1
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Xia Y, Sonneville R, Jenkyn-Bedford M, Ji L, Alabert C, Hong Y, Yeeles JT, Labib KP. DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in Caenorhabditis elegans. Science 2023; 381:eadi4932. [PMID: 37590372 PMCID: PMC7615117 DOI: 10.1126/science.adi4932] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023]
Abstract
Assembly of the CMG (CDC-45-MCM-2-7-GINS) helicase is the key regulated step during eukaryotic DNA replication initiation. Until now, it was unclear whether metazoa require additional factors that are not present in yeast. In this work, we show that Caenorhabditis elegans DNSN-1, the ortholog of human DONSON, functions during helicase assembly in a complex with MUS-101/TOPBP1. DNSN-1 is required to recruit the GINS complex to chromatin, and a cryo-electron microscopy structure indicates that DNSN-1 positions GINS on the MCM-2-7 helicase motor (comprising the six MCM-2 to MCM-7 proteins), by direct binding of DNSN-1 to GINS and MCM-3, using interfaces that we show are important for initiation and essential for viability. These findings identify DNSN-1 as a missing link in our understanding of DNA replication initiation, suggesting that initiation defects underlie the human disease syndrome that results from DONSON mutations.
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Affiliation(s)
- Yisui Xia
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, U.K
| | - Remi Sonneville
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, U.K
| | | | - Liqin Ji
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Constance Alabert
- Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee, U.K
| | - Ye Hong
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, U.K
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Joseph T.P. Yeeles
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, U.K
| | - Karim P.M. Labib
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, U.K
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2
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Heo W, Seo J, Lee Y, Kim Y. Fluid-driven DNA stretching for single-molecule studies on chromatin-associated proteins. Biochem Biophys Res Commun 2022; 634:122-128. [DOI: 10.1016/j.bbrc.2022.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/28/2022]
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3
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Sarni D, Barroso S, Shtrikman A, Irony-Tur Sinai M, Oren YS, Aguilera A, Kerem B. Topoisomerase 1-dependent R-loop deficiency drives accelerated replication and genomic instability. Cell Rep 2022; 40:111397. [PMID: 36170822 PMCID: PMC9532845 DOI: 10.1016/j.celrep.2022.111397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/26/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022] Open
Abstract
DNA replication is a complex process tightly regulated to ensure faithful genome duplication, and its perturbation leads to DNA damage and genomic instability. Replication stress is commonly associated with slow and stalled replication forks. Recently, accelerated replication has emerged as a non-canonical form of replication stress. However, the molecular basis underlying fork acceleration is largely unknown. Here, we show that mutated HRAS activation leads to increased topoisomerase 1 (TOP1) expression, causing aberrant replication fork acceleration and DNA damage by decreasing RNA-DNA hybrids or R-loops. In these cells, restoration of TOP1 expression or mild replication inhibition rescues the perturbed replication and reduces DNA damage. Furthermore, TOP1 or RNaseH1 overexpression induces accelerated replication and DNA damage, highlighting the importance of TOP1 equilibrium in regulating R-loop homeostasis to ensure faithful DNA replication and genome integrity. Altogether, our results dissect a mechanism of oncogene-induced DNA damage by aberrant replication fork acceleration. Increased TOP1 expression by mutated RAS reduces R loops Low R-loop levels promote accelerated replication and DNA damage TOP1 restoration or mild replication inhibition rescue DNA acceleration and damage High TOP1 expression is associated with replication mutagenesis in cancer
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Affiliation(s)
- Dan Sarni
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem 91904, Israel
| | - Sonia Barroso
- Department of Genome Biology, Andalusian Center of Molecular Biology and Regenerative Medicine CABIMER, Seville Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Alon Shtrikman
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem 91904, Israel
| | - Michal Irony-Tur Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem 91904, Israel
| | - Yifat S Oren
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem 91904, Israel
| | - Andrés Aguilera
- Department of Genome Biology, Andalusian Center of Molecular Biology and Regenerative Medicine CABIMER, Seville Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem 91904, Israel.
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4
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Wang W, Klein KN, Proesmans K, Yang H, Marchal C, Zhu X, Borrman T, Hastie A, Weng Z, Bechhoefer J, Chen CL, Gilbert DM, Rhind N. Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication. Mol Cell 2021; 81:2975-2988.e6. [PMID: 34157308 DOI: 10.1016/j.molcel.2021.05.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/08/2021] [Accepted: 05/20/2021] [Indexed: 12/27/2022]
Abstract
The heterogeneous nature of eukaryotic replication kinetics and the low efficiency of individual initiation sites make mapping the location and timing of replication initiation in human cells difficult. To address this challenge, we have developed optical replication mapping (ORM), a high-throughput single-molecule approach, and used it to map early-initiation events in human cells. The single-molecule nature of our data and a total of >2,500-fold coverage of the human genome on 27 million fibers averaging ∼300 kb in length allow us to identify initiation sites and their firing probability with high confidence. We find that the distribution of human replication initiation is consistent with inefficient, stochastic activation of heterogeneously distributed potential initiation complexes enriched in accessible chromatin. These observations are consistent with stochastic models of initiation-timing regulation and suggest that stochastic regulation of replication kinetics is a fundamental feature of eukaryotic replication, conserved from yeast to humans.
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Affiliation(s)
- Weitao Wang
- Institut Curie, PSL Research University, CNRS UMR 3244, Paris 75005, France
| | - Kyle N Klein
- Florida State University, Department of Biological Science, Tallahassee, FL 32306, USA
| | - Karel Proesmans
- Simon Fraser University, Department of Physics, Burnaby, BC V5A 1S6, Canada
| | - Hongbo Yang
- Northwestern University, Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Chicago, IL 60208, USA
| | - Claire Marchal
- Florida State University, Department of Biological Science, Tallahassee, FL 32306, USA
| | - Xiaopeng Zhu
- Carnegie Mellon University, Computational Biology Department, Pittsburgh, PA 15213, USA
| | - Tyler Borrman
- University of Massachusetts Medical School, Program in Bioinformatics and Integrated Biology, Worcester, MA 01605, USA
| | | | - Zhiping Weng
- University of Massachusetts Medical School, Program in Bioinformatics and Integrated Biology, Worcester, MA 01605, USA
| | - John Bechhoefer
- Simon Fraser University, Department of Physics, Burnaby, BC V5A 1S6, Canada.
| | - Chun-Long Chen
- Institut Curie, PSL Research University, CNRS UMR 3244, Paris 75005, France; Sorbonne University, Paris 75005, France.
| | - David M Gilbert
- Florida State University, Department of Biological Science, Tallahassee, FL 32306, USA.
| | - Nicholas Rhind
- University of Massachusetts Medical School, Department of Biochemistry and Molecular Pharmacology, Worcester, MA 01605, USA.
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5
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Miura H, Takahashi S, Shibata T, Nagao K, Obuse C, Okumura K, Ogata M, Hiratani I, Takebayashi SI. Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing. Nat Protoc 2020; 15:4058-4100. [PMID: 33230331 DOI: 10.1038/s41596-020-0378-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/02/2020] [Indexed: 01/03/2023]
Abstract
Replication timing (RT) domains are stable units of chromosome structure that are regulated in the context of development and disease. Conventional genome-wide RT mapping methods require many S-phase cells for either the effective enrichment of replicating DNA through bromodeoxyuridine (BrdU) immunoprecipitation or the determination of copy-number differences during S-phase, which precludes their application to non-abundant cell types and single cells. Here, we provide a simple, cost-effective, and robust protocol for single-cell DNA replication sequencing (scRepli-seq). The scRepli-seq methodology relies on whole-genome amplification (WGA) of genomic DNA (gDNA) from single S-phase cells and next-generation sequencing (NGS)-based determination of copy-number differences that arise between replicated and unreplicated DNA. Haplotype-resolved scRepli-seq, which distinguishes pairs of homologous chromosomes within a single cell, is feasible by using single-nucleotide polymorphism (SNP)/indel information. We also provide computational pipelines for quality control, normalization, and binarization of the scRepli-seq data. The experimental portion of this protocol (before sequencing) takes 3 d.
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Affiliation(s)
- Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Saori Takahashi
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Takahiro Shibata
- Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University, Tsu, Japan.,Laboratory of Molecular & Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Koji Nagao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Katsuzumi Okumura
- Laboratory of Molecular & Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Masato Ogata
- Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University, Tsu, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.
| | - Shin-Ichiro Takebayashi
- Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University, Tsu, Japan. .,Laboratory of Molecular & Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Japan.
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6
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Limiting the DNA Double-Strand Break Resectosome for Genome Protection. Trends Biochem Sci 2020; 45:779-793. [PMID: 32513599 DOI: 10.1016/j.tibs.2020.05.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/20/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022]
Abstract
DNA double-strand break (DSB) resection, once thought to be a simple enzymatic process, is emerging as a highly complex series of coordinated activities required to maintain genome integrity. Progress in cell biology, biochemistry, and genetics has deciphered the precise resecting activities, the regulatory components, and their ability to properly channel the resected DNA to the appropriate DNA repair pathway. Herein, we review the mechanisms of regulation of DNA resection, with an emphasis on negative regulators that prevent single-strand (ss)DNA accumulation to maintain genome stability. Interest in targeting DNA resection inhibitors is emerging because their inactivation leads to poly(ADP-ribose) polymerase inhibitor (PARPi) resistance. We also present detailed regulation of DNA resection machineries, their analysis by functional assays, and their impact on disease and PARPi resistance.
