1
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Ahmad H, Chetlangia N, Prasanth SG. Chromatin's Influence on Pre-Replication Complex Assembly and Function. BIOLOGY 2024; 13:152. [PMID: 38534422 DOI: 10.3390/biology13030152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
In all eukaryotes, the initiation of DNA replication requires a stepwise assembly of factors onto the origins of DNA replication. This is pioneered by the Origin Recognition Complex, which recruits Cdc6. Together, they bring Cdt1, which shepherds MCM2-7 to form the OCCM complex. Sequentially, a second Cdt1-bound hexamer of MCM2-7 is recruited by ORC-Cdc6 to form an MCM double hexamer, which forms a part of the pre-RC. Although the mechanism of ORC binding to DNA varies across eukaryotes, how ORC is recruited to replication origins in human cells remains an area of intense investigation. This review discusses how the chromatin environment influences pre-RC assembly, function, and, eventually, origin activity.
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Affiliation(s)
- Hina Ahmad
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Neha Chetlangia
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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2
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Poulet-Benedetti J, Tonnerre-Doncarli C, Valton AL, Laurent M, Gérard M, Barinova N, Parisis N, Massip F, Picard F, Prioleau MN. Dimeric G-quadruplex motifs-induced NFRs determine strong replication origins in vertebrates. Nat Commun 2023; 14:4843. [PMID: 37563125 PMCID: PMC10415359 DOI: 10.1038/s41467-023-40441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
Replication of vertebrate genomes is tightly regulated to ensure accurate duplication, but our understanding of the interplay between genetic and epigenetic factors in this regulation remains incomplete. Here, we investigated the involvement of three elements enriched at gene promoters and replication origins: guanine-rich motifs potentially forming G-quadruplexes (pG4s), nucleosome-free regions (NFRs), and the histone variant H2A.Z, in the firing of origins of replication in vertebrates. We show that two pG4s on the same DNA strand (dimeric pG4s) are sufficient to induce the assembly of an efficient minimal replication origin without inducing transcription in avian DT40 cells. Dimeric pG4s in replication origins are associated with formation of an NFR next to precisely-positioned nucleosomes enriched in H2A.Z on this minimal origin and genome-wide. Thus, our data suggest that dimeric pG4s are important for the organization and duplication of vertebrate genomes. It supports the hypothesis that a nucleosome close to an NFR is a shared signal for the formation of replication origins in eukaryotes.
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Affiliation(s)
| | | | - Anne-Laure Valton
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Marc Laurent
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Marie Gérard
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Natalja Barinova
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Nikolaos Parisis
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Florian Massip
- MINES ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 75006, Paris, France
- Institut Curie, Paris, Cedex, France
- INSERM, U900, Paris, Cedex, France
| | - Franck Picard
- Laboratory of Biology and Modelling of the Cell, Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France.
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3
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Vouzas AE, Gilbert DM. Replication timing and transcriptional control: beyond cause and effect - part IV. Curr Opin Genet Dev 2023; 79:102031. [PMID: 36905782 PMCID: PMC10035587 DOI: 10.1016/j.gde.2023.102031] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/07/2023] [Accepted: 02/11/2023] [Indexed: 03/11/2023]
Abstract
Decades of work on the spatiotemporal organization of mammalian DNA replication timing (RT) continues to unveil novel correlations with aspects of transcription and chromatin organization but, until recently, mechanisms regulating RT and the biological significance of the RT program had been indistinct. We now know that the RT program is both influenced by and necessary to maintain chromatin structure, forming an epigenetic positive feedback loop. Moreover, the discovery of specific cis-acting elements regulating mammalian RT at both the domain and the whole-chromosome level has revealed multiple cell-type-specific and developmentally regulated mechanisms of RT control. We review recent evidence for diverse mechanisms employed by different cell types to regulate their RT programs and the biological significance of RT regulation during development.
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Affiliation(s)
- Athanasios E Vouzas
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - David M Gilbert
- San Diego Biomedical Research Institute, 3525 John Hopkins Court, San Diego, CA 92121, USA.
