51
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Petryk N, Bultmann S, Bartke T, Defossez PA. Staying true to yourself: mechanisms of DNA methylation maintenance in mammals. Nucleic Acids Res 2021; 49:3020-3032. [PMID: 33300031 PMCID: PMC8034647 DOI: 10.1093/nar/gkaa1154] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 12/16/2022] Open
Abstract
DNA methylation is essential to development and cellular physiology in mammals. Faulty DNA methylation is frequently observed in human diseases like cancer and neurological disorders. Molecularly, this epigenetic mark is linked to other chromatin modifications and it regulates key genomic processes, including transcription and splicing. Each round of DNA replication generates two hemi-methylated copies of the genome. These must be converted back to symmetrically methylated DNA before the next S-phase, or the mark will fade away; therefore the maintenance of DNA methylation is essential. Mechanistically, the maintenance of this epigenetic modification takes place during and after DNA replication, and occurs within the very dynamic context of chromatin re-assembly. Here, we review recent discoveries and unresolved questions regarding the mechanisms, dynamics and fidelity of DNA methylation maintenance in mammals. We also discuss how it could be regulated in normal development and misregulated in disease.
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Affiliation(s)
- Nataliya Petryk
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, F-75013 Paris, France
| | - Sebastian Bultmann
- Department of Biology II, Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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52
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Bonnell E, Pasquier E, Wellinger RJ. Telomere Replication: Solving Multiple End Replication Problems. Front Cell Dev Biol 2021; 9:668171. [PMID: 33869233 PMCID: PMC8047117 DOI: 10.3389/fcell.2021.668171] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/10/2021] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic genomes are highly complex and divided into linear chromosomes that require end protection from unwarranted fusions, recombination, and degradation in order to maintain genomic stability. This is accomplished through the conserved specialized nucleoprotein structure of telomeres. Due to the repetitive nature of telomeric DNA, and the unusual terminal structure, namely a protruding single stranded 3' DNA end, completing telomeric DNA replication in a timely and efficient manner is a challenge. For example, the end replication problem causes a progressive shortening of telomeric DNA at each round of DNA replication, thus telomeres eventually lose their protective capacity. This phenomenon is counteracted by the recruitment and the activation at telomeres of the specialized reverse transcriptase telomerase. Despite the importance of telomerase in providing a mechanism for complete replication of telomeric ends, the majority of telomere replication is in fact carried out by the conventional DNA replication machinery. There is significant evidence demonstrating that progression of replication forks is hampered at chromosomal ends due to telomeric sequences prone to form secondary structures, tightly DNA-bound proteins, and the heterochromatic nature of telomeres. The telomeric loop (t-loop) formed by invasion of the 3'-end into telomeric duplex sequences may also impede the passage of replication fork. Replication fork stalling can lead to fork collapse and DNA breaks, a major cause of genomic instability triggered notably by unwanted repair events. Moreover, at chromosomal ends, unreplicated DNA distal to a stalled fork cannot be rescued by a fork coming from the opposite direction. This highlights the importance of the multiple mechanisms involved in overcoming fork progression obstacles at telomeres. Consequently, numerous factors participate in efficient telomeric DNA duplication by preventing replication fork stalling or promoting the restart of a stalled replication fork at telomeres. In this review, we will discuss difficulties associated with the passage of the replication fork through telomeres in both fission and budding yeasts as well as mammals, highlighting conserved mechanisms implicated in maintaining telomere integrity during replication, thus preserving a stable genome.
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Affiliation(s)
| | | | - Raymund J. Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, QC, Canada
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53
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Sánchez H, McCluskey K, van Laar T, van Veen E, Asscher FM, Solano B, Diffley JFX, Dekker NH. DNA replication origins retain mobile licensing proteins. Nat Commun 2021; 12:1908. [PMID: 33772005 PMCID: PMC7998030 DOI: 10.1038/s41467-021-22216-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/04/2021] [Indexed: 11/22/2022] Open
Abstract
DNA replication in eukaryotes initiates at many origins distributed across each chromosome. Origins are bound by the origin recognition complex (ORC), which, with Cdc6 and Cdt1, recruits and loads the Mcm2-7 (MCM) helicase as an inactive double hexamer during G1 phase. The replisome assembles at the activated helicase in S phase. Although the outline of replisome assembly is understood, little is known about the dynamics of individual proteins on DNA and how these contribute to proper complex formation. Here we show, using single-molecule optical trapping and confocal microscopy, that yeast ORC is a mobile protein that diffuses rapidly along DNA. Origin recognition halts this search process. Recruitment of MCM molecules in an ORC- and Cdc6-dependent fashion results in slow-moving ORC-MCM intermediates and MCMs that rapidly scan the DNA. Following ATP hydrolysis, salt-stable loading of MCM single and double hexamers was seen, both of which exhibit salt-dependent mobility. Our results demonstrate that effective helicase loading relies on an interplay between protein diffusion and origin recognition, and suggest that MCM is stably loaded onto DNA in multiple forms.
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Affiliation(s)
- Humberto Sánchez
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Kaley McCluskey
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Theo van Laar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Edo van Veen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Filip M Asscher
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Belén Solano
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - John F X Diffley
- Chromosome Replication Laboratory, Francis Crick Institute, London, UK.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
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54
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Kirstein N, Buschle A, Wu X, Krebs S, Blum H, Kremmer E, Vorberg IM, Hammerschmidt W, Lacroix L, Hyrien O, Audit B, Schepers A. Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones. eLife 2021; 10:62161. [PMID: 33683199 PMCID: PMC7993996 DOI: 10.7554/elife.62161] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 03/05/2021] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic DNA replication initiates during S phase from origins that have been licensed in the preceding G1 phase. Here, we compare ChIP-seq profiles of the licensing factors Orc2, Orc3, Mcm3, and Mcm7 with gene expression, replication timing, and fork directionality profiles obtained by RNA-seq, Repli-seq, and OK-seq. Both, the origin recognition complex (ORC) and the minichromosome maintenance complex (MCM) are significantly and homogeneously depleted from transcribed genes, enriched at gene promoters, and more abundant in early- than in late-replicating domains. Surprisingly, after controlling these variables, no difference in ORC/MCM density is detected between initiation zones, termination zones, unidirectionally replicating regions, and randomly replicating regions. Therefore, ORC/MCM density correlates with replication timing but does not solely regulate the probability of replication initiation. Interestingly, H4K20me3, a histone modification proposed to facilitate late origin licensing, was enriched in late-replicating initiation zones and gene deserts of stochastic replication fork direction. We discuss potential mechanisms specifying when and where replication initiates in human cells.
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Affiliation(s)
- Nina Kirstein
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Munich, Germany
| | - Alexander Buschle
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health and German Center for Infection Research (DZIF), Munich, Germany
| | - Xia Wu
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the Ludwig-Maximilians Universität (LMU) München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the Ludwig-Maximilians Universität (LMU) München, Munich, Germany
| | - Elisabeth Kremmer
- Institute for Molecular Immunology, Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Ina M Vorberg
- German Center for Neurodegenerative Diseases (DZNE e.V.), Bonn, Germany.,Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health and German Center for Infection Research (DZIF), Munich, Germany
| | - Laurent Lacroix
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Benjamin Audit
- Univ Lyon, ENS de Lyon, Univ. Claude Bernard, CNRS, Laboratoire de Physique, 69342 Lyon, France
| | - Aloys Schepers
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Munich, Germany
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55
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The extrachromosomal elements of the Naegleria genus: How little we know. Plasmid 2021; 115:102567. [PMID: 33617907 DOI: 10.1016/j.plasmid.2021.102567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 11/20/2022]
Abstract
There are currently 47 characterized species in the Naegleria genus of free-living amoebae. Each amoeba has thousands of extrachromosomal elements that are closed circular structures comprised of a single ribosomal DNA (rDNA) copy and a large non-rDNA sequence. Despite the presence of putative open reading frames and introns, ribosomal RNA is the only established transcript. A single origin of DNA replication (ori) has been mapped within the non-rDNA sequence for one species (N. gruberi), a finding that strongly indicates that these episomes replicate independently of the cell's chromosomal DNA component. This article reviews that which has been published about these interesting DNA elements and by analyzing available sequence data, discusses the possibility that different phylogenetically related clusters of Naegleria species individually conserve ori structures and suggests where the rRNA promoter and termination sites may be located.