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7
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Bryan TM. Mechanisms of DNA Replication and Repair: Insights from the Study of G-Quadruplexes. Molecules 2019; 24:E3439. [PMID: 31546714 PMCID: PMC6804030 DOI: 10.3390/molecules24193439] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/18/2019] [Accepted: 09/18/2019] [Indexed: 12/13/2022] Open
Abstract
G-quadruplexes are four-stranded guanine-rich structures that have been demonstrated to occur across the genome in humans and other organisms. They provide regulatory functions during transcription, translation and immunoglobulin gene rearrangement, but there is also a large amount of evidence that they can present a potent barrier to the DNA replication machinery. This mini-review will summarize recent advances in understanding the many strategies nature has evolved to overcome G-quadruplex-mediated replication blockage, including removal of the structure by helicases or nucleases, or circumventing the deleterious effects on the genome through homologous recombination, alternative end-joining or synthesis re-priming. Paradoxically, G-quadruplexes have also recently been demonstrated to provide a positive role in stimulating the initiation of DNA replication. These recent studies have not only illuminated the many roles and consequences of G-quadruplexes, but have also provided fundamental insights into the general mechanisms of DNA replication and its links with genetic and epigenetic stability.
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Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia.
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8
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Shining a Spotlight on DNA: Single-Molecule Methods to Visualise DNA. Molecules 2019; 24:molecules24030491. [PMID: 30704053 PMCID: PMC6384704 DOI: 10.3390/molecules24030491] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/17/2019] [Accepted: 01/29/2019] [Indexed: 11/29/2022] Open
Abstract
The ability to watch single molecules of DNA has revolutionised how we study biological transactions concerning nucleic acids. Many strategies have been developed to manipulate DNA molecules to investigate mechanical properties, dynamics and protein–DNA interactions. Imaging methods using small molecules and protein-based probes to visualise DNA have propelled our understanding of complex biochemical reactions involving DNA. This review focuses on summarising some of the methodological developments made to visualise individual DNA molecules and discusses how these probes have been used in single-molecule biophysical assays.
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9
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Abstract
The maintenance of genome stability in eukaryotic cells relies on accurate and efficient replication along each chromosome following every cell division. The terminal position, repetitive sequence, and structural complexities of the telomeric DNA make the telomere an inherently difficult region to replicate within the genome. Thus, despite functioning to protect genome stability mammalian telomeres are also a source of replication stress and have been recognized as common fragile sites within the genome. Telomere fragility is exacerbated at telomeres that rely on the Alternative Lengthening of Telomeres (ALT) pathway. Like common fragile sites, ALT telomeres are prone to chromosome breaks and are frequent sites of recombination suggesting that ALT telomeres are subjected to chronic replication stress. Here, we will review the features of telomeric DNA that challenge the replication machinery and also how the cell overcomes these challenges to maintain telomere stability and ensure the faithful duplication of the human genome.
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Affiliation(s)
- Emily Mason-Osann
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA
| | - Himabindu Gali
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA
| | - Rachel Litman Flynn
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA.
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10
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da Silva MS, Marin PA, Repolês BM, Elias MC, Machado CR. Analysis of DNA Exchange Using Thymidine Analogs (ADExTA) in Trypanosoma cruzi. Bio Protoc 2018; 8:e3125. [PMID: 34532563 PMCID: PMC8342059 DOI: 10.21769/bioprotoc.3125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 10/20/2018] [Indexed: 11/02/2022] Open
Abstract
Trypanosoma cruzi is a protozoan parasite belonging to the Trypanosomatidae family. Although the trypanosomatids multiply predominantly by clonal generation, the presence of DNA exchange in some of them has been puzzling researchers over the years, mainly because it may represent a novel form that these organisms use to gain variability. Analysis of DNA Exchange using Thymidine Analogs (ADExTA) is a method that allows the in vitro detection and measurement of rates of DNA exchange, particularly in trypanosomatid cells, in a rapid and simple manner by indirect immunofluorescence assay (IFA). The method can be used to detect DNA exchange within one trypanosomatid lineage or among different lineages by paired analysis. The principle of this assay is based on the incorporation of two distinguishable halogenated thymidine analogs called 5'-chloro-2'-deoxyuridine (CldU) and 5'-iodo-2'-deoxyuridine (IdU) during DNA replication. After mixing the two cell cultures that had been previously incorporated with CldU and IdU separately, the presence of these unusual deoxynucleosides in the genome can be detected by specific antibodies. For this, a DNA denaturation step is required to expose the sites of thymidine analogs incorporated. Subsequently, a secondary reaction using fluorochrome-labeled antibodies will generate distinct signals under fluorescence analysis. By using this method, DNA exchange verification (i.e., the presence of both CldU and IdU in the same cell) is possible using a standard fluorescence microscope. It typically takes 2-3 days from the thymidine analogs incorporation to results. Of note, ADExTA is relatively cheap and does not require transfections or harsh genetic manipulation. These features represent an advantage when compared to other time-consuming protocols that demand DNA manipulation to introduce distinct drug-resistance markers in different cells for posterior selection.
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Affiliation(s)
- Marcelo S. da Silva
- Laboratório Especial de Ciclo Celular (LECC), Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Paula A. Marin
- Laboratório Especial de Ciclo Celular (LECC), Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Bruno M. Repolês
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria C. Elias
- Laboratório Especial de Ciclo Celular (LECC), Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Carlos R. Machado
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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11
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Analysis of Fission Yeast Single DNA Molecules on the Megabase Scale Using DNA Combing. Methods Mol Biol 2018; 1721:9-24. [PMID: 29423843 DOI: 10.1007/978-1-4939-7546-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
DNA combing enables the quantitative analysis of DNA replication, DNA recombination, DNA-protein interaction, and DNA methylation along genomic single DNA molecules at 1 kb resolution. However, DNA combing has been restricted to short 200-500 kb long DNA fragments, which introduces significant bias in data analysis. An improved DNA combing methodology that allows to routinely image Mb-scale single DNA molecules and occasionally up to full-length fission yeast chromosomes is presented in this chapter. DNA combing of Mb-scale single DNA molecules can be applied to accurately measure the dynamic properties of DNA replication such as the rate of origin firing, replication fork velocity, fork directionality and the frequency of fork blockage. In addition, Mb-scale single DNA molecules enable the quantitative analysis of complex genomic rearrangements including gross chromosomal translocations, repetitive DNA sequences, large deletions, and duplications, which are difficult to investigate with deep sequencing strategies.
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12
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Sidorova J. A game of substrates: replication fork remodeling and its roles in genome stability and chemo-resistance. Cell Stress 2017; 1:115-133. [PMID: 29355244 PMCID: PMC5771654 DOI: 10.15698/cst2017.12.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/27/2017] [Accepted: 11/29/2017] [Indexed: 01/06/2023] Open
Abstract
During the hours that human cells spend in the DNA synthesis (S) phase of the cell cycle, they may encounter adversities such as DNA damage or shortage of nucleotides. Under these stresses, replication forks in DNA may experience slowing, stalling, and breakage. Fork remodeling mechanisms, which stabilize slow or stalled replication forks and ensure their ability to continue or resume replication, protect cells from genomic instability and carcinogenesis. Fork remodeling includes DNA strand exchanges that result in annealing of newly synthesized strands (fork reversal), controlled DNA resection, and cleavage of DNA strands. Defects in major tumor suppressor genes BRCA1 and BRCA2, and a subset of the Fanconi Anemia genes have been shown to result in deregulation in fork remodeling, and most prominently, loss of kilobases of nascent DNA from stalled replication forks. This phenomenon has recently gained spotlight as a potential marker and mediator of chemo-sensitivity in cancer cells and, conversely, its suppression - as a hallmark of acquired chemo-resistance. Moreover, nascent strand degradation at forks is now known to also trigger innate immune response to self-DNA. An increasingly sophisticated molecular description of these events now points at a combination of unbalanced fork reversal and end-resection as a root cause, yet also reveals the multi-layered complexity and heterogeneity of the underlying processes in normal and cancer cells.
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Affiliation(s)
- Julia Sidorova
- Department of Pathology, University of Washington, Seattle, Washington, USA
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13
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Abstract
Complete duplication of large metazoan chromosomes requires thousands of potential initiation sites, only a small fraction of which are selected in each cell cycle. Assembly of the replication machinery is highly conserved and tightly regulated during the cell cycle, but the sites of initiation are highly flexible, and their temporal order of firing is regulated at the level of large-scale multi-replicon domains. Importantly, the number of replication forks must be quickly adjusted in response to replication stress to prevent genome instability. Here we argue that large genomes are divided into domains for exactly this reason. Once established, domain structure abrogates the need for precise initiation sites and creates a scaffold for the evolution of other chromosome functions.
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Affiliation(s)
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA; Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL 32306-4295, USA.