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4
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Abstract
Immediately following the discovery of the structure of DNA and the semi-conservative replication of the parental DNA sequence into two new DNA strands, it became apparent that DNA replication is organized in a temporal and spatial fashion during the S phase of the cell cycle, correlated with the large-scale organization of chromatin in the nucleus. After many decades of limited progress, technological advances in genomics, genome engineering, and imaging have finally positioned the field to tackle mechanisms underpinning the temporal and spatial regulation of DNA replication and the causal relationships between DNA replication and other features of large-scale chromosome structure and function. In this review, we discuss these major recent discoveries as well as expectations for the coming decade.
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Affiliation(s)
- Athanasios E Vouzas
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
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5
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Seruggia D, Josa S, Fernández A, Montoliu L. The structure and function of the mouse tyrosinase locus. Pigment Cell Melanoma Res 2020; 34:212-221. [DOI: 10.1111/pcmr.12942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/06/2020] [Accepted: 10/14/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Davide Seruggia
- Department of Molecular and Cellular Biology National Centre for Biotechnology (CNB‐CSIC) Madrid Madrid Spain
- CIBERER‐ISCIII Madrid Spain
- Division of Hematology/Oncology Boston Children's HospitalHarvard Medical School Boston MA USA
| | - Santiago Josa
- Department of Molecular and Cellular Biology National Centre for Biotechnology (CNB‐CSIC) Madrid Madrid Spain
- CIBERER‐ISCIII Madrid Spain
| | - Almudena Fernández
- Department of Molecular and Cellular Biology National Centre for Biotechnology (CNB‐CSIC) Madrid Madrid Spain
- CIBERER‐ISCIII Madrid Spain
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology National Centre for Biotechnology (CNB‐CSIC) Madrid Madrid Spain
- CIBERER‐ISCIII Madrid Spain
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6
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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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7
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Control of DNA replication timing in the 3D genome. Nat Rev Mol Cell Biol 2019; 20:721-737. [DOI: 10.1038/s41580-019-0162-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 12/27/2022]
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8
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Rivera-Mulia JC, Kim S, Gabr H, Chakraborty A, Ay F, Kahveci T, Gilbert DM. Replication timing networks reveal a link between transcription regulatory circuits and replication timing control. Genome Res 2019; 29:1415-1428. [PMID: 31434679 PMCID: PMC6724675 DOI: 10.1101/gr.247049.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 08/05/2019] [Indexed: 12/11/2022]
Abstract
DNA replication occurs in a defined temporal order known as the replication timing (RT) program and is regulated during development, coordinated with 3D genome organization and transcriptional activity. However, transcription and RT are not sufficiently coordinated to predict each other, suggesting an indirect relationship. Here, we exploit genome-wide RT profiles from 15 human cell types and intermediate differentiation stages derived from human embryonic stem cells to construct different types of RT regulatory networks. First, we constructed networks based on the coordinated RT changes during cell fate commitment to create highly complex RT networks composed of thousands of interactions that form specific functional subnetwork communities. We also constructed directional regulatory networks based on the order of RT changes within cell lineages, and identified master regulators of differentiation pathways. Finally, we explored relationships between RT networks and transcriptional regulatory networks (TRNs) by combining them into more complex circuitries of composite and bipartite networks. Results identified novel trans interactions linking transcription factors that are core to the regulatory circuitry of each cell type to RT changes occurring in those cell types. These core transcription factors were found to bind cooperatively to sites in the affected replication domains, providing provocative evidence that they constitute biologically significant directional interactions. Our findings suggest a regulatory link between the establishment of cell-type-specific TRNs and RT control during lineage specification.
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Affiliation(s)
- Juan Carlos Rivera-Mulia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Sebo Kim
- Department of Computer and Information Sciences and Engineering, University of Florida, Gainesville, Florida 32611, USA
| | - Haitham Gabr
- Department of Computer and Information Sciences and Engineering, University of Florida, Gainesville, Florida 32611, USA
| | - Abhijit Chakraborty
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA.,School of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Tamer Kahveci
- Department of Computer and Information Sciences and Engineering, University of Florida, Gainesville, Florida 32611, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida, 32306-4295, USA.,Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306, USA
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9
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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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10
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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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11
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Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell 2019; 176:816-830.e18. [PMID: 30595451 PMCID: PMC6546437 DOI: 10.1016/j.cell.2018.11.036] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 10/01/2018] [Accepted: 11/21/2018] [Indexed: 01/09/2023]
Abstract
The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. We created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for RT. CTCF protein depletion weakened most TAD boundaries but had no effect on RT or A/B compartmentalization genome-wide. By contrast, deletion of three intra-TAD CTCF-independent 3D contact sites caused a domain-wide early-to-late RT shift, an A-to-B compartment switch, weakening of TAD architecture, and loss of transcription. The dispensability of TAD boundaries and the necessity of these "early replication control elements" (ERCEs) was validated by deletions and inversions at additional domains. Our results demonstrate that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function.
