that changed their replication timing during development contained a higher proportion of CNVs than developmentally constant regions. Developmentally plastic CNV sites, in particular those that become delayed in their replication timing, were enriched for the clustered protocadherins, a set of genes important for neuronal development that have undergone extensive genetic and epigenetic diversification during zebrafish evolution. In contrast, single nucleotide polymorphism sites replicated consistently early throughout embryonic development, highlighting a unique aspect of the zebrafish genome. Our results uncover a hitherto unrecognized interface between development and evolution.
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Affiliation(s)
- Michelle L Hulke
- Department of Molecular Biology and Genetics, Cornell University
| | - Joseph C Siefert
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation.,Department of Cell Biology, University of Oklahoma Health Sciences Center
| | - Christopher L Sansam
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation.,Department of Cell Biology, University of Oklahoma Health Sciences Center
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University
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8
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Gaboriaud J, Wu PYJ. Insights into the Link between the Organization of DNA Replication and the Mutational Landscape. Genes (Basel) 2019; 10:genes10040252. [PMID: 30934791 PMCID: PMC6523204 DOI: 10.3390/genes10040252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 12/17/2022] Open
Abstract
The generation of a complete and accurate copy of the genetic material during each cell cycle is integral to cell growth and proliferation. However, genetic diversity is essential for adaptation and evolution, and the process of DNA replication is a fundamental source of mutations. Genome alterations do not accumulate randomly, with variations in the types and frequencies of mutations that arise in different genomic regions. Intriguingly, recent studies revealed a striking link between the mutational landscape of a genome and the spatial and temporal organization of DNA replication, referred to as the replication program. In our review, we discuss how this program may contribute to shaping the profile and spectrum of genetic alterations, with implications for genome dynamics and organismal evolution in natural and pathological contexts.
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Affiliation(s)
- Julia Gaboriaud
- CNRS, University of Rennes, Institute of Genetics and Development of Rennes, 35043 Rennes, France.
| | - Pei-Yun Jenny Wu
- CNRS, University of Rennes, Institute of Genetics and Development of Rennes, 35043 Rennes, France.
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9
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Duan C, Huan Q, Chen X, Wu S, Carey LB, He X, Qian W. Reduced intrinsic DNA curvature leads to increased mutation rate. Genome Biol 2018; 19:132. [PMID: 30217230 PMCID: PMC6138893 DOI: 10.1186/s13059-018-1525-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/05/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers our ability to identify positive selection in evolution and to identify driver mutations in tumorigenesis. RESULTS Here, we use a combination of synthetic genes and sequences of thousands of isolated yeast colonies to show that intrinsic DNA curvature is a major cis determinant of mutation rate. Mutation rate negatively correlates with DNA curvature within genes, and a 10% decrease in curvature results in a 70% increase in mutation rate. Consistently, both yeast and humans accumulate mutations in regions with small curvature. We further show that this effect is due to differences in the intrinsic mutation rate, likely due to differences in mutagen sensitivity and not due to differences in the local activity of DNA repair. CONCLUSIONS Our study establishes a framework for understanding the cis properties of DNA sequence in modulating the local mutation rate and identifies a novel causal source of non-uniform mutation rates across the genome.
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Affiliation(s)
- Chaorui Duan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Huan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoshu Chen
- Human Genome Research Institute and Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shaohuan Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lucas B Carey
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Xionglei He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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10
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Gillingham D, Sauter B. Genomic Studies Reveal New Aspects of the Biology of DNA Damaging Agents. Chembiochem 2017; 18:2368-2375. [PMID: 28972683 DOI: 10.1002/cbic.201700520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Indexed: 12/25/2022]
Abstract
A flurry of papers has appeared recently to force a rethinking of our understanding of how chemicals, light, and metal complexes damage our genomes. Conventional wisdom was that damaging agents were indiscriminate and it was statistical bad luck, coupled with evolutionary selection, that drove mutational signatures after exposure of DNA to damaging agents. Recent data, however, suggests that primary DNA damage itself does not drive mutational signatures; instead, it is the selectivity of repair pathways on different regions of the genome that is decisive. In particular, genomic regions shielded by transcription factors or packed densely in nucleosomes are poorly repaired by nucleotide excision repair and are far more susceptible to mutation. There are plenty of approved therapies, the mode-of-action of which is to alkylate DNA, and although historically efforts have been focused on understanding how chemicals modify DNA, these new findings suggest that focus should be shifted to understanding genome-wide repair specificities when different types of alkylation damage occur.
