1
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Zhu X, Kanemaki MT. Replication initiation sites and zones in the mammalian genome: Where are they located and how are they defined? DNA Repair (Amst) 2024; 141:103713. [PMID: 38959715 DOI: 10.1016/j.dnarep.2024.103713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/05/2024]
Abstract
Eukaryotic DNA replication is a tightly controlled process that occurs in two main steps, i.e., licensing and firing, which take place in the G1 and S phases of the cell cycle, respectively. In Saccharomyces cerevisiae, the budding yeast, replication origins contain consensus sequences that are recognized and bound by the licensing factor Orc1-6, which then recruits the replicative Mcm2-7 helicase. By contrast, mammalian initiation sites lack such consensus sequences, and the mammalian ORC does not exhibit sequence specificity. Studies performed over the past decades have identified replication initiation sites in the mammalian genome using sequencing-based assays, raising the question of whether replication initiation occurs at confined sites or in broad zones across the genome. Although recent reports have shown that the licensed MCMs in mammalian cells are broadly distributed, suggesting that ORC-dependent licensing may not determine the initiation sites/zones, they are predominantly located upstream of actively transcribed genes. This review compares the mechanism of replication initiation in yeast and mammalian cells, summarizes the sequencing-based technologies used for the identification of initiation sites/zones, and proposes a possible mechanism of initiation-site/zone selection in mammalian cells. Future directions and challenges in this field are also discussed.
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Affiliation(s)
- Xiaoxuan Zhu
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Shizuoka, Mishima 411-8540, Japan.
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Shizuoka, Mishima 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Shizuoka, Mishima 411-8540, Japan; Department of Biological Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
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2
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Padayachy L, Ntallis SG, Halazonetis TD. RECQL4 is not critical for firing of human DNA replication origins. Sci Rep 2024; 14:7708. [PMID: 38565932 PMCID: PMC10987555 DOI: 10.1038/s41598-024-58404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/28/2024] [Indexed: 04/04/2024] Open
Abstract
Human RECQL4, a member of the RecQ helicase family, plays a role in maintaining genomic stability, but its precise function remains unclear. The N-terminus of RECQL4 has similarity to Sld2, a protein required for the firing of DNA replication origins in budding yeast. Consistent with this sequence similarity, the Xenopus laevis homolog of RECQL4 has been implicated in initiating DNA replication in egg extracts. To determine whether human RECQL4 is required for firing of DNA replication origins, we generated cells in which both RECQL4 alleles were targeted, resulting in either lack of protein expression (knock-out; KO) or expression of a full-length, mutant protein lacking helicase activity (helicase-dead; HD). Interestingly, both the RECQL4 KO and HD cells were viable and exhibited essentially identical origin firing profiles as the parental cells. Analysis of the rate of fork progression revealed increased rates in the RECQL4 KO cells, which might be indicative of decreased origin firing efficiency. Our results are consistent with human RECQL4 having a less critical role in firing of DNA replication origins, than its budding yeast homolog Sld2.
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Affiliation(s)
- Laura Padayachy
- Department of Molecular and Cellular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Sotirios G Ntallis
- Department of Molecular and Cellular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular and Cellular Biology, University of Geneva, 1205, Geneva, Switzerland.
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3
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Berger S, Chistol G. Visualizing the dynamics of DNA replication and repair at the single-molecule level. Methods Cell Biol 2023; 182:109-165. [PMID: 38359974 DOI: 10.1016/bs.mcb.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
During cell division, the genome of each eukaryotic cell is copied by thousands of replisomes-large protein complexes consisting of several dozen proteins. Recent studies suggest that the eukaryotic replisome is much more dynamic than previously thought. To directly visualize replisome dynamics in a physiological context, we recently developed a single-molecule approach for imaging replication proteins in Xenopus egg extracts. These extracts contain all the soluble nuclear proteins and faithfully recapitulate DNA replication and repair in vitro, serving as a powerful platform for studying the mechanisms of genome maintenance. Here we present detailed protocols for conducting single-molecule experiments in nuclear egg extracts and preparing key reagents. This workflow can be easily adapted to visualize the dynamics and function of other proteins implicated in DNA replication and repair.