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14
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Hoory E, Budassi J, Pfeffer E, Cho N, Thalappillil J, Andersen J, Rafailovich M, Sokolov J. Discrimination of Adsorbed Double-Stranded and Single-Stranded DNA Molecules on Surfaces by Fluorescence Emission Spectroscopy Using Acridine Orange Dye. J Fluoresc 2017; 27:2153-2158. [DOI: 10.1007/s10895-017-2154-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/31/2017] [Indexed: 10/19/2022]
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15
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Iyer DR, Rhind N. Replication fork slowing and stalling are distinct, checkpoint-independent consequences of replicating damaged DNA. PLoS Genet 2017; 13:e1006958. [PMID: 28806726 PMCID: PMC5570505 DOI: 10.1371/journal.pgen.1006958] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/24/2017] [Accepted: 08/04/2017] [Indexed: 11/30/2022] Open
Abstract
In response to DNA damage during S phase, cells slow DNA replication. This slowing is orchestrated by the intra-S checkpoint and involves inhibition of origin firing and reduction of replication fork speed. Slowing of replication allows for tolerance of DNA damage and suppresses genomic instability. Although the mechanisms of origin inhibition by the intra-S checkpoint are understood, major questions remain about how the checkpoint regulates replication forks: Does the checkpoint regulate the rate of fork progression? Does the checkpoint affect all forks, or only those encountering damage? Does the checkpoint facilitate the replication of polymerase-blocking lesions? To address these questions, we have analyzed the checkpoint in the fission yeast Schizosaccharomyces pombe using a single-molecule DNA combing assay, which allows us to unambiguously separate the contribution of origin and fork regulation towards replication slowing, and allows us to investigate the behavior of individual forks. Moreover, we have interrogated the role of forks interacting with individual sites of damage by using three damaging agents-MMS, 4NQO and bleomycin-that cause similar levels of replication slowing with very different frequency of DNA lesions. We find that the checkpoint slows replication by inhibiting origin firing, but not by decreasing fork rates. However, the checkpoint appears to facilitate replication of damaged templates, allowing forks to more quickly pass lesions. Finally, using a novel analytic approach, we rigorously identify fork stalling events in our combing data and show that they play a previously unappreciated role in shaping replication kinetics in response to DNA damage.
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Affiliation(s)
- Divya Ramalingam Iyer
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Nicholas Rhind
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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16
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Reinhart M, Cardoso MC. A journey through the microscopic ages of DNA replication. PROTOPLASMA 2017; 254:1151-1162. [PMID: 27943022 PMCID: PMC5376393 DOI: 10.1007/s00709-016-1058-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/01/2016] [Indexed: 06/06/2023]
Abstract
Scientific discoveries and technological advancements are inseparable but not always take place in a coherent chronological manner. In the next, we will provide a seemingly unconnected and serendipitous series of scientific facts that, in the whole, converged to unveil DNA and its duplication. We will not cover here the many and fundamental contributions from microbial genetics and in vitro biochemistry. Rather, in this journey, we will emphasize the interplay between microscopy development culminating on super resolution fluorescence microscopy (i.e., nanoscopy) and digital image analysis and its impact on our understanding of DNA duplication. We will interlace the journey with landmark concepts and experiments that have brought the cellular DNA replication field to its present state.
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Affiliation(s)
- Marius Reinhart
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany.
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17
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Lacroix J, Pélofy S, Blatché C, Pillaire MJ, Huet S, Chapuis C, Hoffmann JS, Bancaud A. Analysis of DNA Replication by Optical Mapping in Nanochannels. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5963-5970. [PMID: 27624455 DOI: 10.1002/smll.201503795] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 06/21/2016] [Indexed: 06/06/2023]
Abstract
DNA replication is essential to maintain genome integrity in S phase of the cell division cycle. Accumulation of stalled replication forks is a major source of genetic instability, and likely constitutes a key driver of tumorigenesis. The mechanisms of regulation of replication fork progression have therefore been extensively investigated, in particular with DNA combing, an optical mapping technique that allows the stretching of single molecules and the mapping of active region for DNA synthesis by fluorescence microscopy. DNA linearization in nanochannels has been successfully used to probe genomic information patterns along single chromosomes, and has been proposed to be a competitive alternative to DNA combing. Yet this conjecture remains to be confirmed experimentally. Here, two complementary techniques are established to detect the genomic distribution of tracks of newly synthesized DNA in human cells by optical mapping in nanochannels. Their respective advantages and limitations are compared, and applied them to detect deregulations of the replication program induced by the antitumor drug hydroxyurea. The developments here thus broaden the field of applications accessible to nanofluidic technologies, and can be used in the future as part for molecular diagnostics in the context of high throughput cancer drug screening.
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Affiliation(s)
- Joris Lacroix
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Sandrine Pélofy
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Charline Blatché
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Marie-Jeanne Pillaire
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
- Equipe "Labellisée LA LIGUE CONTRE LE CANCER 2013" - Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, 2 Avenue Hubert Curien, CS 53717, 31037, Toulouse, France
| | - Sébastien Huet
- CNRS, UMR 6061, Institut Génétique et Développement de Rennes, F-35043, Rennes, France
- Université Rennes 1, UEB, UMR 6290, Faculté de Médecine, F-35043, Rennes, France
| | - Catherine Chapuis
- CNRS, UMR 6061, Institut Génétique et Développement de Rennes, F-35043, Rennes, France
- Université Rennes 1, UEB, UMR 6290, Faculté de Médecine, F-35043, Rennes, France
| | - Jean-Sébastien Hoffmann
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
- Equipe "Labellisée LA LIGUE CONTRE LE CANCER 2013" - Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, 2 Avenue Hubert Curien, CS 53717, 31037, Toulouse, France
| | - Aurélien Bancaud
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
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18
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Giri D, Li Z, Ashraf KM, Collinson MM, Higgins DA. Molecular Combing of λ-DNA using Self-Propelled Water Droplets on Wettability Gradient Surfaces. ACS APPLIED MATERIALS & INTERFACES 2016; 8:24265-24272. [PMID: 27541167 DOI: 10.1021/acsami.6b08607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Surface wettability gradients were used to elongate and align double stranded λ-DNA. Gradients were prepared by vapor phase deposition of octyltrichlorosilane (C8-silane) and fluorinated octyltrichlorosilane (F-silane) precursors. Gradient formation was confirmed by water contact angle and ellipsometric film thickness measurements. Placement of a droplet of aqueous DNA solution on the hydrophobic end of each gradient led to spontaneous motion of the droplet toward the hydrophilic end and deposition of the DNA. Fluorescence imaging of surface-adsorbed YOYO-1 labeled DNA molecules revealed that they are elongated and aligned perpendicular to the droplet-surface contact line at all positions along the gradient, consistent with a dominant role played by surface tension forces in elongating the DNA. The density of adsorbed DNA was found to be greatest on the C8-silane gradient at its hydrophobic end. DNA density decreased toward the hydrophilic end, while the length of the elongated DNA was less dependent on position. The elongation of DNA molecules by spontaneous droplet motion on chemical gradient surfaces has possible applications in DNA barcoding and studies of DNA-protein interactions.
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Affiliation(s)
- Dipak Giri
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
| | - Zi Li
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
| | - Kayesh M Ashraf
- Department of Chemistry, Virginia Commonwealth University , Richmond, Virginia 23284-2006, United States
| | - Maryanne M Collinson
- Department of Chemistry, Virginia Commonwealth University , Richmond, Virginia 23284-2006, United States
| | - Daniel A Higgins
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
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19
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Welcsh P, Kehrli K, Lazarchuk P, Ladiges W, Sidorova J. Application of the microfluidic-assisted replication track analysis to measure DNA repair in human and mouse cells. Methods 2016; 108:99-110. [PMID: 27130890 DOI: 10.1016/j.ymeth.2016.04.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/19/2016] [Accepted: 04/25/2016] [Indexed: 11/25/2022] Open
Abstract
Functional studies of the roles that DNA helicases play in human cells have benefited immensely from DNA fiber (or single molecule) technologies, which enable us to discern minute differences in behaviors of individual replication forks in genomic DNA in vivo. DNA fiber technologies are a group of methods that use different approaches to unravel and stretch genomic DNA to its contour length, and display it on a glass surface in order to immuno-stain nucleoside analog incorporation into DNA to reveal tracks (or tracts) of replication. We have previously adopted a microfluidic approach to DNA stretching and used it to analyze DNA replication. This method was introduced under the moniker maRTA or microfluidic-assisted Replication Track Analysis, and we have since used it to analyze roles of the RECQ helicases WRN and BLM, and other proteins in normal and perturbed replication. Here we describe a novel application of maRTA to detect and measure repair of DNA damage produced by three different agents relevant to etiology or therapy of cancer: methyl-methanesulfonate, UV irradiation, and mitomycin C. Moreover, we demonstrate the utility of this method by analyzing DNA repair in cells with reduced levels of WRN or of the base excision repair protein XRCC1.