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Affiliation(s)
- Jiao Sima
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | | | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Marco Michalski
- Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Kyle N Klein
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Nicolas P Holcomb
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jesse L Turner
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Michelle T Paulsen
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | | | - Daniel A Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Peiyao A Zhao
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Brian K Washburn
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Elphège P Nora
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA
| | - Katerina Kraft
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA; Department of Pediatrics, Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA; Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; UC San Diego, School of Medicine, La Jolla, CA 92037, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
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12
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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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13
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Sima J, Bartlett DA, Gordon MR, Gilbert DM. Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors. Nucleic Acids Res 2018; 46:1810-1820. [PMID: 29294101 PMCID: PMC5829748 DOI: 10.1093/nar/gkx1265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/27/2017] [Accepted: 12/06/2017] [Indexed: 12/11/2022] Open
Abstract
The role of DNA sequence in determining replication timing (RT) and chromatin higher order organization remains elusive. To address this question, we have developed an extra-chromosomal replication system (E-BACs) consisting of ∼200 kb human bacterial artificial chromosomes (BACs) modified with Epstein-Barr virus (EBV) stable segregation elements. E-BACs were stably maintained as autonomous mini-chromosomes in EBNA1-expressing HeLa or human induced pluripotent stem cells (hiPSCs) and established distinct RT patterns. An E-BAC harboring an early replicating chromosomal region replicated early during S phase, while E-BACs derived from RT transition regions (TTRs) and late replicating regions replicated in mid to late S phase. Analysis of E-BAC interactions with cellular chromatin (4C-seq) revealed that the early replicating E-BAC interacted broadly throughout the genome and preferentially with the early replicating compartment of the nucleus. In contrast, mid- to late-replicating E-BACs interacted with more specific late replicating chromosomal segments, some of which were shared between different E-BACs. Together, we describe a versatile system in which to study the structure and function of chromosomal segments that are stably maintained separately from the influence of cellular chromosome context.
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Affiliation(s)
- Jiao Sima
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL 32306, USA
| | - Daniel A Bartlett
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL 32306, USA
| | - Molly R Gordon
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL 32306, USA
| | - David M Gilbert
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL 32306, USA
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14
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Poulet-Benedetti J, Valton AL, Prioleau MN. [G-quadruplex: key controllers of human genome duplication]. Med Sci (Paris) 2017; 33:1063-1070. [PMID: 29261494 DOI: 10.1051/medsci/20173312013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The correct duplication of the human genome is under the control of a spatiotemporal program that determines where and when replication forks start. This regulation thus mainly operates on replication start sites named replication origins. During the S-phase, about 50 000 origins fire in one human cell. However, the normal or perturbed progression of replication forks also strongly impacts on replication. Recently, several studies have put forward the role of a noncanonical DNA structure, the G-quadruplex, in the control of genome duplication. In this review, we describe the major impact of this structure on starting points and on the progression of replication forks.
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Affiliation(s)
- Jérémy Poulet-Benedetti
- Institut Jacques Monod, CNRS UMR7592, université Paris Diderot, Équipe labellisée ARC (Association pour la recherche sur le cancer), 75013 Paris, France
| | - Anne-Laure Valton
- Howard Hughes Medical Institute, Program in systems biology, Department of biochemistry and molecular pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, États-Unis
| | - Marie-Noëlle Prioleau
- Institut Jacques Monod, CNRS UMR7592, université Paris Diderot, Équipe labellisée ARC (Association pour la recherche sur le cancer), 75013 Paris, France
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15
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The impact of replication stress on replication dynamics and DNA damage in vertebrate cells. Nat Rev Genet 2017; 18:535-550. [DOI: 10.1038/nrg.2017.46] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Abstract
In this review, Prioleau and MacAlpine summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages. For more than three decades, investigators have sought to identify the precise locations where DNA replication initiates in mammalian genomes. The development of molecular and biochemical approaches to identify start sites of DNA replication (origins) based on the presence of defining and characteristic replication intermediates at specific loci led to the identification of only a handful of mammalian replication origins. The limited number of identified origins prevented a comprehensive and exhaustive search for conserved genomic features that were capable of specifying origins of DNA replication. More recently, the adaptation of origin-mapping assays to genome-wide approaches has led to the identification of tens of thousands of replication origins throughout mammalian genomes, providing an unprecedented opportunity to identify both genetic and epigenetic features that define and regulate their distribution and utilization. Here we summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages.