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Affiliation(s)
- Scott Berger
- Biophysics Program, Stanford School of Medicine, Stanford, CA, United States
| | - Gheorghe Chistol
- Biophysics Program, Stanford School of Medicine, Stanford, CA, United States; Chemical and Systems Biology Department, Cancer Biology Program, Stanford School of Medicine, Stanford, CA, United States.
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4
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Groelly FJ, Dagg RA, Mailler J, Halazonetis TD, Tarsounas M. High-resolution mapping of mitotic DNA synthesis under conditions of replication stress in cultured cells. STAR Protoc 2023; 4:101970. [PMID: 36598851 PMCID: PMC9826876 DOI: 10.1016/j.xpro.2022.101970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/13/2022] [Accepted: 12/09/2022] [Indexed: 01/05/2023] Open
Abstract
Cells experiencing DNA replication stress enter mitosis with under-replicated DNA, which activates a repair mechanism known as mitotic DNA synthesis (MiDAS). Here we describe a protocol to identify at genome wide and at high resolution the genomic sites where MiDAS occurs in cells exposed to aphidicolin. We use EdU incorporation to label nascent DNA in mitotic cells, followed by isolation of the EdU-labeled DNA and next-generation sequencing. For complete details on the use and execution of this protocol, please refer to Groelly et al. (2022)1 and Macheret et al. (2020).2.
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Affiliation(s)
- Florian J Groelly
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Rebecca A Dagg
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Jonathan Mailler
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland.
| | - Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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5
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Moretton A, Slyskova J, Simaan ME, Arasa-Verge EA, Meyenberg M, Cerrón-Infantes DA, Unterlass MM, Loizou JI. Clickable Cisplatin Derivatives as Versatile Tools to Probe the DNA Damage Response to Chemotherapy. Front Oncol 2022; 12:874201. [PMID: 35719993 PMCID: PMC9202558 DOI: 10.3389/fonc.2022.874201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/29/2022] [Indexed: 12/04/2022] Open
Abstract
Cisplatin induces DNA crosslinks that are highly cytotoxic. Hence, platinum complexes are frequently used in the treatment of a broad range of cancers. Efficiency of cisplatin treatment is limited by the tumor-specific DNA damage response to the generated lesions. We reasoned that better tools to investigate the repair of DNA crosslinks induced by cisplatin would therefore be highly useful in addressing drug limitations. Here, we synthesized a series of cisplatin derivatives that are compatible with click chemistry, thus allowing visualization and isolation of DNA-platinum crosslinks from cells to study cellular responses. We prioritized one alkyne and one azide Pt(II) derivative, Pt-alkyne-53 and Pt-azide-64, for further biological characterization. We demonstrate that both compounds bind DNA and generate DNA lesions and that the viability of treated cells depends on the active DNA repair machinery. We also show that the compounds are clickable with both a fluorescent probe as well as biotin, thus they can be visualized in cells, and their ability to induce crosslinks in genomic DNA can be quantified. Finally, we show that Pt-alkyne-53 can be used to identify DNA repair proteins that bind within its proximity to facilitate its removal from DNA. The compounds we report here can be used as valuable experimental tools to investigate the DNA damage response to platinum complexes and hence might shed light on mechanisms of chemoresistance.