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Affiliation(s)
- Piri Welcsh
- Department of Pathology, Box 357705, University of Washington, 1959 NE Pacific St., Seattle, WA 98195-7705, USA
| | - Keffy Kehrli
- Department of Pathology, Box 357705, University of Washington, 1959 NE Pacific St., Seattle, WA 98195-7705, USA
| | - Pavlo Lazarchuk
- Department of Pathology, Box 357705, University of Washington, 1959 NE Pacific St., Seattle, WA 98195-7705, USA
| | - Warren Ladiges
- Department of Comparative Medicine, Box 357340, University of Washington, 1959 NE Pacific St., Seattle, WA 98195-7340, USA
| | - Julia Sidorova
- Department of Pathology, Box 357705, University of Washington, 1959 NE Pacific St., Seattle, WA 98195-7705, USA.
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20
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Nieminuszczy J, Schwab RA, Niedzwiedz W. The DNA fibre technique - tracking helicases at work. Methods 2016; 108:92-8. [PMID: 27102626 DOI: 10.1016/j.ymeth.2016.04.019] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 10/21/2022] Open
Abstract
Faithful duplication of genetic material during every cell division is essential to ensure accurate transmission of genetic information to daughter cells. DNA helicases play a crucial role in promoting this process by facilitating almost all transactions occurring on DNA, including DNA replication and repair. They are responsible not only for DNA double helix unwinding ahead of progressing replication forks but also for resolution of secondary structures like G4 quadruplexes, HJ branch migration, double HJ dissolution, protein displacement, strand annealing and many more. Their importance in maintaining genome stability is underscored by the fact that many human disorders, including cancer, are associated with mutations in helicase genes. Here we outline how DNA fibre fluorography, a straightforward and inexpensive approach, can be employed to study the in vivo function of helicases in DNA replication and the maintenance of genome stability at a single molecule level. This approach directly visualizes the progression of individual replication forks within living cells and hence provides quantitative information on various aspects of DNA synthesis, such as replication fork processivity (replication speed), fork stalling, origin usage and fork termination.
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Affiliation(s)
- Jadwiga Nieminuszczy
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Rebekka A Schwab
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Wojciech Niedzwiedz
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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21
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Tiram G, Segal E, Krivitsky A, Shreberk-Hassidim R, Ferber S, Ofek P, Udagawa T, Edry L, Shomron N, Roniger M, Kerem B, Shaked Y, Aviel-Ronen S, Barshack I, Calderón M, Haag R, Satchi-Fainaro R. Identification of Dormancy-Associated MicroRNAs for the Design of Osteosarcoma-Targeted Dendritic Polyglycerol Nanopolyplexes. ACS NANO 2016; 10:2028-45. [PMID: 26815014 DOI: 10.1021/acsnano.5b06189] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The presence of dormant, microscopic cancerous lesions poses a major obstacle for the treatment of metastatic and recurrent cancers. While it is well-established that microRNAs play a major role in tumorigenesis, their involvement in tumor dormancy has yet to be fully elucidated. We established and comprehensively characterized pairs of dormant and fast-growing human osteosarcoma models. Using these pairs of mouse tumor models, we identified three novel regulators of osteosarcoma dormancy: miR-34a, miR-93, and miR-200c. This report shows that loss of these microRNAs occurs during the switch from dormant avascular into fast-growing angiogenic phenotype. We validated their downregulation in patients' tumor samples compared to normal bone, making them attractive candidates for osteosarcoma therapy. Successful delivery of miRNAs is a challenge; hence, we synthesized an aminated polyglycerol dendritic nanocarrier, dPG-NH2, and designed dPG-NH2-microRNA polyplexes to target cancer. Reconstitution of these microRNAs using dPG-NH2 polyplexes into Saos-2 and MG-63 cells, which generate fast-growing osteosarcomas, reduced the levels of their target genes, MET proto-oncogene, hypoxia-inducible factor 1α, and moesin, critical to cancer angiogenesis and cancer cells' migration. We further demonstrate that these microRNAs attenuate the angiogenic capabilities of fast-growing osteosarcomas in vitro and in vivo. Treatment with each of these microRNAs using dPG-NH2 significantly prolonged the dormancy period of fast-growing osteosarcomas in vivo. Taken together, these findings suggest that nanocarrier-mediated delivery of microRNAs involved in osteosarcoma tumor-host interactions can induce a dormant-like state.
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Affiliation(s)
- Galia Tiram
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Ehud Segal
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Adva Krivitsky
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Rony Shreberk-Hassidim
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Shiran Ferber
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Paula Ofek
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Taturo Udagawa
- Vertex Pharmaceuticals , Cambridge, Massachusetts 02142, United States
| | - Liat Edry
- Department of Cell & Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Noam Shomron
- Department of Cell & Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Maayan Roniger
- Department of Genetics, The Life Sciences Institute, Edmond J. Safra Campus, The Hebrew University , Jerusalem 91905, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, Edmond J. Safra Campus, The Hebrew University , Jerusalem 91905, Israel
| | - Yuval Shaked
- Department of Molecular Pharmacology, Rappaport Faculty of Medicine, Technion, Israel Institute of Technology , Haifa 32000, Israel
| | - Sarit Aviel-Ronen
- Department of Pathology, Sheba Medical Center , Tel Hashomer 52621, Israel
- Talpiot Medical Leadership Program, Sheba Medical Center , Tel Hashomer 52621, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center , Tel Hashomer 52621, Israel
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Marcelo Calderón
- Institut für Chemie und Biochemie, Freie Universität Berlin , Berlin 14195, Germany
| | - Rainer Haag
- Institut für Chemie und Biochemie, Freie Universität Berlin , Berlin 14195, Germany
| | - Ronit Satchi-Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv 69978, Israel
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22
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Urban JM, Foulk MS, Casella C, Gerbi SA. The hunt for origins of DNA replication in multicellular eukaryotes. F1000PRIME REPORTS 2015; 7:30. [PMID: 25926981 PMCID: PMC4371235 DOI: 10.12703/p7-30] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope that features for ORI specification might emerge. These methods are reviewed here with analysis of their advantages and shortcomings. The various factors that may influence ORI selection for initiation of DNA replication are discussed.
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Affiliation(s)
- John M. Urban
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
| | - Michael S. Foulk
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Department of Biology, Mercyhurst University501 East 38th Street, Erie, PA 16546USA
| | - Cinzia Casella
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Institute for Molecular Medicine, University of Southern DenmarkJB Winsloews Vej 25, 5000 Odense CDenmark
| | - Susan A. Gerbi
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
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23
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Baldwin KA, Fairhurst DJ. Classifying dynamic contact line modes in drying drops. SOFT MATTER 2015; 11:1628-1633. [PMID: 25599376 DOI: 10.1039/c4sm02642j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Although the evaporation mode of sessile droplets is almost universally characterized as either constant contact radius (CCR) or constant contact angle (CCA), here we investigate two alternatives where the contact line speed is either constant or inversely proportional to the droplet radius. We present supporting evidence from our experiments on poly(ethylene oxide) (PEO) polymer solutions and blood, and from literature on pure and binary liquids, colloidal suspensions, soft substrates, reactive dewetting and hole nucleation. We introduce the use of novel "clock-drop" images to visualize droplet evolution and dimensionless height-radius plots to characterize the evaporative pathways. Combining these with a simple scaling argument, we show that receding speed is inversely proportional to the three-phase contact radius R, with a constant of proportionality A, which is dependent on the drying conditions and drop shape, but independent of drop volume. We have shown that this is equivalent to a linear decrease in contact area with time. By varying only A, which we achieved experimentally by choosing solutions whose precipitate constricts after deposition, the evaporation mode can be altered continuously to include the two established modes CCR and CCA, and two new modes which we term "slowly receding" and "rapidly receding", which are characterised by fully dried "doughnut" and "pillar" deposits respectively.
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Affiliation(s)
- Kyle Anthony Baldwin
- School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, UK.
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24
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Cruz-García A, López-Saavedra A, Huertas P. BRCA1 accelerates CtIP-mediated DNA-end resection. Cell Rep 2014; 9:451-9. [PMID: 25310973 DOI: 10.1016/j.celrep.2014.08.076] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/10/2014] [Accepted: 08/27/2014] [Indexed: 01/08/2023] Open
Abstract
DNA-end resection is a highly regulated and critical step in the response and repair of DNA double-strand breaks. In higher eukaryotes, CtIP regulates resection by integrating cellular signals via its posttranslational modifications and protein-protein interactions, including cell-cycle-controlled interaction with BRCA1. The role of BRCA1 in DNA-end resection is not clear. Here, we develop an assay to study DNA resection in higher eukaryotes at high resolution. We demonstrate that the BRCA1-CtIP interaction, albeit not essential for resection, modulates the speed at which this process takes place.
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Affiliation(s)
- Andrés Cruz-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), 41092 Sevilla, Spain; Departamento de Genética, Universidad de Sevilla, 41080, Sevilla, Spain
| | - Ana López-Saavedra
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), 41092 Sevilla, Spain; Departamento de Genética, Universidad de Sevilla, 41080, Sevilla, Spain
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), 41092 Sevilla, Spain; Departamento de Genética, Universidad de Sevilla, 41080, Sevilla, Spain.