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Affiliation(s)
- Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Basilius Sauter
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
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11
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Blumenfeld B, Ben-Zimra M, Simon I. Perturbations in the Replication Program Contribute to Genomic Instability in Cancer. Int J Mol Sci 2017; 18:E1138. [PMID: 28587102 PMCID: PMC5485962 DOI: 10.3390/ijms18061138] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/08/2017] [Accepted: 05/21/2017] [Indexed: 12/14/2022] Open
Abstract
Cancer and genomic instability are highly impacted by the deoxyribonucleic acid (DNA) replication program. Inaccuracies in DNA replication lead to the increased acquisition of mutations and structural variations. These inaccuracies mainly stem from loss of DNA fidelity due to replication stress or due to aberrations in the temporal organization of the replication process. Here we review the mechanisms and impact of these major sources of error to the replication program.
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Affiliation(s)
- Britny Blumenfeld
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| | - Micha Ben-Zimra
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
- Pharmacology and Experimental Therapeutics Unit, The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel.
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.
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12
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Seplyarskiy VB, Bazykin GA, Soldatov RA. Polymerase ζ Activity Is Linked to Replication Timing in Humans: Evidence from Mutational Signatures. Mol Biol Evol 2015; 32:3158-72. [PMID: 26376651 DOI: 10.1093/molbev/msv184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Replication timing is an important determinant of germline mutation patterns, with a higher rate of point mutations in late replicating regions. Mechanisms underlying this association remain elusive. One of the suggested explanations is the activity of error-prone DNA polymerases in late-replicating regions. Polymerase zeta (pol ζ), an essential error-prone polymerase biased toward transversions, also has a tendency to produce dinucleotide mutations (DNMs), complex mutational events that simultaneously affect two adjacent nucleotides. Experimental studies have shown that pol ζ is strongly biased toward GC→AA/TT DNMs. Using primate divergence data, we show that the GC→AA/TT pol ζ mutational signature is the most frequent among DNMs, and its rate exceeds the mean rate of other DNM types by a factor of approximately 10. Unlike the overall rate of DNMs, the pol ζ signature drastically increases with the replication time in the human genome. Finally, the pol ζ signature is enriched in transcribed regions, and there is a strong prevalence of GC→TT over GC→AA DNMs on the nontemplate strand, indicating association with transcription. A recurrently occurring GC→TT DNM in HRAS and SOD1 genes causes the Costello syndrome and amyotrophic lateral sclerosis correspondently; we observe an approximately 1 kb long mutation hotspot enriched by transversions near these DNMs in both cases, suggesting a link between these diseases and pol ζ activity. This study uncovers the genomic preferences of pol ζ, shedding light on a novel cause of mutational heterogeneity along the genome.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia
| | - Georgii A Bazykin
- Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ruslan A Soldatov
- Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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13
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Lubelsky Y, Prinz JA, DeNapoli L, Li Y, Belsky JA, MacAlpine DM. DNA replication and transcription programs respond to the same chromatin cues. Genome Res 2015; 24:1102-14. [PMID: 24985913 PMCID: PMC4079966 DOI: 10.1101/gr.160010.113] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA replication is a dynamic process that occurs in a temporal order along each of the chromosomes. A consequence of the temporally coordinated activation of replication origins is the establishment of broad domains (>100 kb) that replicate either early or late in S phase. This partitioning of the genome into early and late replication domains is important for maintaining genome stability, gene dosage, and epigenetic inheritance; however, the molecular mechanisms that define and establish these domains are poorly understood. The modENCODE Project provided an opportunity to investigate the chromatin features that define the Drosophila replication timing program in multiple cell lines. The majority of early and late replicating domains in the Drosophila genome were static across all cell lines; however, a small subset of domains was dynamic and exhibited differences in replication timing between the cell lines. Both origin selection and activation contribute to defining the DNA replication program. Our results suggest that static early and late replicating domains were defined at the level of origin selection (ORC binding) and likely mediated by chromatin accessibility. In contrast, dynamic domains exhibited low ORC densities in both cell types, suggesting that origin activation and not origin selection governs the plasticity of the DNA replication program. Finally, we show that the male-specific early replication of the X chromosome is dependent on the dosage compensation complex (DCC), suggesting that the transcription and replication programs respond to the same chromatin cues. Specifically, MOF-mediated hyperacetylation of H4K16 on the X chromosome promotes both the up-regulation of male-specific transcription and origin activation.