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Affiliation(s)
- Amandine Moretton
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jana Slyskova
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marwan E Simaan
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Materials Chemistry, Technische Universität Wien, Vienna, Austria.,Institute of Applied Synthetic Chemistry, Technische Universität Wien, Vienna, Austria
| | - Emili A Arasa-Verge
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Mathilde Meyenberg
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - D Alonso Cerrón-Infantes
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Materials Chemistry, Technische Universität Wien, Vienna, Austria.,Institute of Applied Synthetic Chemistry, Technische Universität Wien, Vienna, Austria.,Department of Chemistry, Solid State Chemistry, Universität Konstanz, Konstanz, Germany
| | - Miriam M Unterlass
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Materials Chemistry, Technische Universität Wien, Vienna, Austria.,Institute of Applied Synthetic Chemistry, Technische Universität Wien, Vienna, Austria.,Department of Chemistry, Solid State Chemistry, Universität Konstanz, Konstanz, Germany
| | - Joanna I Loizou
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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6
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Tipping WJ, Merchant AS, Fearon R, Tomkinson NCO, Faulds K, Graham D. Temporal imaging of drug dynamics in live cells using stimulated Raman scattering microscopy and a perfusion cell culture system. RSC Chem Biol 2022; 3:1154-1164. [PMID: 36128503 PMCID: PMC9428671 DOI: 10.1039/d2cb00160h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Multimodal imaging of drug uptake and cell viability analysis in the same live cell population is enabled using a perfusion cell culture system.
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Affiliation(s)
- William J. Tipping
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, UK
| | - Andrew S. Merchant
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, UK
| | - Rebecca Fearon
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, UK
| | | | - Karen Faulds
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, UK
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow G1 1RD, UK
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7
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St Germain C, Zhao H, Sinha V, Sanz LA, Chédin F, Barlow J. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2051-2073. [PMID: 35100392 PMCID: PMC8887484 DOI: 10.1093/nar/gkac035] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 01/05/2022] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
Abstract
Conflicts between transcription and replication machinery are a potent source of replication stress and genome instability; however, no technique currently exists to identify endogenous genomic locations prone to transcription–replication interactions. Here, we report a novel method to identify genomic loci prone to transcription–replication interactions termed transcription–replication immunoprecipitation on nascent DNA sequencing, TRIPn-Seq. TRIPn-Seq employs the sequential immunoprecipitation of RNA polymerase 2 phosphorylated at serine 5 (RNAP2s5) followed by enrichment of nascent DNA previously labeled with bromodeoxyuridine. Using TRIPn-Seq, we mapped 1009 unique transcription–replication interactions (TRIs) in mouse primary B cells characterized by a bimodal pattern of RNAP2s5, bidirectional transcription, an enrichment of RNA:DNA hybrids, and a high probability of forming G-quadruplexes. TRIs are highly enriched at transcription start sites and map to early replicating regions. TRIs exhibit enhanced Replication Protein A association and TRI-associated genes exhibit higher replication fork termination than control transcription start sites, two marks of replication stress. TRIs colocalize with double-strand DNA breaks, are enriched for deletions, and accumulate mutations in tumors. We propose that replication stress at TRIs induces mutations potentially contributing to age-related disease, as well as tumor formation and development.
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Affiliation(s)
- Commodore P St Germain
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
- School of Mathematics and Science, Solano Community College, 4000 Suisun Valley Road, Fairfield, CA 94534, USA
| | - Hongchang Zhao
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Vrishti Sinha
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Lionel A Sanz
- Department of Molecular and Cellular Biology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jacqueline H Barlow
- To whom correspondence should be addressed. Tel: +1 530 752 9529; Fax: +1 530 752 9014;
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8
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A transcription-based mechanism for oncogenic β-catenin-induced lethality in BRCA1/2-deficient cells. Nat Commun 2021; 12:4919. [PMID: 34389725 PMCID: PMC8363664 DOI: 10.1038/s41467-021-25215-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
BRCA1 or BRCA2 germline mutations predispose to breast, ovarian and other cancers. High-throughput sequencing of tumour genomes revealed that oncogene amplification and BRCA1/2 mutations are mutually exclusive in cancer, however the molecular mechanism underlying this incompatibility remains unknown. Here, we report that activation of β-catenin, an oncogene of the WNT signalling pathway, inhibits proliferation of BRCA1/2-deficient cells. RNA-seq analyses revealed β-catenin-induced discrete transcriptome alterations in BRCA2-deficient cells, including suppression of CDKN1A gene encoding the CDK inhibitor p21. This accelerates G1/S transition, triggering illegitimate origin firing and DNA damage. In addition, β-catenin activation accelerates replication fork progression in BRCA2-deficient cells, which is critically dependent on p21 downregulation. Importantly, we find that upregulated p21 expression is essential for the survival of BRCA2-deficient cells and tumours. Thus, our work demonstrates that β-catenin toxicity in cancer cells with compromised BRCA1/2 function is driven by transcriptional alterations that cause aberrant replication and inflict DNA damage. Germline mutations in BRCA1 or BRCA2 tumour suppressor genes predispose to different cancers, as does oncogene activation. Here the authors reveal that aberrant transcription of specific genes triggered by activation of the oncogene β-catenin causes replication failure and cell death in the context of BRCA1/2 deficiency.