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56
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Abstract
The Origin Recognition Complex (ORC) is an evolutionarily conserved six-subunit protein complex that binds specific sites at many locations to coordinately replicate the entire eukaryote genome. Though highly conserved in structure, ORC’s selectivity for replication origins has diverged tremendously between yeasts and humans to adapt to vastly different life cycles. In this work, we demonstrate that the selectivity determinant of ORC for DNA binding lies in a 19-amino acid insertion helix in the Orc4 subunit, which is present in yeast but absent in human. Removal of this motif from Orc4 transforms the yeast ORC, which selects origins based on base-specific binding at defined locations, into one whose selectivity is dictated by chromatin landscape and afforded with plasticity, as reported for human. Notably, the altered yeast ORC has acquired an affinity for regions near transcriptional start sites (TSSs), which the human ORC also favors. In most model yeast species the Origin Recognition Complex (ORC) binds defined and species-specific base sequences while in humans what determines the binding appears to be more complex. Here the authors reveal that the yeast’s ORC complex binding specificity is dependent on a 19-amino acid insertion helix in the Orc4 subunit which is lost in human.
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57
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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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58
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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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59
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Falbo L, Costanzo V. Epigenetic regulation of replication origin assembly: A role for histone H1 and chromatin remodeling factors. Bioessays 2020; 43:e2000181. [PMID: 33165968 DOI: 10.1002/bies.202000181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 12/18/2022]
Abstract
During early embryonic development in several metazoans, accurate DNA replication is ensured by high number of replication origins. This guarantees rapid genome duplication coordinated with fast cell divisions. In Xenopus laevis embryos this program switches to one with a lower number of origins at a developmental stage known as mid-blastula transition (MBT) when cell cycle length increases and gene transcription starts. Consistent with this regulation, somatic nuclei replicate poorly when transferred to eggs, suggesting the existence of an epigenetic memory suppressing replication assembly origins at all available sites. Recently, it was shown that histone H1 imposes a non-permissive chromatin configuration preventing replication origin assembly on somatic nuclei. This somatic state can be erased by SSRP1, a subunit of the FACT complex. Here, we further develop the hypothesis that this novel form of epigenetic memory might impact on different areas of vertebrate biology going from nuclear reprogramming to cancer development.
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Affiliation(s)
- Lucia Falbo
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, Milan, 20139, Italy
| | - Vincenzo Costanzo
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, Milan, 20139, Italy.,Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
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60
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Ding Q, Koren A. Positive and Negative Regulation of DNA Replication Initiation. Trends Genet 2020; 36:868-879. [PMID: 32739030 PMCID: PMC7572746 DOI: 10.1016/j.tig.2020.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
Genomic DNA is replicated every cell cycle by the programmed activation of replication origins at specific times and chromosomal locations. The factors that define the locations of replication origins and their typical activation times in eukaryotic cells are poorly understood. Previous studies highlighted the role of activating factors and epigenetic modifications in regulating replication initiation. Here, we review the role that repressive pathways - and their alleviation - play in establishing the genomic landscape of replication initiation. Several factors mediate this repression, in particular, factors associated with inactive chromatin. Repression can support organized, yet stochastic, replication initiation, and its absence could explain instances of rapid and random replication or re-replication.
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Affiliation(s)
- Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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61
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Irwin NAT, Pittis AA, Mathur V, Howe LJ, Keeling PJ, Lynn DH, Bourland WA. The Function and Evolution of Motile DNA Replication Systems in Ciliates. Curr Biol 2020; 31:66-76.e6. [PMID: 33125869 DOI: 10.1016/j.cub.2020.09.077] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/09/2020] [Accepted: 09/25/2020] [Indexed: 01/31/2023]
Abstract
DNA replication is a ubiquitous and conserved cellular process. However, regulation of DNA replication is only understood in a small fraction of organisms that poorly represent the diversity of genetic systems in nature. Here we used computational and experimental approaches to examine the function and evolution of one such system, the replication band (RB) in spirotrich ciliates, which is a localized, motile hub that traverses the macronucleus while replicating DNA. We show that the RB can take unique forms in different species, from polar bands to a "replication envelope," where replication initiates at the nuclear periphery before advancing inward. Furthermore, we identify genes involved in cellular transport, including calcium transporters and cytoskeletal regulators, that are associated with the RB and may be involved in its function and translocation. These findings highlight the evolution and diversity of DNA replication systems and provide insights into the regulation of nuclear organization and processes.
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Affiliation(s)
- Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Alexandros A Pittis
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - LeAnn J Howe
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Denis H Lynn
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - William A Bourland
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA.
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62
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Hu Y, Tareen A, Sheu YJ, Ireland WT, Speck C, Li H, Joshua-Tor L, Kinney JB, Stillman B. Evolution of DNA replication origin specification and gene silencing mechanisms. Nat Commun 2020; 11:5175. [PMID: 33056978 PMCID: PMC7560902 DOI: 10.1038/s41467-020-18964-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/22/2020] [Indexed: 02/08/2023] Open
Abstract
DNA replication in eukaryotic cells initiates from replication origins that bind the Origin Recognition Complex (ORC). Origin establishment requires well-defined DNA sequence motifs in Saccharomyces cerevisiae and some other budding yeasts, but most eukaryotes lack sequence-specific origins. A 3.9 Å structure of S. cerevisiae ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) bound to origin DNA revealed that a loop within Orc2 inserts into a DNA minor groove and an α-helix within Orc4 inserts into a DNA major groove. Using a massively parallel origin selection assay coupled with a custom mutual-information-based modeling approach, and a separate analysis of whole-genome replication profiling, here we show that the Orc4 α-helix contributes to the DNA sequence-specificity of origins in S. cerevisiae and Orc4 α-helix mutations change genome-wide origin firing patterns. The DNA sequence specificity of replication origins, mediated by the Orc4 α-helix, has co-evolved with the gain of ORC-Sir4-mediated gene silencing and the loss of RNA interference. Contrary to most eukaryotes that lack sequence-specific origins of replication, S. cerevisiae origins are defined by specific DNA sequence motifs. Here the authors reveal that multiple subunits of ORC, including Orc2 and Orc4, contribute to the sequence-specificity of origins in S. cerevisiae.
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Affiliation(s)
- Y Hu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.,Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - A Tareen
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Y-J Sheu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - W T Ireland
- Department of Physics, California Institute of Technology, Pasadena, CA, 91125, USA
| | - C Speck
- DNA Replication Group, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, W12 0NN, London, UK
| | - H Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - L Joshua-Tor
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.,W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, NY, 11724, USA
| | - J B Kinney
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - B Stillman
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
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63
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Yuan Z, Li H. Molecular mechanisms of eukaryotic origin initiation, replication fork progression, and chromatin maintenance. Biochem J 2020; 477:3499-3525. [PMID: 32970141 PMCID: PMC7574821 DOI: 10.1042/bcj20200065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022]
Abstract
Eukaryotic DNA replication is a highly dynamic and tightly regulated process. Replication involves several dozens of replication proteins, including the initiators ORC and Cdc6, replicative CMG helicase, DNA polymerase α-primase, leading-strand DNA polymerase ε, and lagging-strand DNA polymerase δ. These proteins work together in a spatially and temporally controlled manner to synthesize new DNA from the parental DNA templates. During DNA replication, epigenetic information imprinted on DNA and histone proteins is also copied to the daughter DNA to maintain the chromatin status. DNA methyltransferase 1 is primarily responsible for copying the parental DNA methylation pattern into the nascent DNA. Epigenetic information encoded in histones is transferred via a more complex and less well-understood process termed replication-couple nucleosome assembly. Here, we summarize the most recent structural and biochemical insights into DNA replication initiation, replication fork elongation, chromatin assembly and maintenance, and related regulatory mechanisms.