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25
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Ben-David E, Bester AC, Shifman S, Kerem B. Transcriptional dynamics in colorectal carcinogenesis: new insights into the role of c-Myc and miR17 in benign to cancer transformation. Cancer Res 2014; 74:5532-40. [PMID: 25125661 DOI: 10.1158/0008-5472.can-14-0932] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Colorectal cancer develops in a sequential, evolutionary process, leading to a heterogenic tumor. Comprehensive molecular studies of colorectal cancer have been previously performed; still, the process of carcinogenesis is not fully understood. We utilized gene expression patterns from 94 samples including normal, adenoma, and adenocarcinoma colon biopsies and performed a coexpression network analysis to determine gene expression trajectories of 8,000 genes across carcinogenesis. We found that the majority of gene expression changes occur in the transition from normal tissue to adenoma. The upregulated genes, known to be involved in cellular proliferation, included c-Myc along with its targets. In a cellular model system, we show that physiologic upregulation of c-Myc can lead to cellular proliferation without DNA replication stress. Our analysis also found that carcinogenesis involves a progressive downregulation of genes that are markers of colonic tissue and propose that this reflects a perturbed differentiation of colon cells during carcinogenesis. The analysis of miRNAs targets pointed toward the involvement of miR17 in the regulation of colon cell differentiation. Finally, we found that copy-number variations (CNV) enriched in colon adenocarcinoma tend to occur in genes whose expression changes already in adenoma, with deletions occurring in genes downregulated and duplications in genes upregulated in adenomas. We suggest that the CNVs are selected to reinforce changes in gene expression, rather than initiate them. Together, these findings shed new light into the molecular processes that underlie the transformation of colon tissue from normal to cancer and add a temporal context that has been hitherto lacking.
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Affiliation(s)
- Eyal Ben-David
- Department of Genetics, The Life Sciences Institute, Edmond J. Safra Campus, The Hebrew University, Jerusalem, Israel
| | - Assaf C Bester
- Department of Genetics, The Life Sciences Institute, Edmond J. Safra Campus, The Hebrew University, Jerusalem, Israel. Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
| | - Sagiv Shifman
- Department of Genetics, The Life Sciences Institute, Edmond J. Safra Campus, The Hebrew University, Jerusalem, Israel.
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, Edmond J. Safra Campus, The Hebrew University, Jerusalem, Israel
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26
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Infection with retroviral vectors leads to perturbed DNA replication increasing vector integrations into fragile sites. Sci Rep 2014; 3:2189. [PMID: 23852038 PMCID: PMC3711054 DOI: 10.1038/srep02189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/18/2013] [Indexed: 01/16/2023] Open
Abstract
Genome instability is a hallmark of cancer. Common fragile sites (CFSs) are specific regions in the human genome that are sensitive to replication stress and are prone to genomic instability in different cancer types. Here we molecularly cloned a new CFS, FRA11H, in 11q13. The genomic region of FRA11H harbors a hotspot of chromosomal breakpoints found in different types of cancer, indicating that this region is unstable during cancer development. We further found that FRA11H is a hotspot for integrations of Murine Leukemia Virus (MLV)-based vectors, following CD34+ infections in vitro as well as ex-vivo during gene therapy trials. Importantly, we found that the MLV-based vector infection in-vitro leads to replication perturbation, DNA damage and increased CFS expression. This suggests that infection by MLV-based vectors leads to replication-induced genome instability, raising further concerns regarding the use of retroviral vectors in gene therapy trials.
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27
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Zarkov A, Stoynov S, Nedelcheva-Veleva M. Novel glass slide preparation system for single DNA molecules analysis. BIOTECHNOL BIOTEC EQ 2014; 28:112-117. [PMID: 26019496 PMCID: PMC4434140 DOI: 10.1080/13102818.2014.901687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Here we propose an easy to build up and apply glass slide preparation system for single DNA molecules stretching. It is based on fast and simple coating of a solid glass with a cocktail of acrylic monomers that are easily polymerized via ultraviolet illumination. The acrylated slides are used to successfully stretch DNA molecules in a broader pH range compared to that of the commonly used amino-silanes. Moreover, the single DNA molecules that are stretched on the acrylated slides give a brighter and more photostable signal when visualized under a fluorescent microscope.
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28
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Sherstyuk VV, Shevchenko AI, Zakian SM. Epigenetic landscape for initiation of DNA replication. Chromosoma 2013; 123:183-99. [PMID: 24337246 DOI: 10.1007/s00412-013-0448-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 11/27/2013] [Accepted: 12/02/2013] [Indexed: 02/07/2023]
Abstract
The key genetic process of DNA replication is initiated at specific sites referred to as replication origins. In eukaryotes, origins of DNA replication are not specified by a defined nucleotide sequence. Recent studies have shown that the structural context and topology of DNA sequence, chromatin features, and its transcriptional activity play an important role in origin choice. During differentiation and development, significant changes in chromatin organization and transcription occur, influencing origin activity and choice. In the last few years, a number of different genome-wide studies have broadened the understanding of replication origin regulation. In this review, we discuss the epigenetic factors and mechanisms that modulate origin choice and firing.
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Affiliation(s)
- Vladimir V Sherstyuk
- Russian Academy of Sciences, Siberian Branch, Institute of Cytology and Genetics, pr. Akad. Lavrentieva 10, Novosibirsk, 630090, Russia
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29
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Zarkov A, Vasilev A, Deligeorgiev T, Stoynov S, Nedelcheva-Veleva M. Novel Fluorescent Dyes for Single DNA Molecule Techniques. Mol Imaging 2013. [DOI: 10.2310/7290.2012.00018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Alexander Zarkov
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Aleksey Vasilev
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Todor Deligeorgiev
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Stoyno Stoynov
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Marina Nedelcheva-Veleva
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
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30
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The response of mammalian cells to UV-light reveals Rad54-dependent and independent pathways of homologous recombination. DNA Repair (Amst) 2011; 10:1095-105. [DOI: 10.1016/j.dnarep.2011.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 08/08/2011] [Indexed: 11/17/2022]
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31
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Nucleotide deficiency promotes genomic instability in early stages of cancer development. Cell 2011; 145:435-46. [PMID: 21529715 DOI: 10.1016/j.cell.2011.03.044] [Citation(s) in RCA: 623] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 01/18/2011] [Accepted: 03/29/2011] [Indexed: 12/28/2022]
Abstract
Chromosomal instability in early cancer stages is caused by stress on DNA replication. The molecular basis for replication perturbation in this context is currently unknown. We studied the replication dynamics in cells in which a regulator of S phase entry and cell proliferation, the Rb-E2F pathway, is aberrantly activated. Aberrant activation of this pathway by HPV-16 E6/E7 or cyclin E oncogenes significantly decreased the cellular nucleotide levels in the newly transformed cells. Exogenously supplied nucleosides rescued the replication stress and DNA damage and dramatically decreased oncogene-induced transformation. Increased transcription of nucleotide biosynthesis genes, mediated by expressing the transcription factor c-myc, increased the nucleotide pool and also rescued the replication-induced DNA damage. Our results suggest a model for early oncogenesis in which uncoordinated activation of factors regulating cell proliferation leads to insufficient nucleotides that fail to support normal replication and genome stability.
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Yang SCH, Rhind N, Bechhoefer J. Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing. Mol Syst Biol 2011; 6:404. [PMID: 20739926 PMCID: PMC2950085 DOI: 10.1038/msb.2010.61] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 07/16/2010] [Indexed: 11/09/2022] Open
Abstract
We developed analytical models of DNA replication that include probabilistic initiation of origins, fork progression, passive replication, and asynchrony. We fit the model to budding yeast genome-wide microarray data probing the replication fraction and found that initiation times correlate with the precision of timing. We extracted intrinsic origin properties, such as potential origin efficiency and firing-time distribution, which cannot be done using phenomenological approaches. We propose that origin timing is controlled by stochastically activated initiators bound to origin sites rather than explicit time-measuring mechanisms.