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9
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Monitoring genome-wide replication fork directionality by Okazaki fragment sequencing in mammalian cells. Nat Protoc 2021; 16:1193-1218. [PMID: 33442052 DOI: 10.1038/s41596-020-00454-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/25/2020] [Indexed: 11/08/2022]
Abstract
The ability to monitor DNA replication fork directionality at the genome-wide scale is paramount for a greater understanding of how genetic and environmental perturbations can impact replication dynamics in human cells. Here we describe a detailed protocol for isolating and sequencing Okazaki fragments from asynchronously growing mammalian cells, termed Okazaki fragment sequencing (Ok-seq), for the purpose of quantitatively determining replication initiation and termination frequencies around specific genomic loci by meta-analyses. Briefly, cells are pulsed with 5-ethynyl-2'-deoxyuridine (EdU) to label newly synthesized DNA, and collected for DNA extraction. After size fractionation on a sucrose gradient, Okazaki fragments are concentrated and purified before click chemistry is used to tag the EdU label with a biotin conjugate that is cleavable under mild conditions. Biotinylated Okazaki fragments are then captured on streptavidin beads and ligated to Illumina adapters before library preparation for Illumina sequencing. The use of Ok-seq to interrogate genome-wide replication fork initiation and termination efficiencies can be applied to all unperturbed, asynchronously growing mammalian cells or under conditions of replication stress, and the assay can be performed in less than 2 weeks.
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10
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Strobino M, Wenda JM, Padayachy L, Steiner FA. Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans. Genome Res 2020; 30:1740-1751. [PMID: 33172964 PMCID: PMC7706726 DOI: 10.1101/gr.260794.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Histone H3.3 is a replication-independent variant of histone H3 with important roles in development, differentiation, and fertility. Here, we show that loss of H3.3 results in replication defects in Caenorhabditis elegans embryos at elevated temperatures. To characterize these defects, we adapt methods to determine replication timing, map replication origins, and examine replication fork progression. Our analysis of the spatiotemporal regulation of DNA replication shows that despite the very rapid embryonic cell cycle, the genome is replicated from early and late firing origins and is partitioned into domains of early and late replication. We find that under temperature stress conditions, additional replication origins become activated. Moreover, loss of H3.3 results in altered replication fork progression around origins, which is particularly evident at stress-activated origins. These replication defects are accompanied by replication checkpoint activation, a delayed cell cycle, and increased lethality in checkpoint-compromised embryos. Our comprehensive analysis of DNA replication in C. elegans reveals the genomic location of replication origins and the dynamics of their firing, and uncovers a role of H3.3 in the regulation of replication origins under stress conditions.