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Affiliation(s)
- Zuanning Yuan
- Structural Biology Program, Van Andel Institute, Grand Rapids, Michigan, U.S.A
| | - Huilin Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, Michigan, U.S.A
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64
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Huang TT, Brill E, Nair JR, Zhang X, Wilson KM, Chen L, Thomas CJ, Lee JM. Targeting the PI3K/mTOR Pathway Augments CHK1 Inhibitor-Induced Replication Stress and Antitumor Activity in High-Grade Serous Ovarian Cancer. Cancer Res 2020; 80:5380-5392. [PMID: 32998994 DOI: 10.1158/0008-5472.can-20-1439] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/04/2020] [Accepted: 09/18/2020] [Indexed: 01/08/2023]
Abstract
High-grade serous ovarian carcinoma (HGSOC) is the most lethal gynecologic malignancy in industrialized countries and has limited treatment options. Targeting ataxia-telangiectasia and Rad3-related/cell-cycle checkpoint kinase 1 (CHK1)-mediated S-phase and G2-M-phase cell-cycle checkpoints has been a promising therapeutic strategy in HGSOC. To improve the efficacy of CHK1 inhibitor (CHK1i), we conducted a high-throughput drug combination screening in HGSOC cells. PI3K/mTOR pathway inhibitors (PI3K/mTORi) showed supra-additive cytotoxicity with CHK1i. Combined treatment with CHK1i and PI3K/mTORi significantly attenuated cell viability and increased DNA damage, chromosomal breaks, and mitotic catastrophe compared with monotherapy. PI3K/mTORi decelerated fork speed by promoting new origin firing via increased CDC45, thus potentiating CHK1i-induced replication stress. PI3K/mTORi also augmented CHK1i-induced DNA damage by attenuating DNA homologous recombination repair activity and RAD51 foci formation. High expression of replication stress markers was associated with poor prognosis in patients with HGSOC. Our findings indicate that combined PI3K/mTORi and CHK1i induces greater cell death in HGSOC cells and in vivo models by causing lethal replication stress and DNA damage. This insight can be translated therapeutically by further developing combinations of PI3K and cell-cycle pathway inhibitors in HGSOC. SIGNIFICANCE: Dual inhibition of CHK1 and PI3K/mTOR pathways yields potent synthetic lethality by causing lethal replication stress and DNA damage in HGSOC, warranting further clinical development.
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Affiliation(s)
- Tzu-Ting Huang
- Women's Malignancies Branch, Center for Cancer Research, NCI, Bethesda, Maryland.
| | - Ethan Brill
- Women's Malignancies Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Jayakumar R Nair
- Women's Malignancies Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Xiaohu Zhang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Bethesda, Maryland
| | - Kelli M Wilson
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Bethesda, Maryland
| | - Lu Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Bethesda, Maryland
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Bethesda, Maryland.,Lymphoid Malignancies Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Jung-Min Lee
- Women's Malignancies Branch, Center for Cancer Research, NCI, Bethesda, Maryland
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65
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Brossas C, Valton AL, Venev SV, Chilaka S, Counillon A, Laurent M, Goncalves C, Duriez B, Picard F, Dekker J, Prioleau MN. Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain. EMBO J 2020; 39:e99520. [PMID: 32935369 PMCID: PMC7604622 DOI: 10.15252/embj.201899520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/31/2020] [Accepted: 08/25/2020] [Indexed: 12/27/2022] Open
Abstract
Vertebrate genomes replicate according to a precise temporal program strongly correlated with their organization into A/B compartments. Until now, the molecular mechanisms underlying the establishment of early-replicating domains remain largely unknown. We defined two minimal cis-element modules containing a strong replication origin and chromatin modifier binding sites capable of shifting a targeted mid-late-replicating region for earlier replication. The two origins overlap with a constitutive or a silent tissue-specific promoter. When inserted side-by-side, these modules advance replication timing over a 250 kb region through the cooperation with one endogenous origin located 30 kb away. Moreover, when inserted at two chromosomal sites separated by 30 kb, these two modules come into close physical proximity and form an early-replicating domain establishing more contacts with active A compartments. The synergy depends on the presence of the active promoter/origin. Our results show that clustering of strong origins located at active promoters can establish early-replicating domains.
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Affiliation(s)
- Caroline Brossas
- CNRS, Institut Jacques Monod, Equipe Labellisée Association Pour la Recherche sur le Cancer, Université de Paris, Paris, France
| | - Anne-Laure Valton
- Department of Biochemistry and Molecular Pharmacology, Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sergey V Venev
- Department of Biochemistry and Molecular Pharmacology, Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Antonin Counillon
- CNRS, Institut Jacques Monod, Equipe Labellisée Association Pour la Recherche sur le Cancer, Université de Paris, Paris, France
| | - Marc Laurent
- CNRS, Institut Jacques Monod, Equipe Labellisée Association Pour la Recherche sur le Cancer, Université de Paris, Paris, France
| | - Coralie Goncalves
- CNRS, Institut Jacques Monod, Equipe Labellisée Association Pour la Recherche sur le Cancer, Université de Paris, Paris, France
| | - Bénédicte Duriez
- CNRS, Institut Jacques Monod, Equipe Labellisée Association Pour la Recherche sur le Cancer, Université de Paris, Paris, France
| | - Franck Picard
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Job Dekker
- Department of Biochemistry and Molecular Pharmacology, Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Marie-Noëlle Prioleau
- CNRS, Institut Jacques Monod, Equipe Labellisée Association Pour la Recherche sur le Cancer, Université de Paris, Paris, France
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66
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Gadgil RY, Romer EJ, Goodman CC, Rider SD, Damewood FJ, Barthelemy JR, Shin-Ya K, Hanenberg H, Leffak M. Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication. J Biol Chem 2020; 295:15378-15397. [PMID: 32873711 DOI: 10.1074/jbc.ra120.013495] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/23/2020] [Indexed: 12/12/2022] Open
Abstract
Short tandemly repeated DNA sequences, termed microsatellites, are abundant in the human genome. These microsatellites exhibit length instability and susceptibility to DNA double-strand breaks (DSBs) due to their tendency to form stable non-B DNA structures. Replication-dependent microsatellite DSBs are linked to genome instability signatures in human developmental diseases and cancers. To probe the causes and consequences of microsatellite DSBs, we designed a dual-fluorescence reporter system to detect DSBs at expanded (CTG/CAG) n and polypurine/polypyrimidine (Pu/Py) mirror repeat structures alongside the c-myc replication origin integrated at a single ectopic chromosomal site. Restriction cleavage near the (CTG/CAG)100 microsatellite leads to homology-directed single-strand annealing between flanking AluY elements and reporter gene deletion that can be detected by flow cytometry. However, in the absence of restriction cleavage, endogenous and exogenous replication stressors induce DSBs at the (CTG/CAG)100 and Pu/Py microsatellites. DSBs map to a narrow region at the downstream edge of the (CTG)100 lagging-strand template. (CTG/CAG) n chromosome fragility is repeat length-dependent, whereas instability at the (Pu/Py) microsatellites depends on replication polarity. Strikingly, restriction-generated DSBs and replication-dependent DSBs are not repaired by the same mechanism. Knockdown of DNA damage response proteins increases (Rad18, polymerase (Pol) η, Pol κ) or decreases (Mus81) the sensitivity of the (CTG/CAG)100 microsatellites to replication stress. Replication stress and DSBs at the ectopic (CTG/CAG)100 microsatellite lead to break-induced replication and high-frequency mutagenesis at a flanking thymidine kinase gene. Our results show that non-B structure-prone microsatellites are susceptible to replication-dependent DSBs that cause genome instability.
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Affiliation(s)
- Rujuta Yashodhan Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Eric J Romer
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Caitlin C Goodman
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - S Dean Rider
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - French J Damewood
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Joanna R Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Kazuo Shin-Ya
- Biomedical Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, Düsseldorf, Germany; Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA.
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67
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Villar-Fernández MA, Cardoso da Silva R, Firlej M, Pan D, Weir E, Sarembe A, Raina VB, Bange T, Weir JR, Vader G. Biochemical and functional characterization of a meiosis-specific Pch2/ORC AAA+ assembly. Life Sci Alliance 2020; 3:3/11/e201900630. [PMID: 32826290 PMCID: PMC7442955 DOI: 10.26508/lsa.201900630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
The AAA+ protein Pch2 forms a biochemical complex with Orc1/ORC to suppress DNA break formation in the meiotic G2/prophase. Pch2 is a meiosis-specific AAA+ protein that controls several important chromosomal processes. We previously demonstrated that Orc1, a subunit of the ORC, functionally interacts with budding yeast Pch2. The ORC (Orc1-6) AAA+ complex loads the AAA+ MCM helicase to origins of replication, but whether and how ORC collaborates with Pch2 remains unclear. Here, we show that a Pch2 hexamer directly associates with ORC during the meiotic G2/prophase. Biochemical analysis suggests that Pch2 uses its non-enzymatic NH2-terminal domain and AAA+ core and likely engages the interface of ORC that also binds to Cdc6, a factor crucial for ORC-MCM binding. Canonical ORC function requires association with origins, but we show here that despite causing efficient removal of Orc1 from origins, nuclear depletion of Orc2 and Orc5 does not trigger Pch2/Orc1-like meiotic phenotypes. This suggests that the function for Orc1/Pch2 in meiosis can be executed without efficient association of ORC with origins of replication. In conclusion, we uncover distinct functionalities for Orc1/ORC that drive the establishment of a non-canonical, meiosis-specific AAA+ assembly with Pch2.