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Affiliation(s)
- Yoav Lubelsky
- Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Joseph A Prinz
- Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Leyna DeNapoli
- Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Yulong Li
- Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Jason A Belsky
- Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - David M MacAlpine
- Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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14
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Abstract
Mutational heterogeneity must be taken into account when reconstructing evolutionary histories, calibrating molecular clocks, and predicting links between genes and disease. Selective pressures and various DNA transactions have been invoked to explain the heterogeneous distribution of genetic variation between species, within populations, and in tissue-specific tumors. To examine relationships between such heterogeneity and variations in leading- and lagging-strand replication fidelity and mismatch repair, we accumulated 40,000 spontaneous mutations in eight diploid yeast strains in the absence of selective pressure. We found that replicase error rates vary by fork direction, coding state, nucleosome proximity, and sequence context. Further, error rates and DNA mismatch repair efficiency both vary by mismatch type, responsible polymerase, replication time, and replication origin proximity. Mutation patterns implicate replication infidelity as one driver of variation in somatic and germline evolution, suggest mechanisms of mutual modulation of genome stability and composition, and predict future observations in specific cancers.
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15
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Makunin IV, Kolesnikova TD, Andreyenkova NG. Underreplicated regions in Drosophila melanogaster are enriched with fast-evolving genes and highly conserved noncoding sequences. Genome Biol Evol 2014; 6:2050-60. [PMID: 25062918 PMCID: PMC4159006 DOI: 10.1093/gbe/evu156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Many late replicating regions are underreplicated in polytene chromosomes of Drosophila melanogaster. These regions contain silenced chromatin and overlap long syntenic blocks of conserved gene order in drosophilids. In this report we show that in D. melanogaster the underreplicated regions are enriched with fast-evolving genes lacking homologs in distant species such as mosquito or human, indicating that the phylogenetic conservation of genes correlates with replication timing and chromatin status. Drosophila genes without human homologs located in the underreplicated regions have higher nonsynonymous substitution rate and tend to encode shorter proteins when compared with those in the adjacent regions. At the same time, the underreplicated regions are enriched with ultraconserved elements and highly conserved noncoding sequences, especially in introns of very long genes indicating the presence of an extensive regulatory network that may be responsible for the conservation of gene order in these regions. The regions have a modest preference for long noncoding RNAs but are depleted for small nucleolar RNAs, microRNAs, and transfer RNAs. Our results demonstrate that the underreplicated regions have a specific genic composition and distinct pattern of evolution.