The kinetics of DNA replication must be controlled for cells to develop properly. Although the biochemical mechanisms of origin initiations are increasingly well understood, the organization of initiation timing as a genome-wide program is still a mystery. With the advance of technology, researchers have been able to generate large amounts of data revealing aspects of replication kinetics. In particular, the use of microarrays to probe the replication fraction of budding yeast genome wide has been a successful first step towards unraveling the details of the replication program (Raghuraman et al, 2001; Alvino et al, 2007; McCune et al, 2008). On the surface, the microarray data shows apparent patterns of early and late replicating regions and seems to support the prevailing picture of eukaryotic replication—origins are positioned at defined sites and initiated at defined, preprogrammed times (Donaldson, 2005). Molecular combing, a single-molecule technique, however, showed that the initiation of origins is stochastic (Czajkowsky et al, 2008). Motivated by these conflicting viewpoints, we developed a model that is flexible enough to describe both deterministic and stochastic initiation. We modeled origin initiation as probabilistic events. We first propose a model where each origin is allowed to have its distinct ‘firing-time distribution.' Origins that have well-determined initiation times have narrow distributions, whereas more stochastic origins have wider distributions. Similar models based on simulations have previously been proposed (Lygeros et al, 2008; Blow and Ge, 2009; de Moura et al, 2010); however, our model is novel in that it is analytic. It is much faster than simulations and allowed us, for the first time, to fit genome-wide microarray data and extract parameters that describe the replication program in unprecedented detail (Figure 2). Our main result is this: origins that fire early, on average, have precisely defined initiation times, whereas origins that fire late, on average, do not have a well-defined initiation time and initiate throughout S phase. What kind of global controlling mechanism can account for this trend? We propose a second model where an origin is composed of multiple initiators, each of which fires independently and identically. A good candidate for the initiator is the minichromosome maintenance (MCM) complex, as it is found to be associated with origin firing and loaded in abundance (Hyrien et al, 2003). We show that the aforementioned relationship can be explained quantitatively if the earlier-firing origins have more MCM complexes. This model offers a new view of replication: controlled origin timing can emerge from stochastic firing and does not need an explicit time-measuring mechanism, a ‘clock.' This model provides a new, detailed, plausible, and testable mechanism for replication timing control. Our models also capture the effects of passive replication, which is often neglected in phenomenological approaches (Eshaghi et al, 2007). There are two ways an origin site can be replicated. The site can be replicated by the origin binding to it but can also be passively replicated by neighboring origins. This complication makes it difficult to extract the intrinsic properties of origins. By modeling passive replication, we can separate the contribution from each origin and extract the potential efficiency of origins, i.e., the efficiency of the origin given that there is no passive replication. We found that while most origins are potentially highly efficient, their observed efficiency varies greatly. This implies that many origins, though capable of initiating, are often passively replicated and appear dormant. Such a design makes the replication process robust against replication stress such as fork stalling (Blow and Ge, 2009). If two approaching forks stall, normally dormant origins in the region, not being passively replicated, will initiate to replicate the gap. With the advance of the microarray and molecular-combing technology, experiments have been done to probe many different types of cells, and large amounts of replication fraction data have been generated. Our model can be applied to spatiotemporally resolved replication fraction data for any organism, as the model is flexible enough to capture a wide range of replication kinetics. The analytical model is also much faster than simulation-based models. For these reasons, we believe that the model is a powerful tool for analyzing these large datasets. This work opens the possibility for understanding the replication program across species in more rigor and detail (Goldar et al, 2009). Microarrays are powerful tools to probe genome-wide replication kinetics. The rich data sets that result contain more information than has been extracted by current methods of analysis. In this paper, we present an analytical model that incorporates probabilistic initiation of origins and passive replication. Using the model, we performed least-squares fits to a set of recently published time course microarray data on Saccharomyces cerevisiae. We extracted the distribution of firing times for each origin and found that the later an origin fires on average, the greater the variation in firing times. To explain this trend, we propose a model where earlier-firing origins have more initiator complexes loaded and a more accessible chromatin environment. The model demonstrates how initiation can be stochastic and yet occur at defined times during S phase, without an explicit timing program. Furthermore, we hypothesize that the initiators in this model correspond to loaded minichromosome maintenance complexes. This model is the first to suggest a detailed, testable, biochemically plausible mechanism for the regulation of replication timing in eukaryotes.
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Chastain PD, Nakamura J, Rao S, Chu H, Ibrahim JG, Swenberg JA, Kaufman DG. Abasic sites preferentially form at regions undergoing DNA replication. FASEB J 2010; 24:3674-80. [PMID: 20511393 DOI: 10.1096/fj.09-145276] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We investigated whether apurinic/apyrimidinic (AP/abasic) sites were more frequent in regions of DNA replication in cells and whether their number increased during oxidative stress. DNA fiber spreading and fluorescent immunostaining were used to detect areas of DNA replication and sites of AP lesions in extended DNA fibers. The distribution of AP sites was determined in DNA fibers from vertebrate cells maintained under normal culture conditions or stressed with exogenous H(2)O(2). AP lesions per unit length were enumerated in bulk DNA or at replication sites. The background density of AP sites in DNA fibers was 5.4 AP sites/10(6) nt, while newly replicated DNA contained 12.9 AP sites/10(6) nt. In cells exposed to 20 μM H(2)O(2), AP sites in newly replicated DNA increased to 20.8/10(6) nt. Determinations of AP site density in bulk DNA by fiber analysis or standard slot blot assays agreed to within 10%. Our findings show that the fiber assay not only accurately determines the frequency of AP sites but also shows their distribution. They also reveal that there is increased susceptibility to oxidative damage in DNA regions undergoing replication, which may explain the previously observed clustering of AP sites.
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Affiliation(s)
- Paul D Chastain
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7525, USA.
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Kang SH, Lee S, Yeung ES. Digestion of individual DNA molecules by lambda-exonuclease at liquid-solid interface. Analyst 2010; 135:1759-64. [PMID: 20436973 DOI: 10.1039/c0an00145g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzyme digestion of single DNA molecules was directly observed in real time by dual-color total internal reflection fluorescence microscopy (TIRFM). Individual lambda-DNA molecules labeled with the fluorescent dye, YOYO-1, were stretched in a laminar flow stream and immobilized on a bare fused-silica prism surface based on hydrophobic and electrostatic interactions. Enzyme digestion was initiated by the influx of lambda-exonuclease enzyme via capillary force. When the dye : bp ratio was higher than 1 : 20, the exact digestion rate could not be measured because of induced photocleavage of the DNA molecules. At a dye : bp ratio of 1 : 50, shortening of the DNA strand was recorded in real time. Unlike previous studies, the length-based digestion rate of lambda-exonuclease showed 3 distinct values in the range of 0.173(+/-0.024) to 0.462(+/-0.152) microm s(-1) at 37 degrees C. That is, different enzyme molecules exhibit different digestion dynamics. Digestion was also monitored based on the decrease in fluorescence intensity, but uncertainties were much larger due to the distance dependent excitation intensity in the TIRF mode.
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Affiliation(s)
- Seong Ho Kang
- Ames Laboratory-USDOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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Abstract
The DNA double helix has become a modern icon which symbolizes our understanding of the molecular basis of life. It is less widely recognized that the double helix proposed by Watson and Crick more than half a century ago is a remarkably adaptable molecule that can undergo major conformational rearrangements without being irreversibly damaged. Indeed, DNA deformation is an intrinsic feature of many of the biological processes in which it is involved. Over the last two decades, single-molecule experiments coupled with molecular modeling have transformed our understanding of DNA flexibility, while the accumulation of high-resolution structures of DNA-protein complexes have demonstrated how organisms can exploit this property as a useful feature for preserving, reading, replicating, and packaging the genetic message. In this Minireview we summarize the information now available on the extreme--and the less extreme--deformations of the double helix.
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Affiliation(s)
- Chantal Prévost
- Laboratoire de Biochimie Théorique-UPR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, France.
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Sidorova JM, Li N, Schwartz DC, Folch A, Monnat RJ. Microfluidic-assisted analysis of replicating DNA molecules. Nat Protoc 2009; 4:849-61. [PMID: 19444242 DOI: 10.1038/nprot.2009.54] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Single molecule-based protocols have been gaining popularity as a way to visualize DNA replication at the global genomic- and locus-specific levels. These protocols take advantage of the ability of many organisms to incorporate nucleoside analogs during DNA replication, together with a method to display stretched DNA on glass for immunostaining and microscopy. We describe here a microfluidic platform that can be used to stretch and to capture labeled DNA molecules for replication analyses. This platform consists of parallel arrays of three-sided, 3- or 4-microm high, variable-width capillary channels fabricated from polydimethylsiloxane by conventional soft lithography, and of silane-modified glass coverslips to reversibly seal the open side of the channels. Capillary tension in these microchannels facilitates DNA loading, stretching and glass coverslip deposition from microliter-scale DNA samples. The simplicity and extensibility of this platform should facilitate DNA replication analyses using small samples from a variety of biological and clinical sources.
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Affiliation(s)
- Julia M Sidorova
- Department of Pathology, University of Washington, Seattle, Washington, USA.
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Schwartz M, Oren YS, Bester AC, Rahat A, Sfez R, Yitzchaik S, de Villartay JP, Kerem B. Impaired replication stress response in cells from immunodeficiency patients carrying Cernunnos/XLF mutations. PLoS One 2009; 4:e4516. [PMID: 19223975 PMCID: PMC2637976 DOI: 10.1371/journal.pone.0004516] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2008] [Accepted: 01/09/2009] [Indexed: 11/18/2022] Open
Abstract
Non-Homologous End Joining (NHEJ) is one of the two major pathways of DNA Double Strand Breaks (DSBs) repair. Mutations in human NHEJ genes can lead to immunodeficiency due to its role in V(D)J recombination in the immune system. In addition, most patients carrying mutations in NHEJ genes display developmental anomalies which are likely the result of a general defect in repair of endogenously induced DSBs such as those arising during normal DNA replication. Cernunnos/XLF is a recently identified NHEJ gene which is mutated in immunodeficiency with microcephaly patients. Here we aimed to investigate whether Cernunnos/XLF mutations disrupt the ability of patient cells to respond to replication stress conditions. Our results demonstrate that Cernunnos/XLF mutated cells and cells downregulated for Cernunnos/XLF have increased sensitivity to conditions which perturb DNA replication. In addition, under replication stress, these cells exhibit impaired DSB repair and increased accumulation of cells in G2/M. Moreover Cernunnos/XLF mutated and down regulated cells display greater chromosomal instability, particularly at fragile sites, under replication stress conditions. These results provide evidence for the role of Cernunnos/XLF in repair of DSBs and maintenance of genomic stability under replication stress conditions. This is the first study of a NHEJ syndrome showing association with impaired cellular response to replication stress conditions. These findings may be related to the clinical features in these patients which are not due to the V(D)J recombination defect. Additionally, in light of the emerging important role of replication stress in the early stages of cancer development, our findings may provide a mechanism for the role of NHEJ in preventing tumorigenesis.