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Affiliation(s)
- María Ascensión Villar-Fernández
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,International Max Planck Research School in Chemical and Molecular Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Richard Cardoso da Silva
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Dongqing Pan
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Elisabeth Weir
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Annika Sarembe
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Vivek B Raina
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,International Max Planck Research School in Chemical and Molecular Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Tanja Bange
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - John R Weir
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Friedrich Miescher Laboratory, Tübingen, Germany
| | - Gerben Vader
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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68
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Jaremko MJ, On KF, Thomas DR, Stillman B, Joshua-Tor L. The dynamic nature of the human origin recognition complex revealed through five cryoEM structures. eLife 2020; 9:e58622. [PMID: 32808929 PMCID: PMC7467728 DOI: 10.7554/elife.58622] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022] Open
Abstract
Genome replication is initiated from specific origin sites established by dynamic events. The Origin Recognition Complex (ORC) is necessary for orchestrating the initiation process by binding to origin DNA, recruiting CDC6, and assembling the MCM replicative helicase on DNA. Here we report five cryoEM structures of the human ORC (HsORC) that illustrate the native flexibility of the complex. The absence of ORC1 revealed a compact, stable complex of ORC2-5. Introduction of ORC1 opens the complex into several dynamic conformations. Two structures revealed dynamic movements of the ORC1 AAA+ and ORC2 winged-helix domains that likely impact DNA incorporation into the ORC core. Additional twist and pinch motions were observed in an open ORC conformation revealing a hinge at the ORC5·ORC3 interface that may facilitate ORC binding to DNA. Finally, a structure of ORC was determined with endogenous DNA bound in the core revealing important differences between human and yeast origin recognition.
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Affiliation(s)
- Matt J Jaremko
- W. M. Keck Structural Biology LaboratoryNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
- Cold Spring Harbor LaboratoryNew YorkUnited States
| | - Kin Fan On
- W. M. Keck Structural Biology LaboratoryNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
- Cold Spring Harbor LaboratoryNew YorkUnited States
| | - Dennis R Thomas
- W. M. Keck Structural Biology LaboratoryNew YorkUnited States
- Cold Spring Harbor LaboratoryNew YorkUnited States
| | | | - Leemor Joshua-Tor
- W. M. Keck Structural Biology LaboratoryNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
- Cold Spring Harbor LaboratoryNew YorkUnited States
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69
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Chromatin and Nuclear Architecture: Shaping DNA Replication in 3D. Trends Genet 2020; 36:967-980. [PMID: 32713597 DOI: 10.1016/j.tig.2020.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022]
Abstract
In eukaryotes, DNA replication progresses through a finely orchestrated temporal and spatial program. The 3D genome structure and nuclear architecture have recently emerged as fundamental determinants of the replication program. Factors with established roles in replication have been recognized as genome organization regulators. Exploiting paradigms from yeasts and mammals, we discuss how DNA replication is regulated in time and space through DNA-associated trans-acting factors, diffusible limiting replication initiation factors, higher-order chromatin folding, dynamic origin localization, and specific nuclear microenvironments. We present an integrated model for the regulation of DNA replication in 3D and highlight the importance of accurate spatio-temporal regulation of DNA replication in physiology and disease.
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70
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de Araujo CB, da Cunha JPC, Inada DT, Damasceno J, Lima ARJ, Hiraiwa P, Marques C, Gonçalves E, Nishiyama-Junior MY, McCulloch R, Elias MC. Replication origin location might contribute to genetic variability in Trypanosoma cruzi. BMC Genomics 2020; 21:414. [PMID: 32571205 PMCID: PMC7310030 DOI: 10.1186/s12864-020-06803-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/05/2020] [Indexed: 11/29/2022] Open
Abstract
Background DNA replication in trypanosomatids operates in a uniquely challenging environment, since most of their genomes are constitutively transcribed. Trypanosoma cruzi, the etiological agent of Chagas disease, presents high variability in both chromosomes size and copy number among strains, though the underlying mechanisms are unknown. Results Here we have mapped sites of DNA replication initiation across the T. cruzi genome using Marker Frequency Analysis, which has previously only been deployed in two related trypanosomatids. The putative origins identified in T. cruzi show a notable enrichment of GC content, a preferential position at subtelomeric regions, coinciding with genes transcribed towards the telomeres, and a pronounced enrichment within coding DNA sequences, most notably in genes from the Dispersed Gene Family 1 (DGF-1). Conclusions These findings suggest a scenario where collisions between DNA replication and transcription are frequent, leading to increased genetic variability, as seen by the increase SNP levels at chromosome subtelomeres and in DGF-1 genes containing putative origins.
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Affiliation(s)
- Christiane Bezerra de Araujo
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil.,Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil. .,Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.
| | - Davi Toshio Inada
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil.,Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Jeziel Damasceno
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Alex Ranieri Jerônimo Lima
- Laboratório de Tecnologia Biomolecular - Bioinformática, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | | | - Catarina Marques
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Evonnildo Gonçalves
- Laboratório de Tecnologia Biomolecular - Bioinformática, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Milton Yutaka Nishiyama-Junior
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.,Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Maria Carolina Elias
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil. .,Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.
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71
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Yella VR, Vanaja A, Kulandaivelu U, Kumar A. Delving into Eukaryotic Origins of Replication Using DNA Structural Features. ACS OMEGA 2020; 5:13601-13611. [PMID: 32566825 PMCID: PMC7301376 DOI: 10.1021/acsomega.0c00441] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/15/2020] [Indexed: 05/18/2023]
Abstract
DNA replication in eukaryotes is an intricate process, which is precisely synchronized by a set of regulatory proteins, and the replication fork emanates from discrete sites on chromatin called origins of replication (Oris). These spots are considered as the gateway to chromosomal replication and are stereotyped by sequence motifs. The cognate sequences are noticeable in a small group of entire origin regions or totally absent across different metazoans. Alternatively, the use of DNA secondary structural features can provide additional information compared to the primary sequence. In this article, we report the trends in DNA sequence-based structural properties of origin sequences in nine eukaryotic systems representing different families of life. Biologically relevant DNA secondary structural properties, namely, stability, propeller twist, flexibility, and minor groove shape were studied in the sequences flanking replication start sites. Results indicate that Oris in yeasts show lower stability, more rigidity, and narrow minor groove preferences compared to genomic sequences surrounding them. Yeast Oris also show preference for A-tracts and the promoter element TATA box in the vicinity of replication start sites. On the contrary, Drosophila melanogaster, humans, and Arabidopsis thaliana do not have such features in their Oris, and instead, they show high preponderance of G-rich sequence motifs such as putative G-quadruplexes or i-motifs and CpG islands. Our extensive study applies the DNA structural feature computation to delve into origins of replication across organisms ranging from yeasts to mammals and including a plant. Insights from this study would be significant in understanding origin architecture and help in designing new algorithms for predicting DNA trans-acting factor recognition events.
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Affiliation(s)
- Venkata Rajesh Yella
- Department
of Biotechnology, Koneru Lakshmaiah Education
Foundation, Guntur 522502, Andhra Pradesh, India
| | - Akkinepally Vanaja
- Department
of Biotechnology, Koneru Lakshmaiah Education
Foundation, Guntur 522502, Andhra Pradesh, India
- KL
College of Pharmacy, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur 522502, Andhra Pradesh, India
| | - Umasankar Kulandaivelu
- KL
College of Pharmacy, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur 522502, Andhra Pradesh, India
| | - Aditya Kumar
- Department
of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
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72
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Qiu L, Zeng X, Han J. Histone variant H2A.Z facilitates DNA replication. SCIENCE CHINA-LIFE SCIENCES 2020; 63:788-790. [PMID: 32215843 DOI: 10.1007/s11427-020-1673-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/06/2020] [Indexed: 02/05/2023]
Affiliation(s)
- Lei Qiu
- Department of Abdominal Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Xinyi Zeng
- Department of Abdominal Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Junhong Han
- Department of Abdominal Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
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73
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Zhang W, Feng J, Li Q. The replisome guides nucleosome assembly during DNA replication. Cell Biosci 2020; 10:37. [PMID: 32190287 PMCID: PMC7066812 DOI: 10.1186/s13578-020-00398-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/29/2020] [Indexed: 12/18/2022] Open
Abstract
Nucleosome assembly during DNA replication is tightly coupled to ongoing DNA synthesis. This process, termed DNA replication-coupled (RC) nucleosome assembly, is essential for chromatin replication and has a great impact on both genome stability maintenance and epigenetic inheritance. This review discusses a set of recent findings regarding the role of replisome components contributing to RC nucleosome assembly. Starting with a brief introduction to the factors involved in nucleosome assembly and some aspects of the architecture of the eukaryotic replisome, we discuss studies from yeast to mammalian cells and the interactions of replisome components with histones and histone chaperones. We describe the proposed functions of replisome components during RC nucleosome assembly and discuss their impacts on histone segregation and implications for epigenetic inheritance.