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Affiliation(s)
- Igor V Makunin
- Research Computing Centre, The University of Queensland, St Lucia, Queensland, AustraliaInstitute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatyana D Kolesnikova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaNovosibirsk State University, Russia
| | - Natalya G Andreyenkova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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16
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Sima J, Gilbert DM. Complex correlations: replication timing and mutational landscapes during cancer and genome evolution. Curr Opin Genet Dev 2014; 25:93-100. [PMID: 24598232 DOI: 10.1016/j.gde.2013.11.022] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/29/2013] [Indexed: 12/23/2022]
Abstract
A recent flurry of reports correlates replication timing (RT) with mutation rates during both evolution and cancer. Specifically, point mutations and copy number losses correlate with late replication, while copy number gains and other rearrangements correlate with early replication. In some cases, plausible mechanisms have been proposed. Point mutation rates may reflect temporal variation in repair mechanisms. Transcription-induced double-strand breaks are expected to occur in transcriptionally active early replicating chromatin. Fusion partners are generally in close proximity, and chromatin in close proximity replicates at similar times. However, temporal enrichment of copy number gains and losses remains an enigma. Moreover, many conclusions are compromised by a lack of matched RT and sequence datasets, the filtering out of developmental variation in RT, and the use of somatic cell lines to make inferences about germline evolution.
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Affiliation(s)
- Jiao Sima
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
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17
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Andreyenkova NG, Kolesnikova TD, Makunin IV, Pokholkova GV, Boldyreva LV, Zykova TY, Zhimulev IF, Belyaeva ES. Late replication domains are evolutionary conserved in the Drosophila genome. PLoS One 2013; 8:e83319. [PMID: 24391753 PMCID: PMC3877026 DOI: 10.1371/journal.pone.0083319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 11/01/2013] [Indexed: 12/20/2022] Open
Abstract
Drosophila chromosomes are organized into distinct domains differing in their predominant chromatin composition, replication timing and evolutionary conservation. We show on a genome-wide level that genes whose order has remained unaltered across 9 Drosophila species display late replication timing and frequently map to the regions of repressive chromatin. This observation is consistent with the existence of extensive domains of repressive chromatin that replicate extremely late and have conserved gene order in the Drosophila genome. We suggest that such repressive chromatin domains correspond to a handful of regions that complete replication at the very end of S phase. We further demonstrate that the order of genes in these regions is rarely altered in evolution. Substantial proportion of such regions significantly coincide with large synteny blocks. This indicates that there are evolutionary mechanisms maintaining the integrity of these late-replicating chromatin domains. The synteny blocks corresponding to the extremely late-replicating regions in the D. melanogaster genome consistently display two-fold lower gene density across different Drosophila species.
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Affiliation(s)
- Natalya G. Andreyenkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatyana D. Kolesnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Igor V. Makunin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Research Computing Centre, The University of Queensland, Brisbane, St Lucia, QLD, Australia
| | - Galina V. Pokholkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lidiya V. Boldyreva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatyana Yu. Zykova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Igor F. Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- * E-mail:
| | - Elena S. Belyaeva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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18
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Juan D, Rico D, Marques-Bonet T, Fernández-Capetillo Ó, Valencia A. Late-replicating CNVs as a source of new genes. Biol Open 2013; 2:1402-11. [PMID: 24285712 PMCID: PMC3863426 DOI: 10.1242/bio.20136924] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 10/23/2013] [Indexed: 01/09/2023] Open
Abstract
Asynchronous replication of the genome has been associated with different rates of point mutation and copy number variation (CNV) in human populations. Here, our aim was to investigate whether the bias in the generation of CNV that is associated with DNA replication timing might have conditioned the birth of new protein-coding genes during evolution. We show that genes that were duplicated during primate evolution are more commonly found among the human genes located in late-replicating CNV regions. We traced the relationship between replication timing and the evolutionary age of duplicated genes. Strikingly, we found that there is a significant enrichment of evolutionary younger duplicates in late-replicating regions of the human and mouse genome. Indeed, the presence of duplicates in late-replicating regions gradually decreases as the evolutionary time since duplication extends. Our results suggest that the accumulation of recent duplications in late-replicating CNV regions is an active process influencing genome evolution.