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Affiliation(s)
- Maude Strobino
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Joanna M Wenda
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Laura Padayachy
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
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11
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Macheret M, Bhowmick R, Sobkowiak K, Padayachy L, Mailler J, Hickson ID, Halazonetis TD. High-resolution mapping of mitotic DNA synthesis regions and common fragile sites in the human genome through direct sequencing. Cell Res 2020; 30:997-1008. [PMID: 32561860 PMCID: PMC7784693 DOI: 10.1038/s41422-020-0358-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/31/2020] [Indexed: 12/22/2022] Open
Abstract
DNA replication stress, a feature of human cancers, often leads to instability at specific genomic loci, such as the common fragile sites (CFSs). Cells experiencing DNA replication stress may also exhibit mitotic DNA synthesis (MiDAS). To understand the physiological function of MiDAS and its relationship to CFSs, we mapped, at high resolution, the genomic sites of MiDAS in cells treated with the DNA polymerase inhibitor aphidicolin. Sites of MiDAS were evident as well-defined peaks that were largely conserved between cell lines and encompassed all known CFSs. The MiDAS peaks mapped within large, transcribed, origin-poor genomic regions. In cells that had been treated with aphidicolin, these regions remained unreplicated even in late S phase; MiDAS then served to complete their replication after the cells entered mitosis. Interestingly, leading and lagging strand synthesis were uncoupled in MiDAS, consistent with MiDAS being a form of break-induced replication, a repair mechanism for collapsed DNA replication forks. Our results provide a better understanding of the mechanisms leading to genomic instability at CFSs and in cancer cells.
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Affiliation(s)
- Morgane Macheret
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Rahul Bhowmick
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Katarzyna Sobkowiak
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Laura Padayachy
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Jonathan Mailler
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark.
| | - Thanos D Halazonetis
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland.
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12
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Nonrandom DNA Segregation Detection under Replication Stress. STAR Protoc 2020; 1:100143. [PMID: 33377037 PMCID: PMC7757299 DOI: 10.1016/j.xpro.2020.100143] [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: 11/23/2022] Open
Abstract
Nonrandom DNA segregation (NDS) is a mitotic event in which sister chromatids carrying the old (parent) DNA strands are distributed exclusively to one of the two daughter cells. Although this phenomenon occurs in multiple organisms, the low frequency poses an obstacle to observation. Here, we present an improved protocol to induce NDS under replication stress. This protocol can be modified to accommodate various cell lines. For complete details on the use and execution of this protocol, please refer to Xing et al. (2020). Nonrandom DNA segregation is of significant relevance but difficult to observe Efficient induction of nonrandom DNA segregation by replication stress A step-by-step protocol for nonrandom DNA segregation detection by immunofluorescence
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13
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Tamayo-Orrego L, Gallo D, Racicot F, Bemmo A, Mohan S, Ho B, Salameh S, Hoang T, Jackson AP, Brown GW, Charron F. Sonic hedgehog accelerates DNA replication to cause replication stress promoting cancer initiation in medulloblastoma. ACTA ACUST UNITED AC 2020; 1:840-854. [DOI: 10.1038/s43018-020-0094-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 06/12/2020] [Indexed: 01/02/2023]
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14
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DNA copy-number measurement of genome replication dynamics by high-throughput sequencing: the sort-seq, sync-seq and MFA-seq family. Nat Protoc 2020; 15:1255-1284. [PMID: 32051615 DOI: 10.1038/s41596-019-0287-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/16/2019] [Indexed: 12/20/2022]
Abstract
Genome replication follows a defined temporal programme that can change during cellular differentiation and disease onset. DNA replication results in an increase in DNA copy number that can be measured by high-throughput sequencing. Here we present a protocol to determine genome replication dynamics using DNA copy-number measurements. Cell populations can be obtained in three variants of the method. First, sort-seq reveals the average replication dynamics across S phase in an unperturbed cell population; FACS is used to isolate replicating and non-replicating subpopulations from asynchronous cells. Second, sync-seq measures absolute replication time at specific points during S phase using a synchronized cell population. Third, marker frequency analysis can be used to reveal the average replication dynamics using copy-number analysis in any proliferating asynchronous cell culture. These approaches have been used to reveal genome replication dynamics in prokaryotes, archaea and a wide range of eukaryotes, including yeasts and mammalian cells. We have found this approach straightforward to apply to other organisms and highlight example studies from across the three domains of life. Here we present a Saccharomyces cerevisiae version of the protocol that can be performed in 7-10 d. It requires basic molecular and cellular biology skills, as well as a basic understanding of Unix and R.
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