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Affiliation(s)
- Wenshuo Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
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74
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Hulke ML, Massey DJ, Koren A. Genomic methods for measuring DNA replication dynamics. Chromosome Res 2020; 28:49-67. [PMID: 31848781 PMCID: PMC7131883 DOI: 10.1007/s10577-019-09624-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/30/2019] [Accepted: 12/03/2019] [Indexed: 12/27/2022]
Abstract
Genomic DNA replicates according to a defined temporal program in which early-replicating loci are associated with open chromatin, higher gene density, and increased gene expression levels, while late-replicating loci tend to be heterochromatic and show higher rates of genomic instability. The ability to measure DNA replication dynamics at genome scale has proven crucial for understanding the mechanisms and cellular consequences of DNA replication timing. Several methods, such as quantification of nucleotide analog incorporation and DNA copy number analyses, can accurately reconstruct the genomic replication timing profiles of various species and cell types. More recent developments have expanded the DNA replication genomic toolkit to assays that directly measure the activity of replication origins, while single-cell replication timing assays are beginning to reveal a new level of replication timing regulation. The combination of these methods, applied on a genomic scale and in multiple biological systems, promises to resolve many open questions and lead to a holistic understanding of how eukaryotic cells replicate their genomes accurately and efficiently.
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Affiliation(s)
- Michelle L Hulke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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75
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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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76
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Massip F, Laurent M, Brossas C, Fernández-Justel JM, Gómez M, Prioleau MN, Duret L, Picard F. Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints. Nucleic Acids Res 2019; 47:5114-5125. [PMID: 30916335 PMCID: PMC6547456 DOI: 10.1093/nar/gkz182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/28/2019] [Accepted: 03/11/2019] [Indexed: 01/03/2023] Open
Abstract
The replication program of vertebrate genomes is driven by the chromosomal distribution and timing of activation of tens of thousands of replication origins. Genome-wide studies have shown the association of origins with promoters and CpG islands, and their enrichment in G-quadruplex motifs (G4). However, the genetic determinants driving their activity remain poorly understood. To gain insight on the constraints operating on origins, we conducted the first evolutionary comparison of origins across vertebrates. We generated a genome-wide map of chicken origins (the first of a bird genome), and performed a comparison with human and mouse maps. The analysis of intra-species polymorphism revealed a strong depletion of genetic diversity at the core of replication initiation loci. This depletion is not linked to the presence of G4 motifs, promoters or CpG islands. In contrast, we show that origins experienced a rapid turnover during vertebrate evolution, since pairwise comparisons of origin maps revealed that <24% of them are conserved among vertebrates. This study unravels the existence of a novel determinant of origins, the precise functional role of which remains to be determined. Despite the importance of replication initiation for the fitness of organisms, the distribution of origins along vertebrate chromosomes is highly flexible.
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Affiliation(s)
- Florian Massip
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villleurbanne, France.,Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Marc Laurent
- Institut Jacques Monod, CNRS UMR7592, Université Paris Diderot, Equipe Labellisée Association pour la Recherche sur le Cancer, Paris, France
| | - Caroline Brossas
- Institut Jacques Monod, CNRS UMR7592, Université Paris Diderot, Equipe Labellisée Association pour la Recherche sur le Cancer, Paris, France
| | | | - María Gómez
- Centro de Biología Molecular Severo Ochoa CBMSO (CSIC/UAM). Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Marie-Noelle Prioleau
- Institut Jacques Monod, CNRS UMR7592, Université Paris Diderot, Equipe Labellisée Association pour la Recherche sur le Cancer, Paris, France
| | - Laurent Duret
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villleurbanne, France
| | - Franck Picard
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villleurbanne, France
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77
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Lynch KL, Alvino GM, Kwan EX, Brewer BJ, Raghuraman MK. The effects of manipulating levels of replication initiation factors on origin firing efficiency in yeast. PLoS Genet 2019; 15:e1008430. [PMID: 31584938 PMCID: PMC6795477 DOI: 10.1371/journal.pgen.1008430] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/16/2019] [Accepted: 09/17/2019] [Indexed: 12/22/2022] Open
Abstract
Chromosome replication in Saccharomyces cerevisiae is initiated from ~300 origins that are regulated by DNA sequence and by the limited abundance of six trans-acting initiation proteins (Sld2, Sld3, Dpb11, Dbf4, Sld7 and Cdc45). We set out to determine how the levels of individual factors contribute to time of origin activation and/or origin efficiency using induced depletion of single factors and overexpression of sets of multiple factors. Depletion of Sld2 or Sld3 slows growth and S phase progression, decreases origin efficiency across the genome and impairs viability as a result of incomplete replication of the rDNA. We find that the most efficient early origins are relatively unaffected by depletion of either Sld2 or Sld3. However, Sld3 levels, and to a lesser extent Sld2 levels, are critical for firing of the less efficient early origins. Overexpression of Sld3 simultaneously with Sld2, Dpb11 and Dbf4 preserves the relative efficiency of origins. Only when Cdc45 and Sld7 are also overexpressed is origin efficiency equalized between early- and late-firing origins. Our data support a model in which Sld3 together with Cdc45 (and/or Sld7) is responsible for the differential efficiencies of origins across the yeast genome. Eukaryotic chromosome duplication begins at sites called origins of replication along the chromosomal DNA. A conserved property of eukaryotic origins is that they vary in efficiency—the proportion of cells in a population in which they “fire”—and in the average time of activation within S phase, but the molecular details underlying this variation are not well understood. Previous work has shown that limiting concentrations of a set of conserved replication initiation proteins referred to as “SSDDCS” (Sld2, Sld3, Dbf4, Dpb11, Cdc45, and Sld7) are rate limiting for origin activation in budding yeast and other eukaryotes; combined overexpression of these proteins increases and/or advances origin firing. However, it remained possible that different factors affect different aspects of origin activation (e.g., timing vs. efficiency). Here, by depleting individual factors or by overexpressing sets of factors in budding yeast, we demonstrate that it is levels of Sld3, Cdc45 and/or Sld7 levels are primarily responsible for modulating the differences in relative origin efficiency and timing. This work gives further insights into what shapes the landscape of genome duplication.
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Affiliation(s)
- Kelsey L. Lynch
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Gina M. Alvino
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Elizabeth X. Kwan
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Bonita J. Brewer
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - M. K. Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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78
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Limas JC, Cook JG. Preparation for DNA replication: the key to a successful S phase. FEBS Lett 2019; 593:2853-2867. [PMID: 31556113 PMCID: PMC6817399 DOI: 10.1002/1873-3468.13619] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/09/2019] [Accepted: 09/17/2019] [Indexed: 12/13/2022]
Abstract
Successful genome duplication is required for cell proliferation and demands extraordinary precision and accuracy. The mechanisms by which cells enter, progress through, and exit S phase are intense areas of focus in the cell cycle and genome stability fields. Key molecular events in the G1 phase of the cell division cycle, especially origin licensing, are essential for pre-establishing conditions for efficient DNA replication during the subsequent S phase. If G1 events are poorly regulated or disordered, then DNA replication can be compromised leading to genome instability, a hallmark of tumorigenesis. Upon entry into S phase, coordinated origin firing and replication progression ensure complete, timely, and precise chromosome replication. Both G1 and S phase progressions are controlled by master cell cycle protein kinases and ubiquitin ligases that govern the activity and abundance of DNA replication factors. In this short review, we describe current understanding and recent developments related to G1 progression and S phase entrance and exit with a particular focus on origin licensing regulation in vertebrates.
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Affiliation(s)
- Juanita C Limas
- Department of Pharmacology, University of North Carolina at Chapel Hill, NC, USA
| | - Jeanette Gowen Cook
- Department of Pharmacology, University of North Carolina at Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC, USA
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79
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Abstract
In all kingdoms of life, DNA is used to encode hereditary information. Propagation of the genetic material between generations requires timely and accurate duplication of DNA by semiconservative replication prior to cell division to ensure each daughter cell receives the full complement of chromosomes. DNA synthesis of daughter strands starts at discrete sites, termed replication origins, and proceeds in a bidirectional manner until all genomic DNA is replicated. Despite the fundamental nature of these events, organisms have evolved surprisingly divergent strategies that control replication onset. Here, we discuss commonalities and differences in replication origin organization and recognition in the three domains of life.