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Affiliation(s)
- David Juan
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Daniel Rico
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Tomas Marques-Bonet
- Institut Catala de Recerca i Estudis Avancats (ICREA) and Institut de Biologia Evolutiva (UPF/CSIC), Dr Aiguader 88, PRBB, 08003 Barcelona, Spain
| | - Óscar Fernández-Capetillo
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Alfonso Valencia
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Center (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
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19
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Hawkins M, Retkute R, Müller CA, Saner N, Tanaka TU, de Moura APS, Nieduszynski CA. High-resolution replication profiles define the stochastic nature of genome replication initiation and termination. Cell Rep 2013; 5:1132-41. [PMID: 24210825 PMCID: PMC3898788 DOI: 10.1016/j.celrep.2013.10.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/18/2013] [Accepted: 10/07/2013] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic genome replication is stochastic, and each cell uses a different cohort of replication origins. We demonstrate that interpreting high-resolution Saccharomyces cerevisiae genome replication data with a mathematical model allows quantification of the stochastic nature of genome replication, including the efficiency of each origin and the distribution of termination events. Single-cell measurements support the inferred values for stochastic origin activation time. A strain, in which three origins were inactivated, confirmed that the distribution of termination events is primarily dictated by the stochastic activation time of origins. Cell-to-cell variability in origin activity ensures that termination events are widely distributed across virtually the whole genome. We propose that the heterogeneity in origin usage contributes to genome stability by limiting potentially deleterious events from accumulating at particular loci. Deep sequencing reveals a high-resolution view of genome replication dynamics Genome-wide modeling and single-cell imaging reveal stochastic origin activity Origin activity determines the location of replication termination events Termination events are widely distributed across the whole genome
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Affiliation(s)
- Michelle Hawkins
- Centre for Genetics and Genomics, School of Life Sciences, Queen's Medical Centre, The University of Nottingham, Nottingham NG7 2UH, UK
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20
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Newman TJ, Mamun MA, Nieduszynski CA, Blow JJ. Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts. Nucleic Acids Res 2013; 41:9705-18. [PMID: 23963700 PMCID: PMC3834809 DOI: 10.1093/nar/gkt728] [Citation(s) in RCA: 39] [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: 05/15/2013] [Revised: 07/24/2013] [Accepted: 07/25/2013] [Indexed: 01/21/2023] Open
Abstract
During S phase, the entire genome must be precisely duplicated, with no sections of DNA left unreplicated. Here, we develop a simple mathematical model to describe the probability of replication failing due to the irreversible stalling of replication forks. We show that the probability of complete genome replication is maximized if replication origins are evenly spaced, the largest inter-origin distances are minimized, and the end-most origins are positioned close to chromosome ends. We show that origin positions in the yeast Saccharomyces cerevisiae genome conform to all three predictions thereby maximizing the probability of complete replication if replication forks stall. Origin positions in four other yeasts-Kluyveromyces lactis, Lachancea kluyveri, Lachancea waltii and Schizosaccharomyces pombe-also conform to these predictions. Equating failure rates at chromosome ends with those in chromosome interiors gives a mean per nucleotide fork stall rate of ∼5 × 10(-8), which is consistent with experimental estimates. Using this value in our theoretical predictions gives replication failure rates that are consistent with data from replication origin knockout experiments. Our theory also predicts that significantly larger genomes, such as those of mammals, will experience a much greater probability of replication failure genome-wide, and therefore will likely require additional compensatory mechanisms.