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Affiliation(s)
- Michal Schwartz
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
| | - Yifat S. Oren
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
| | - Assaf C. Bester
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
| | - Ayelet Rahat
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
| | - Ruthy Sfez
- Department of Inorganic and Analytical Chemistry, The Hebrew University, Jerusalem, Israel
| | - Shlomo Yitzchaik
- Department of Inorganic and Analytical Chemistry, The Hebrew University, Jerusalem, Israel
| | - Jean-Pierre de Villartay
- Institut National de la Santé et de la Recherche Médicale, U768, Paris, France
- Université Paris-Descartes, Faculté de Médecine René Descartes, Site Necker, IFR 94, Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants Malades, Service d'Immunologie et d'Hématologie Pédiatrique, Paris, France
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
- * E-mail:
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Herrick J, Bensimon A. Introduction to molecular combing: genomics, DNA replication, and cancer. Methods Mol Biol 2009; 521:71-101. [PMID: 19563102 DOI: 10.1007/978-1-60327-815-7_5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The sequencing of the human genome inaugurated a new era in both fundamental and applied genetics. At the same time, the emergence of new technologies for probing the genome has transformed the field of pharmaco-genetics and made personalized genomic profiling and high-throughput screening of new therapeutic agents all but a matter of routine. One of these technologies, molecular combing, has served to bridge the technical gap between the examination of gross chromosomal abnormalities and sequence-specific alterations. Molecular combing provides a new perspective on the structure and dynamics of the human genome at the whole genome and sub-chromosomal levels with a resolution ranging from a few kilobases up to a megabase and more. Originally developed to study genetic rearrangements and to map genes for positional cloning, recent advances have extended the spectrum of its applications to studying the real-time dynamics of the replication of the genome. Understanding how the genome is replicated is essential for elucidating the mechanisms that both maintain genome integrity and result in the instabilities leading to human genetic disease and cancer. In the following, we will examine recent discoveries and advances due to the application of molecular combing to new areas of research in the fields of molecular cytogenetics and cancer genomics.
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Yang SCH, Bechhoefer J. How Xenopus laevis embryos replicate reliably: investigating the random-completion problem. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:041917. [PMID: 18999465 DOI: 10.1103/physreve.78.041917] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Indexed: 05/27/2023]
Abstract
DNA synthesis in Xenopus frog embryos initiates stochastically in time at many sites (origins) along the chromosome. Stochastic initiation implies fluctuations in the time to complete and may lead to cell death if replication takes longer than the cell cycle time ( approximately 25 min) . Surprisingly, although the typical replication time is about 20 min , in vivo experiments show that replication fails to complete only about 1 in 300 times. How is replication timing accurately controlled despite the stochasticity? Biologists have proposed two solutions to this "random-completion problem." The first solution uses randomly located origins but increases their rate of initiation as S phase proceeds, while the second uses regularly spaced origins. In this paper, we investigate the random-completion problem using a type of model first developed to describe the kinetics of first-order phase transitions. Using methods from the field of extreme-value statistics, we derive the distribution of replication-completion times for a finite genome. We then argue that the biologists' first solution to the problem is not only consistent with experiment but also nearly optimizes the use of replicative proteins. We also show that spatial regularity in origin placement does not alter significantly the distribution of replication times and, thus, is not needed for the control of replication timing.
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Affiliation(s)
- Scott Cheng-Hsin Yang
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6.
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Sibani S, Rampakakis E, Di Paola D, Zannis-Hadjopoulos M. Fine mapping and functional activity of the adenosine deaminase origin in murine embryonic fibroblasts. J Cell Biochem 2008; 104:773-84. [PMID: 18181156 DOI: 10.1002/jcb.21662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
DNA replication initiates at origins within the genome. The late-firing murine adenosine deaminase (mAdA) origin is located within a 2 kb fragment of DNA, making it difficult to examine by realtime technology. In this study, fine mapping of the mAdA region by measuring the abundance of nascent strand DNA identified two origins, mAdA-1 and mAdA-C, located 397 bp apart from each other. Both origins conferred autonomous replication to plasmids transfected in murine embryonic fibroblasts (MEFs), and exhibited similar activities in vivo and in vitro. Furthermore, both were able to recruit the DNA replication initiator proteins Cdc6 and Ku in vitro, similar to other bona fide replication origins. When tested in a murine Ku80(-/-) cell line, both origins exhibited replication activities comparable to those observed in wildtype cells, as did the hypoxanthine-guanine phosphoribosyltransferase (HPRT) and c-myc origins. This contrasts with previously published studies using Ku80-deficient human cells lines and suggests differences in the mechanism of initiation of DNA replication between the murine and human systems.
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Affiliation(s)
- Sahar Sibani
- McGill Cancer Center and Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6
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41
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Montagnoli A, Valsasina B, Croci V, Menichincheri M, Rainoldi S, Marchesi V, Tibolla M, Tenca P, Brotherton D, Albanese C, Patton V, Alzani R, Ciavolella A, Sola F, Molinari A, Volpi D, Avanzi N, Fiorentini F, Cattoni M, Healy S, Ballinari D, Pesenti E, Isacchi A, Moll J, Bensimon A, Vanotti E, Santocanale C. A Cdc7 kinase inhibitor restricts initiation of DNA replication and has antitumor activity. Nat Chem Biol 2008; 4:357-65. [PMID: 18469809 DOI: 10.1038/nchembio.90] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2008] [Accepted: 04/11/2008] [Indexed: 12/30/2022]
Abstract
Cdc7 is an essential kinase that promotes DNA replication by activating origins of replication. Here, we characterized the potent Cdc7 inhibitor PHA-767491 (1) in biochemical and cell-based assays, and we tested its antitumor activity in rodents. We found that the compound blocks DNA synthesis and affects the phosphorylation of the replicative DNA helicase at Cdc7-dependent phosphorylation sites. Unlike current DNA synthesis inhibitors, PHA-767491 prevents the activation of replication origins but does not impede replication fork progression, and it does not trigger a sustained DNA damage response. Treatment with PHA-767491 results in apoptotic cell death in multiple cancer cell types and tumor growth inhibition in preclinical cancer models. To our knowledge, PHA-767491 is the first molecule that directly affects the mechanisms controlling initiation as opposed to elongation in DNA replication, and its activities suggest that Cdc7 kinase inhibition could be a new strategy for the development of anticancer therapeutics.
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Affiliation(s)
- Alessia Montagnoli
- Nerviano Medical Sciences Oncology, Via Pasteur 10, 20014 Nerviano, Italy
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Lam L, Iino R, Tabata KV, Noji H. Highly sensitive restriction enzyme assay and analysis: a review. Anal Bioanal Chem 2008; 391:2423-32. [PMID: 18427787 DOI: 10.1007/s00216-008-2099-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 02/13/2008] [Accepted: 03/20/2008] [Indexed: 11/27/2022]
Abstract
Biological assays at the single molecule level are crucial to fundamental studies of DNA-protein mechanisms. In order to cater for high throughput applications, one area of immense research potential is single-molecule bioassays where miniaturized devices are developed to perform rapid and effective biological reactions and analyses. With the success of various emerging technologies for engineering miniaturized structures down to the nanoscale level, supported by specialized equipment for detection, many investigations in the field of life science that were once thought impossible can now be actively explored. In this review, the significance of downscaling to the single-molecule level is firstly presented in selected examples, with the focus placed on restriction enzyme assays. To determine the effectiveness of single-molecule restriction enzyme reactions, simple and direct analytical methods based on DNA stretching have often been reliably employed. DNA stretching can be realized based on a number of working principles related to the physical forces exerted on the DNA samples. We then discuss two examples of a nanochannel system and a microchamber system where single-molecule restriction enzyme digestion and DNA stretching have been integrated, which possess prospective capabilities of developing into highly sensitive and high-throughput restriction enzyme assays. Finally, we take a brief look at the general trends in technological development in this field by comparing the advantages and disadvantages of performing assays at bulk, microscale and single-molecule levels.
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Affiliation(s)
- Liza Lam
- The Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan.
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Frum RA, Chastain PD, Qu P, Cohen SM, Kaufman DG. DNA replication in early S phase pauses near newly activated origins. Cell Cycle 2008; 7:1440-8. [PMID: 18418075 DOI: 10.4161/cc.7.10.5879] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During the S phase of the cell cycle, the entire genome is replicated. There is a high level of orderliness to this process through the temporally and topologically coordinated activation of many replication origins situated along chromosomes. We investigated the program of replication from origins initiating in early S phase by labeling synchronized normal human fibroblasts (NHF1) with nucleotide analogs for various pulse times and measuring labeled tracks in combed DNA fibers. Our analysis showed that replication forks progress 9-35 kilobases from newly initiated origins, followed by a pause in synthesis before replication resumes. Pausing was not observed near origins that initiated in the middle of S phase. No evidence for pausing near origins was found at the beginning of the S phase in glioblastoma T98G cells. Treatment with the S phase checkpoint inhibitor caffeine abrogated pausing in NHF1 cells in early S phase. This suggests that pausing may comprise a novel aspect of the intra-S phase checkpoint pathway or a related new early S checkpoint. Further, it is possible that the loss of this regulatory process in cancer cells such as T98G could be a contributing factor in the genetic instability that typifies cancers.