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Affiliation(s)
- Marie-Noëlle Prioleau
- Institut Jacques Monod, UMR7592, Centre National de la Recherche Scientifique, Universite Paris Diderot, Equipe Labellisee Association pour la Recherche sur le Cancer, Paris 75013, France
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710. USA
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17
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Prioleau MN. G-Quadruplexes and DNA Replication Origins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:273-286. [DOI: 10.1007/978-981-10-6955-0_13] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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18
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Marks AB, Fu H, Aladjem MI. Regulation of Replication Origins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:43-59. [PMID: 29357052 DOI: 10.1007/978-981-10-6955-0_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In eukaryotes, genome duplication starts concomitantly at many replication initiation sites termed replication origins. The replication initiation program is spatially and temporally coordinated to ensure accurate, efficient DNA synthesis that duplicates the entire genome while maintaining other chromatin-dependent functions. Unlike in prokaryotes, not all potential replication origins in eukaryotes are needed for complete genome duplication during each cell cycle. Instead, eukaryotic cells vary the use of initiation sites so that only a fraction of potential replication origins initiate replication each cell cycle. Flexibility in origin choice allows each eukaryotic cell type to utilize different initiation sites, corresponding to unique nuclear DNA packaging patterns. These patterns coordinate replication with gene expression and chromatin condensation. Budding yeast replication origins share a consensus sequence that marks potential initiation sites. Metazoan origins, on the other hand, lack a consensus sequence. Rather, they are associated with a collection of structural features, chromatin packaging features, histone modifications, transcription, and DNA-DNA/DNA-protein interactions. These features confer cell type-specific replication and expression and play an essential role in maintaining genomic stability.
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Affiliation(s)
- Anna B Marks
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Haiqing Fu
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA.
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19
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Valton AL, Prioleau MN. G-Quadruplexes in DNA Replication: A Problem or a Necessity? Trends Genet 2016; 32:697-706. [DOI: 10.1016/j.tig.2016.09.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/01/2016] [Indexed: 10/21/2022]
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20
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Rivera-Mulia JC, Gilbert DM. Replication timing and transcriptional control: beyond cause and effect-part III. Curr Opin Cell Biol 2016; 40:168-178. [PMID: 27115331 DOI: 10.1016/j.ceb.2016.03.022] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/24/2016] [Accepted: 03/29/2016] [Indexed: 11/17/2022]
Abstract
DNA replication is essential for faithful transmission of genetic information and is intimately tied to chromosome structure and function. Genome duplication occurs in a defined temporal order known as the replication-timing (RT) program, which is regulated during the cell cycle and development in discrete units referred to as replication domains (RDs). RDs correspond to topologically-associating domains (TADs) and are spatio-temporally compartmentalized in the nucleus. While improvements in experimental tools have begun to reveal glimpses of causality, they have also unveiled complex context-dependent relationships that challenge long recognized correlations of RT to chromatin organization and gene regulation. In particular, RDs/TADs that switch RT during development march to the beat of a different drummer.
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Affiliation(s)
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA; Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL, USA.
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21
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Marks AB, Smith OK, Aladjem MI. Replication origins: determinants or consequences of nuclear organization? Curr Opin Genet Dev 2016; 37:67-75. [PMID: 26845042 PMCID: PMC4914405 DOI: 10.1016/j.gde.2015.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/20/2022]
Abstract
Chromosome replication, gene expression and chromatin assembly all occur on the same template, necessitating a tight spatial and temporal coordination to maintain genomic stability. The distribution of replication initiation events is responsive to local and global changes in chromatin structure and is affected by transcriptional activity. Concomitantly, replication origin sequences, which determine the locations of replication initiation events, can affect chromatin structure and modulate transcriptional efficiency. The flexibility observed in the replication initiation landscape might help achieve complete and accurate genome duplication while coordinating the DNA replication program with transcription and other nuclear processes in a cell-type specific manner. This review discusses the relationships among replication origin distribution, local and global chromatin structures and concomitant nuclear metabolic processes.