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Affiliation(s)
- Timothy J. Newman
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK, School of Engineering, Physics and Mathematics, University of Dundee, Dundee, DD1 4HN, UK and Centre for Genetics and Genomics, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Mohammed A. Mamun
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK, School of Engineering, Physics and Mathematics, University of Dundee, Dundee, DD1 4HN, UK and Centre for Genetics and Genomics, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Conrad A. Nieduszynski
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK, School of Engineering, Physics and Mathematics, University of Dundee, Dundee, DD1 4HN, UK and Centre for Genetics and Genomics, University of Nottingham, Nottingham, NG7 2UH, UK
| | - J. Julian Blow
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK, School of Engineering, Physics and Mathematics, University of Dundee, Dundee, DD1 4HN, UK and Centre for Genetics and Genomics, University of Nottingham, Nottingham, NG7 2UH, UK
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21
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Abstract
Although distinct chromatin types have been long known to replicate at different timepoints of S phase, fine replication control has only recently become considered as an epigenetic phenomenon. It is now clear that in course of differentiation significant changes in genome replication timing occur, and these changes are intimately linked with the changes in transcriptional activity and nuclear architecture. Temporally coordinate replication is organized spatially into discrete units having specific chromosomal organization and function. Even though the functional aspects of such tight control of replication timing remain to be explored, one can confidently consider the replication program as yet another fundamental feature characteristic of the given differentiation state. The present review touches upon the molecular mechanisms of spatial and temporal control of replication timing, involving individual replication origins as well as large chromatin domains.
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22
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Terekhanova NV, Bazykin GA, Neverov A, Kondrashov AS, Seplyarskiy VB. Prevalence of multinucleotide replacements in evolution of primates and Drosophila. Mol Biol Evol 2013; 30:1315-25. [PMID: 23447710 PMCID: PMC3649671 DOI: 10.1093/molbev/mst036] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution of sequences mostly involves independent changes at different sites. However, substitutions at neighboring sites may co-occur as multinucleotide replacement events (MNRs). Here, we compare noncoding sequences of several species of primates, and of three species of Drosophila fruit flies, in a phylogenetic analysis of the replacements that occurred between species at nearby nucleotide sites. Both in primates and in Drosophila, the frequency of single-nucleotide replacements is substantially elevated within 10 nucleotides from other replacements that occurred on the same lineage but not on another lineage. The data imply that dinucleotide replacements (DNRs) affecting sites at distances of up to 10 nucleotides from each other are responsible for 2.3% of single-nucleotide replacements in primate genomes and for 5.6% in Drosophila genomes. Among these DNRs, 26% and 69%, respectively, are in fact parts of replacements of three or more trinucleotide replacements (TNRs). The plurality of MNRs affect nearby nucleotides, so that at least six times as many DNRs affect two adjacent nucleotide sites than sites 10 nucleotides apart. Still, approximately 60% of DNRs, and approximately 90% of TNRs, span distances more than two (or three) nucleotides. MNRs make a major contribution to the observed clustering of substitutions: In the human–chimpanzee comparison, DNRs are responsible for 50% of cases when two nearby replacements are observed on the human lineage, and TNRs are responsible for 83% of cases when three replacements at three immediately adjacent sites are observed on the human lineage. The prevalence of MNRs matches that is observed in data on de novo mutations and is also observed in the regions with the lowest sequence conservation, suggesting that MNRs mainly have mutational origin; however, epistatic selection and/or gene conversion may also play a role.
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Affiliation(s)
- Nadezhda V Terekhanova
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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23
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Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J, Sunyaev SR, McCarroll SA. Differential relationship of DNA replication timing to different forms of human mutation and variation. Am J Hum Genet 2012. [PMID: 23176822 DOI: 10.1016/j.ajhg.2012.10.018] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human genetic variation is distributed nonrandomly across the genome, though the principles governing its distribution are only partially known. DNA replication creates opportunities for mutation, and the timing of DNA replication correlates with the density of SNPs across the human genome. To enable deeper investigation of how DNA replication timing relates to human mutation and variation, we generated a high-resolution map of the human genome's replication timing program and analyzed its relationship to point mutations, copy number variations, and the meiotic recombination hotspots utilized by males and females. DNA replication timing associated with point mutations far more strongly than predicted from earlier analyses and showed a stronger relationship to transversion than transition mutations. Structural mutations arising from recombination-based mechanisms and recombination hotspots used more extensively by females were enriched in early-replicating parts of the genome, though these relationships appeared to relate more strongly to the genomic distribution of causative sequence features. These results indicate differential and sex-specific relationship of DNA replication timing to different forms of mutation and recombination.
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Affiliation(s)
- Amnon Koren
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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