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Affiliation(s)
- Babatunde Ekundayo
- Quantitative Biology, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Franziska Bleichert
- Quantitative Biology, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- * E-mail:
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80
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Casar Tena T, Maerz LD, Szafranski K, Groth M, Blätte TJ, Donow C, Matysik S, Walther P, Jeggo PA, Burkhalter MD, Philipp M. Resting cells rely on the DNA helicase component MCM2 to build cilia. Nucleic Acids Res 2019; 47:134-151. [PMID: 30329080 PMCID: PMC6326816 DOI: 10.1093/nar/gky945] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 10/04/2018] [Indexed: 12/24/2022] Open
Abstract
Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding the DNA double strand. Interestingly, the number of MCM hexamers greatly exceeds the number of firing origins suggesting additional roles of MCMs. Here we show a hitherto unanticipated function of MCM2 in cilia formation in human cells and zebrafish that is uncoupled from replication. Zebrafish depleted of MCM2 develop ciliopathy-phenotypes including microcephaly and aberrant heart looping due to malformed cilia. In non-cycling human fibroblasts, loss of MCM2 promotes transcription of a subset of genes, which cause cilia shortening and centriole overduplication. Chromatin immunoprecipitation experiments show that MCM2 binds to transcription start sites of cilia inhibiting genes. We propose that such binding may block RNA polymerase II-mediated transcription. Depletion of a second MCM (MCM7), which functions in complex with MCM2 during its canonical functions, reveals an overlapping cilia-deficiency phenotype likely unconnected to replication, although MCM7 appears to regulate a distinct subset of genes and pathways. Our data suggests that MCM2 and 7 exert a role in ciliogenesis in post-mitotic tissues.
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Affiliation(s)
- Teresa Casar Tena
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Lars D Maerz
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Karol Szafranski
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Tamara J Blätte
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Cornelia Donow
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Sabrina Matysik
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany
| | - Penelope A Jeggo
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Martin D Burkhalter
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Melanie Philipp
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
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81
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Platel M, Narassimprakash H, Ciardo D, Haccard O, Marheineke K. Genome wide decrease of DNA replication eye density at the midblastula transition of Xenopus laevis. Cell Cycle 2019; 18:1458-1472. [PMID: 31130065 PMCID: PMC6592225 DOI: 10.1080/15384101.2019.1618641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/03/2019] [Accepted: 05/08/2019] [Indexed: 02/04/2023] Open
Abstract
During the first rapid divisions of early development in many species, the DNA:cytoplasm ratio increases until the midblastula transition (MBT) when transcription resumes and cell cycles lengthen. S phase is very rapid in early embryos, about 20-30 times faster than in differentiated cells. Using a combination of DNA fiber studies and a Xenopus laevis embryonic in vitro replication system, we show that S phase slows down shortly after the MBT owing to a genome wide decrease of replication eye density. Increasing the dNTP pool did not accelerate S phase or increase replication eye density implying that dNTPs are not rate limiting for DNA replication at the Xenopus MBT. Increasing the ratio of DNA:cytoplasm in egg extracts faithfully recapitulates changes in the spatial replication program in embryos, supporting the hypothesis that titration of soluble limiting factors could explain the observed changes in the DNA replication program at the MBT in Xenopus laevis.
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Affiliation(s)
- Marie Platel
- Department of Genome Biology, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris‐Sud, University Paris‐Saclay, Gif‐sur‐Yvette, France
| | - Hemalatha Narassimprakash
- Department of Genome Biology, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris‐Sud, University Paris‐Saclay, Gif‐sur‐Yvette, France
| | - Diletta Ciardo
- Department of Genome Biology, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris‐Sud, University Paris‐Saclay, Gif‐sur‐Yvette, France
| | - Olivier Haccard
- Department of Genome Biology, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris‐Sud, University Paris‐Saclay, Gif‐sur‐Yvette, France
| | - Kathrin Marheineke
- Department of Genome Biology, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris‐Sud, University Paris‐Saclay, Gif‐sur‐Yvette, France
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82
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Dorsett D. The Many Roles of Cohesin in Drosophila Gene Transcription. Trends Genet 2019; 35:542-551. [PMID: 31130395 PMCID: PMC6571051 DOI: 10.1016/j.tig.2019.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/20/2022]
Abstract
The cohesin protein complex mediates sister chromatid cohesion to ensure accurate chromosome segregation, and also influences gene transcription in higher eukaryotes. Modest deficits in cohesin function that do not alter chromosome segregation cause significant birth defects. The mechanisms by which cohesin participates in gene regulation have been studied in Drosophila, revealing that it is involved in gene activation by transcriptional enhancers and epigenetic gene silencing mediated by Polycomb group proteins. Recent studies reveal that early DNA replication origins are important for determining which genes associate with cohesin, and suggest that cohesin at replication origins is important for establishing both sister chromatid cohesion and enhancer-promoter communication.
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Affiliation(s)
- Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
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83
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Abstract
DNA replication starts with the opening of DNA at sites called DNA replication origins. From the single sequence-specific DNA replication origin of the small Escherichia coli genome, up to thousands of origins that are necessary to replicate the large human genome, strict sequence specificity has been lost. Nevertheless, genome-wide analyses performed in the recent years, using different mapping methods, demonstrated that there are precise locations along the metazoan genome from which replication initiates. These sites contain relaxed sequence consensus and epigenetic features. There is flexibility in the choice of origins to be used during a given cell cycle, probably imposed by evolution and developmental constraints. Here, we will briefly describe their main features.
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84
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Duriez B, Chilaka S, Bercher JF, Hercul E, Prioleau MN. Replication dynamics of individual loci in single living cells reveal changes in the degree of replication stochasticity through S phase. Nucleic Acids Res 2019; 47:5155-5169. [PMID: 30926993 PMCID: PMC6547449 DOI: 10.1093/nar/gkz220] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/18/2019] [Accepted: 03/21/2019] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic genomes are replicated under the control of a highly sophisticated program during the restricted time period corresponding to S phase. The most widely used replication timing assays, which are performed on populations of millions of cells, suggest that most of the genome is synchronously replicated on homologous chromosomes. We investigated the stochastic nature of this temporal program, by comparing the precise replication times of allelic loci within single vertebrate cells progressing through S phase at six loci replicated from very early to very late. We show that replication timing is strictly controlled for the three loci replicated in the first half of S phase. Out of the three loci replicated in the second part of S phase, two present a significantly more stochastic pattern. Surprisingly, we find that the locus replicated at the very end of S phase, presents stochasticity similar to those replicated in early S phase. We suggest that the richness of loci in efficient origins of replication, which decreases from early- to late-replicating regions, and the strength of interaction with the nuclear lamina may underlie the variation of timing control during S phase.
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Affiliation(s)
- Bénédicte Duriez
- Domaines Chromatiniens et Réplication, Institut Jacques Monod, UMR7592 CNRS – Université Paris Diderot, Paris, France, Equipe labellisée ARC
| | - Sabarinadh Chilaka
- Domaines Chromatiniens et Réplication, Institut Jacques Monod, UMR7592 CNRS – Université Paris Diderot, Paris, France, Equipe labellisée ARC
| | | | - Eslande Hercul
- Domaines Chromatiniens et Réplication, Institut Jacques Monod, UMR7592 CNRS – Université Paris Diderot, Paris, France, Equipe labellisée ARC
| | - Marie-Noëlle Prioleau
- Domaines Chromatiniens et Réplication, Institut Jacques Monod, UMR7592 CNRS – Université Paris Diderot, Paris, France, Equipe labellisée ARC
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85
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Mullican JC, Chapman NM, Tracy S. Mapping the Single Origin of Replication in the Naegleria gruberi Extrachromosomal DNA Element. Protist 2019; 170:141-152. [DOI: 10.1016/j.protis.2019.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/28/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
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86
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Kolesnikova TD, Antonenko OV, Makunin IV. Replication timing in Drosophila and its peculiarities in polytene chromosomes. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Drosophila melanogaster is one of the popular model organisms in DNA replication studies. Since the 1960s, DNA replication of polytene chromosomes has been extensively studied by cytological methods. In the recent two decades, the progress in our understanding of DNA replication was associated with new techniques. Use of fluorescent dyes increased the resolution of cytological methods significantly. High-throughput methods allowed analysis of DNA replication on a genome scale, as well as its correlation with chromatin structure and gene activi ty. Precise mapping of the cytological structures of polytene chromosomes to the genome assembly allowed comparison of replication between polytene chromosomes and chromosomes of diploid cells. New features of replication characteristic for D. melanogaster were described for both diploid and polytene chromosomes. Comparison of genomic replication profiles revealed a significant similarity between Drosophila and other well-studi ed eukaryotic species, such as human. Early replication is often confined to intensely transcribed gene-dense regions characterized by multiple replication initiation sites. Features of DNA replication in Drosophila might be explained by a compact genome. The organization of replication in polytene chromosomes has much in common with the organization of replication in chromosomes in diploid cells. The most important feature of replication in polytene chromosomes is its low rate and the dependence of S-phase duration on many factors: external and internal, local and global. The speed of replication forks in D. melanogaster polytene chromosomes is affected by SUUR and Rif1 proteins. It is not known yet how universal the mechanisms associated with these factors are, but their study is very promising.