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Affiliation(s)
- Rebecca A Frum
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7525, USA
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Herrick J, Bensimon A. Global regulation of genome duplication in eukaryotes: an overview from the epifluorescence microscope. Chromosoma 2008; 117:243-60. [PMID: 18197411 DOI: 10.1007/s00412-007-0145-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 12/14/2007] [Accepted: 12/17/2007] [Indexed: 01/15/2023]
Abstract
In eukaryotes, DNA replication is initiated along each chromosome at multiple sites called replication origins. Locally, each replication origin is "licensed" or specified at the end of the M and the beginning of the G1 phases of the cell cycle. During the S phase when DNA synthesis takes place, origins are activated in stages corresponding to early and late-replicating domains. The staged and progressive activation of replication origins reflects the need to maintain a strict balance between the number of active replication forks and the rate at which DNA synthesis proceeds. This suggests that origin densities (frequency of initiation) and replication fork movement (rates of elongation) must be coregulated to guarantee the efficient and complete duplication of each subchromosomal domain. Emerging evidence supports this proposal and suggests that the ATM/ATR intra-S phase checkpoint plays an important role in the coregulation of initiation frequencies and rates of elongation. In this paper, we review recent results concerning the mechanisms governing the global regulation of DNA replication and discuss the roles these mechanisms play in maintaining genome stability during both a normal and perturbed S phase.
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Affiliation(s)
- John Herrick
- Genomic Vision, 29, rue Faubourg St. Jacques, Paris 75014, France.
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Rao VA, Conti C, Guirouilh-Barbat J, Nakamura A, Miao ZH, Davies SL, Saccá B, Hickson ID, Bensimon A, Pommier Y. Endogenous γ-H2AX-ATM-Chk2 Checkpoint Activation in Bloom's Syndrome Helicase–Deficient Cells Is Related to DNA Replication Arrested Forks. Mol Cancer Res 2007; 5:713-24. [PMID: 17634426 DOI: 10.1158/1541-7786.mcr-07-0028] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Bloom syndrome helicase (BLM) is critical for genomic stability. A defect in BLM activity results in the cancer-predisposing Bloom syndrome (BS). Here, we report that BLM-deficient cell lines and primary fibroblasts display an endogenously activated DNA double-strand break checkpoint response with prominent levels of phosphorylated histone H2AX (gamma-H2AX), Chk2 (p(T68)Chk2), and ATM (p(S1981)ATM) colocalizing in nuclear foci. Interestingly, the mitotic fraction of gamma-H2AX foci did not seem to be higher in BLM-deficient cells, indicating that these lesions form transiently during interphase. Pulse labeling with iododeoxyuridine and immunofluorescence microscopy showed the colocalization of gamma-H2AX, ATM, and Chk2 together with replication foci. Those foci costained for Rad51, indicating homologous recombination at these replication sites. We therefore analyzed replication in BS cells using a single molecule approach on combed DNA fibers. In addition to a higher frequency of replication fork barriers, BS cells displayed a reduced average fork velocity and global reduction of interorigin distances indicative of an elevated frequency of origin firing. Because BS is one of the most penetrant cancer-predisposing hereditary diseases, it is likely that the lack of BLM engages the cells in a situation similar to precancerous tissues with replication stress. To our knowledge, this is the first report of high ATM-Chk2 kinase activation and its linkage to replication defects in a BS model.
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Affiliation(s)
- V Ashutosh Rao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
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Conti C, Saccà B, Herrick J, Lalou C, Pommier Y, Bensimon A. Replication fork velocities at adjacent replication origins are coordinately modified during DNA replication in human cells. Mol Biol Cell 2007; 18:3059-67. [PMID: 17522385 PMCID: PMC1949372 DOI: 10.1091/mbc.e06-08-0689] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The spatial organization of replicons into clusters is believed to be of critical importance for genome duplication in higher eukaryotes, but its functional organization still remains to be fully clarified. The coordinated activation of origins is insufficient on its own to account for a timely completion of genome duplication when interorigin distances vary significantly and fork velocities are constant. Mechanisms coordinating origin distribution with fork progression are still poorly elucidated, because of technical difficulties of visualizing the process. Taking advantage of a single molecule approach, we delineated and compared the DNA replication kinetics at the genome level in human normal primary and malignant cells. Our results show that replication forks moving from one origin, as well as from neighboring origins, tend to exhibit the same velocity, although the plasticity of the replication program allows for their adaptation to variable interorigin distances. We also found that forks that emanated from closely spaced origins tended to move slower than those associated with long replicons. Taken together, our results indicate a functional role for origin clustering in the dynamic regulation of genome duplication.
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Affiliation(s)
- Chiara Conti
- *Department of Genome Stability, Pasteur Institute, Paris F-75724, France
| | - Barbara Saccà
- *Department of Genome Stability, Pasteur Institute, Paris F-75724, France
| | - John Herrick
- *Department of Genome Stability, Pasteur Institute, Paris F-75724, France
| | - Claude Lalou
- Institut National de la Santé et de la Recherche Médicale U532, Hôpital Saint-Louis, Paris 75010, France; and
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817
| | - Aaron Bensimon
- *Department of Genome Stability, Pasteur Institute, Paris F-75724, France
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Chan TF, Ha C, Phong A, Cai D, Wan E, Leung L, Kwok PY, Xiao M. A simple DNA stretching method for fluorescence imaging of single DNA molecules. Nucleic Acids Res 2006; 34:e113. [PMID: 16971459 PMCID: PMC1635263 DOI: 10.1093/nar/gkl593] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Stretching or aligning DNA molecules onto a surface by means of molecular combing techniques is one of the critical steps in single DNA molecule analysis. However, many of the current studies have focused on λ-DNA, or other large DNA molecules. There are very few studies on stretching methodologies for DNA molecules generated via PCR (typically smaller than 20 kb). Here we describe a simple method of stretching DNA molecules up to 18 kb in size on a modified glass surface. The very low background fluorescence allows efficient detection of single fluorescent dye labels incorporated into the stretched DNA molecules.
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Affiliation(s)
| | | | | | | | | | | | | | - Ming Xiao
- To whom correspondence should be addressed. 513 Parnassus Avenue, HSW-901A, San Francisco, CA 94143, USA. Tel: +1 4155143876; Fax: +1 4154762956;
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49
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Liberi G, Cotta-Ramusino C, Lopes M, Sogo J, Conti C, Bensimon A, Foiani M. Methods to study replication fork collapse in budding yeast. Methods Enzymol 2006; 409:442-62. [PMID: 16793417 DOI: 10.1016/s0076-6879(05)09026-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Replication of the eukaryotic genome is a difficult task, as cells must coordinate chromosome replication with chromatin remodeling, DNA recombination, DNA repair, transcription, cell cycle progression, and sister chromatid cohesion. Yet, DNA replication is a potentially genotoxic process, particularly when replication forks encounter a bulge in the template: forks under these conditions may stall and restart or even break down leading to fork collapse. It is now clear that fork collapse stimulates chromosomal rearrangements and therefore represents a potential source of DNA damage. Hence, the comprehension of the mechanisms that preserve replication fork integrity or that promote fork collapse are extremely relevant for the understanding of the cellular processes controlling genome stability. Here we describe some experimental approaches that can be used to physically visualize the quality of replication forks in the yeast S. cerevisiae and to distinguish between stalled and collapsed forks.
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Affiliation(s)
- Giordano Liberi
- F.I.R.C. Institute of Molecular Oncology Foundation and DSBB-University of Milan, Milan, Italy
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50
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Patel PK, Arcangioli B, Baker SP, Bensimon A, Rhind N. DNA replication origins fire stochastically in fission yeast. Mol Biol Cell 2005; 17:308-16. [PMID: 16251353 PMCID: PMC1345668 DOI: 10.1091/mbc.e05-07-0657] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
DNA replication initiates at discrete origins along eukaryotic chromosomes. However, in most organisms, origin firing is not efficient; a specific origin will fire in some but not all cell cycles. This observation raises the question of how individual origins are selected to fire and whether origin firing is globally coordinated to ensure an even distribution of replication initiation across the genome. We have addressed these questions by determining the location of firing origins on individual fission yeast DNA molecules using DNA combing. We show that the firing of replication origins is stochastic, leading to a random distribution of replication initiation. Furthermore, origin firing is independent between cell cycles; there is no epigenetic mechanism causing an origin that fires in one cell cycle to preferentially fire in the next. Thus, the fission yeast strategy for the initiation of replication is different from models of eukaryotic replication that propose coordinated origin firing.
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Affiliation(s)
- Prasanta K Patel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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