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Affiliation(s)
- T. D. Kolesnikova
- Institute of Molecular and Cellular Biology, SB RAS. Novosibirsk State University
| | | | - I. V. Makunin
- Institute of Molecular and Cellular Biology, SB RAS; Research Computing Centre, The University of Queensland
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87
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Hiratani I, Takahashi S. DNA Replication Timing Enters the Single-Cell Era. Genes (Basel) 2019; 10:genes10030221. [PMID: 30884743 PMCID: PMC6470765 DOI: 10.3390/genes10030221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 12/20/2022] Open
Abstract
In mammalian cells, DNA replication timing is controlled at the level of megabase (Mb)-sized chromosomal domains and correlates well with transcription, chromatin structure, and three-dimensional (3D) genome organization. Because of these properties, DNA replication timing is an excellent entry point to explore genome regulation at various levels and a variety of studies have been carried out over the years. However, DNA replication timing studies traditionally required at least tens of thousands of cells, and it was unclear whether the replication domains detected by cell population analyses were preserved at the single-cell level. Recently, single-cell DNA replication profiling methods became available, which revealed that the Mb-sized replication domains detected by cell population analyses were actually well preserved in individual cells. In this article, we provide a brief overview of our current knowledge on DNA replication timing regulation in mammals based on cell population studies, outline the findings from single-cell DNA replication profiling, and discuss future directions and challenges.
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Affiliation(s)
- Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.
| | - Saori Takahashi
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.
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88
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Mathematical description of eukaryotic chromosome replication. Proc Natl Acad Sci U S A 2019; 116:4776-4778. [PMID: 30782813 DOI: 10.1073/pnas.1900968116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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89
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Genome-wide stability of the DNA replication program in single mammalian cells. Nat Genet 2019; 51:529-540. [PMID: 30804559 DOI: 10.1038/s41588-019-0347-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 01/09/2019] [Indexed: 11/09/2022]
Abstract
Here, we report a single-cell DNA replication sequencing method, scRepli-seq, a genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication-domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct profiles, which were also conserved among cells. Haplotype-resolved scRepli-seq revealed similar replication profiles of homologous autosomes, while the inactive X chromosome was clearly replicated later than its active counterpart. However, a small degree of cell-to-cell replication-timing heterogeneity was present, which was smallest at the beginning and the end of S phase. In addition, developmentally regulated domains were found to deviate from others and showed a higher degree of heterogeneity, thus suggesting a link to developmental plasticity. Moreover, allelic expression imbalance was found to strongly associate with replication-timing asynchrony. Our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into three-dimensional genome organization.
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90
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H3K9 Promotes Under-Replication of Pericentromeric Heterochromatin in Drosophila Salivary Gland Polytene Chromosomes. Genes (Basel) 2019; 10:genes10020093. [PMID: 30700014 PMCID: PMC6409945 DOI: 10.3390/genes10020093] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 12/11/2022] Open
Abstract
Chromatin structure and its organization contributes to the proper regulation and timing of DNA replication. Yet, the precise mechanism by which chromatin contributes to DNA replication remains incompletely understood. This is particularly true for cell types that rely on polyploidization as a developmental strategy for growth and high biosynthetic capacity. During Drosophila larval development, cells of the salivary gland undergo endoreplication, repetitive rounds of DNA synthesis without intervening cell division, resulting in ploidy values of ~1350C. S phase of these endocycles displays a reproducible pattern of early and late replicating regions of the genome resulting from the activity of the same replication initiation factors that are used in diploid cells. However, unlike diploid cells, the latest replicating regions of polyploid salivary gland genomes, composed primarily of pericentric heterochromatic enriched in H3K9 methylation, are not replicated each endocycle, resulting in under-replicated domains with reduced ploidy. Here, we employ a histone gene replacement strategy in Drosophila to demonstrate that mutation of a histone residue important for heterochromatin organization and function (H3K9) but not mutation of a histone residue important for euchromatin function (H4K16), disrupts proper endoreplication in Drosophila salivary gland polyploid genomes thereby leading to DNA copy gain in pericentric heterochromatin. These findings reveal that H3K9 is necessary for normal levels of under-replication of pericentric heterochromatin and suggest that under-replication at pericentric heterochromatin is mediated through H3K9 methylation.
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91
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Control of Eukaryotic DNA Replication Initiation-Mechanisms to Ensure Smooth Transitions. Genes (Basel) 2019; 10:genes10020099. [PMID: 30700044 PMCID: PMC6409694 DOI: 10.3390/genes10020099] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 02/06/2023] Open
Abstract
DNA replication differs from most other processes in biology in that any error will irreversibly change the nature of the cellular progeny. DNA replication initiation, therefore, is exquisitely controlled. Deregulation of this control can result in over-replication characterized by repeated initiation events at the same replication origin. Over-replication induces DNA damage and causes genomic instability. The principal mechanism counteracting over-replication in eukaryotes is a division of replication initiation into two steps—licensing and firing—which are temporally separated and occur at distinct cell cycle phases. Here, we review this temporal replication control with a specific focus on mechanisms ensuring the faultless transition between licensing and firing phases.
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92
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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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93
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Transcription shapes DNA replication initiation and termination in human cells. Nat Struct Mol Biol 2018; 26:67-77. [PMID: 30598550 PMCID: PMC6320713 DOI: 10.1038/s41594-018-0171-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/19/2018] [Indexed: 12/21/2022]
Abstract
Although DNA replication is a fundamental aspect of biology, it is not known what determines where DNA replication starts and stops in the human genome. Here we directly identify and quantitatively compare sites of replication initiation and termination in untransformed human cells. We report that replication preferentially initiates at the transcription start site of genes occupied by high levels of RNA polymerase II, and terminates at their polyadenylation sites, thus ensuring global co-directionality of transcription and replication, particularly at gene 5’ ends. During replication stress, replication initiation is stimulated downstream of genes and termination is redistributed to gene bodies; this globally re-orients replication relative to transcription around gene 3’ ends. These data suggest that replication initiation and termination are coupled to transcription in human cells, and propose a model for the impact of replication stress on genome integrity.
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94
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Transcription-dependent regulation of replication dynamics modulates genome stability. Nat Struct Mol Biol 2018; 26:58-66. [PMID: 30598553 DOI: 10.1038/s41594-018-0170-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 11/16/2018] [Indexed: 01/17/2023]
Abstract
Common fragile sites (CFSs) are loci that are hypersensitive to replication stress and hotspots for chromosomal rearrangements in cancers. CFSs replicate late in S phase, are cell-type specific and nest in large genes. The relative impact of transcription-replication conflicts versus a low density in initiation events on fragility is currently debated. Here we addressed the relationships between transcription, replication, and instability by manipulating the transcription of endogenous large genes in chicken and human cells. We found that inducing low transcription with a weak promoter destabilized large genes, whereas stimulating their transcription with strong promoters alleviated instability. Notably, strong promoters triggered a switch to an earlier replication timing, supporting a model in which high transcription levels give cells more time to complete replication before mitosis. Transcription could therefore contribute to maintaining genome integrity, challenging the dominant view that it is exclusively a threat.
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95
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Debatisse M, Rosselli F. A journey with common fragile sites: From S phase to telophase. Genes Chromosomes Cancer 2018; 58:305-316. [PMID: 30387289 DOI: 10.1002/gcc.22704] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 10/25/2018] [Indexed: 12/17/2022] Open
Abstract
Some regions of the genome, notably common fragile sites (CFSs), are hypersensitive to replication stress and often involved in the generation of gross chromosome rearrangements in cancer cells. CFSs nest within very large genes and display cell-type-dependent instability. Fragile or not, large genes tend to replicate late in S-phase. A number of data now show that transcription perturbs replication completion across the body of large genes, particularly upon replication stress. However, the molecular mechanisms by which transcription elicits such under-replication and subsequent instability remain unclear. We present here our view of the mechanisms responsible for CFS under-replication and those allowing the cells to cope with this problem in G2 and mitosis. We notably focus on the major role played by the FANC proteins in the protection of CFSs from S phase up to late mitosis. We finally discuss a possible rationale for the conservation of large genes across vertebrate evolution.
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Affiliation(s)
- Michelle Debatisse
- CNRS UMR 8200, Equipe labellisée "La ligue Contre le Cancer", Villejuif, France.,Sorbonne Universités, UPMC Univ Paris 06, Paris, France.,Gustave Roussy Cancer Center, Villejuif, France
| | - Filippo Rosselli
- CNRS UMR 8200, Equipe labellisée "La ligue Contre le Cancer", Villejuif, France.,Gustave Roussy Cancer Center, Villejuif, France.,Université Paris Saclay - Paris Sud, Orsay, France
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96
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Courtot L, Hoffmann JS, Bergoglio V. The Protective Role of Dormant Origins in Response to Replicative Stress. Int J Mol Sci 2018; 19:ijms19113569. [PMID: 30424570 PMCID: PMC6274952 DOI: 10.3390/ijms19113569] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023] Open
Abstract
Genome stability requires tight regulation of DNA replication to ensure that the entire genome of the cell is duplicated once and only once per cell cycle. In mammalian cells, origin activation is controlled in space and time by a cell-specific and robust program called replication timing. About 100,000 potential replication origins form on the chromatin in the gap 1 (G1) phase but only 20⁻30% of them are active during the DNA replication of a given cell in the synthesis (S) phase. When the progress of replication forks is slowed by exogenous or endogenous impediments, the cell must activate some of the inactive or "dormant" origins to complete replication on time. Thus, the many origins that may be activated are probably key to protect the genome against replication stress. This review aims to discuss the role of these dormant origins as safeguards of the human genome during replicative stress.
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Affiliation(s)
- Lilas Courtot
- CRCT, Université de Toulouse, Inserm, CNRS, UPS; Equipe labellisée Ligue Contre le Cancer, Laboratoire d'excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France.
| | - Jean-Sébastien Hoffmann
- CRCT, Université de Toulouse, Inserm, CNRS, UPS; Equipe labellisée Ligue Contre le Cancer, Laboratoire d'excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France.
| | - Valérie Bergoglio
- CRCT, Université de Toulouse, Inserm, CNRS, UPS; Equipe labellisée Ligue Contre le Cancer, Laboratoire d'excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France.
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97
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Aze A, Maiorano D. Recent advances in understanding DNA replication: cell type-specific adaptation of the DNA replication program. F1000Res 2018; 7. [PMID: 30228862 PMCID: PMC6117848 DOI: 10.12688/f1000research.15408.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/20/2018] [Indexed: 12/11/2022] Open
Abstract
DNA replication is an essential process occurring prior to cell division. Cell division coupled to proliferation ensures the growth and renewal of a large variety of specialized cell types generated during embryonic development. Changes in the DNA replication program occur during development. Embryonic undifferentiated cells show a high replication rate and fast proliferation, whereas more differentiated cells are characterized by reduced DNA synthesis and a low proliferation rate. Hence, the DNA replication program must adapt to the specific features of cells committed to different fates. Recent findings on DNA synthesis regulation in different cell types open new perspectives for developing efficient and more adapted therapies to treat various diseases such as genetic diseases and cancer. This review will put the emphasis on recent progress made in this field.
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Affiliation(s)
- Antoine Aze
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, Montpellier, 34396 Cedex 5, France
| | - Domenico Maiorano
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, Montpellier, 34396 Cedex 5, France
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98
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Shoaib M, Walter D, Gillespie PJ, Izard F, Fahrenkrog B, Lleres D, Lerdrup M, Johansen JV, Hansen K, Julien E, Blow JJ, Sørensen CS. Histone H4K20 methylation mediated chromatin compaction threshold ensures genome integrity by limiting DNA replication licensing. Nat Commun 2018; 9:3704. [PMID: 30209253 PMCID: PMC6135857 DOI: 10.1038/s41467-018-06066-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/09/2018] [Indexed: 11/20/2022] Open
Abstract
The decompaction and re-establishment of chromatin organization immediately after mitosis is essential for genome regulation. Mechanisms underlying chromatin structure control in daughter cells are not fully understood. Here we show that a chromatin compaction threshold in cells exiting mitosis ensures genome integrity by limiting replication licensing in G1 phase. Upon mitotic exit, chromatin relaxation is controlled by SET8-dependent methylation of histone H4 on lysine 20. In the absence of either SET8 or H4K20 residue, substantial genome-wide chromatin decompaction occurs allowing excessive loading of the origin recognition complex (ORC) in the daughter cells. ORC overloading stimulates aberrant recruitment of the MCM2-7 complex that promotes single-stranded DNA formation and DNA damage. Restoring chromatin compaction restrains excess replication licensing and loss of genome integrity. Our findings identify a cell cycle-specific mechanism whereby fine-tuned chromatin relaxation suppresses excessive detrimental replication licensing and maintains genome integrity at the cellular transition from mitosis to G1 phase.
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Affiliation(s)
- Muhammad Shoaib
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - David Walter
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Peter J Gillespie
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Fanny Izard
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, University of Montpellier, Institut Régional du Cancer (ICM), F-34298, Montpellier, France
| | - Birthe Fahrenkrog
- Institute for Molecular Biology and Medicine, Universite Libré de Bruxelles, Charleroi, 6041, Belgium
| | - David Lleres
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, 34293, France
| | - Mads Lerdrup
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Klaus Hansen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Eric Julien
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, University of Montpellier, Institut Régional du Cancer (ICM), F-34298, Montpellier, France
- Centre National de la Recherche Scientifique (CNRS), Montpellier, 34000, France
| | - J Julian Blow
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Claus S Sørensen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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99
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Dynamic changes in ORC localization and replication fork progression during tissue differentiation. BMC Genomics 2018; 19:623. [PMID: 30134926 PMCID: PMC6103881 DOI: 10.1186/s12864-018-4992-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/02/2018] [Indexed: 12/23/2022] Open
Abstract
Background Genomic regions repressed for DNA replication, resulting in either delayed replication in S phase or underreplication in polyploid cells, are thought to be controlled by inhibition of replication origin activation. Studies in Drosophila polytene cells, however, raised the possibility that impeding replication fork progression also plays a major role. Results We exploited genomic regions underreplicated (URs) with tissue specificity in Drosophila polytene cells to analyze mechanisms of replication repression. By localizing the Origin Recognition Complex (ORC) in the genome of the larval fat body and comparing this to ORC binding in the salivary gland, we found that sites of ORC binding show extensive tissue specificity. In contrast, there are common domains nearly devoid of ORC in the salivary gland and fat body that also have reduced density of ORC binding sites in diploid cells. Strikingly, domains lacking ORC can still be replicated in some polytene tissues, showing absence of ORC and origins is insufficient to repress replication. Analysis of the width and location of the URs with respect to ORC position indicates that whether or not a genomic region lacking ORC is replicated is controlled by whether replication forks formed outside the region are inhibited. Conclusions These studies demonstrate that inhibition of replication fork progression can block replication across genomic regions that constitutively lack ORC. Replication fork progression can be inhibited in both tissue-specific and genome region-specific ways. Consequently, when evaluating sources of genome instability it is important to consider altered control of replication forks in response to differentiation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4992-3) contains supplementary material, which is available to authorized users.
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100
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Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse. Cell 2018; 174:1127-1142.e19. [PMID: 30078706 DOI: 10.1016/j.cell.2018.07.011] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/25/2018] [Accepted: 07/06/2018] [Indexed: 12/30/2022]
Abstract
Replication origins, fragile sites, and rDNA have been implicated as sources of chromosomal instability. However, the defining genomic features of replication origins and fragile sites are among the least understood elements of eukaryote genomes. Here, we map sites of replication initiation and breakage in primary cells at high resolution. We find that replication initiates between transcribed genes within nucleosome-depleted structures established by long asymmetrical poly(dA:dT) tracts flanking the initiation site. Paradoxically, long (>20 bp) (dA:dT) tracts are also preferential sites of polar replication fork stalling and collapse within early-replicating fragile sites (ERFSs) and late-replicating common fragile sites (CFSs) and at the rDNA replication fork barrier. Poly(dA:dT) sequences are fragile because long single-strand poly(dA) stretches at the replication fork are unprotected by the replication protein A (RPA). We propose that the evolutionary expansion of poly(dA:dT) tracts in eukaryotic genomes promotes replication initiation, but at the cost of chromosome fragility.
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