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Affiliation(s)
- Anna B Marks
- Developmental Therapeutics Branch, NCI, NIH, Bethesda, MD, USA
| | - Owen K Smith
- Developmental Therapeutics Branch, NCI, NIH, Bethesda, MD, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, NCI, NIH, Bethesda, MD, USA.
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22
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Schiavone D, Guilbaud G, Murat P, Papadopoulou C, Sarkies P, Prioleau MN, Balasubramanian S, Sale JE. Determinants of G quadruplex-induced epigenetic instability in REV1-deficient cells. EMBO J 2014; 33:2507-20. [PMID: 25190518 PMCID: PMC4282387 DOI: 10.15252/embj.201488398] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
REV1-deficient chicken DT40 cells are compromised in replicating G quadruplex (G4)-forming DNA. This results in localised, stochastic loss of parental chromatin marks and changes in gene expression. We previously proposed that this epigenetic instability arises from G4-induced replication fork stalls disrupting the accurate propagation of chromatin structure through replication. Here, we test this model by showing that a single G4 motif is responsible for the epigenetic instability of the BU-1 locus in REV1-deficient cells, despite its location 3.5 kb from the transcription start site (TSS). The effect of the G4 is dependent on it residing on the leading strand template, but is independent of its in vitro thermal stability. Moving the motif to more than 4 kb from the TSS stabilises expression of the gene. However, loss of histone modifications (H3K4me3 and H3K9/14ac) around the transcription start site correlates with the position of the G4 motif, expression being lost only when the promoter is affected. This supports the idea that processive replication is required to maintain the histone modification pattern and full transcription of this model locus.
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Affiliation(s)
- Davide Schiavone
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Pierre Murat
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Peter Sarkies
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK The Gurdon Institute, Cambridge, UK
| | | | | | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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23
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Fernandez-Vidal A, Guitton-Sert L, Cadoret JC, Drac M, Schwob E, Baldacci G, Cazaux C, Hoffmann JS. A role for DNA polymerase θ in the timing of DNA replication. Nat Commun 2014; 5:4285. [PMID: 24989122 DOI: 10.1038/ncomms5285] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 06/03/2014] [Indexed: 01/01/2023] Open
Abstract
Although DNA polymerase θ (Pol θ) is known to carry out translesion synthesis and has been implicated in DNA repair, its physiological function under normal growth conditions remains unclear. Here we present evidence that Pol θ plays a role in determining the timing of replication in human cells. We find that Pol θ binds to chromatin during early G1, interacts with the Orc2 and Orc4 components of the Origin recognition complex and that the association of Mcm proteins with chromatin is enhanced in G1 when Pol θ is downregulated. Pol θ-depleted cells exhibit a normal density of activated origins in S phase, but early-to-late and late-to-early shifts are observed at a number of replication domains. Pol θ overexpression, on the other hand, causes delayed replication. Our results therefore suggest that Pol θ functions during the earliest steps of DNA replication and influences the timing of replication initiation.
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Affiliation(s)
- Anne Fernandez-Vidal
- 1] Equipe Labellisée Ligue contre le Cancer 2013 INSERM Unit 1037; CNRS ERL 5294; CRCT (Cancer Research Center of Toulouse), BP3028, CHU Purpan, Toulouse 31024, France [2] Université Paul Sabatier, University of Toulouse III, Toulouse F-31062, France [3]
| | - Laure Guitton-Sert
- 1] Equipe Labellisée Ligue contre le Cancer 2013 INSERM Unit 1037; CNRS ERL 5294; CRCT (Cancer Research Center of Toulouse), BP3028, CHU Purpan, Toulouse 31024, France [2] Université Paul Sabatier, University of Toulouse III, Toulouse F-31062, France [3]
| | - Jean-Charles Cadoret
- 1] Institut Jacques Monod, UMR7592, CNRS and University Paris-Diderot, 15 Rue Hélène Brion, Paris, Cedex 13 75205, France [2]
| | - Marjorie Drac
- Institut of Molecular Genetics, CNRS UMR5535 and University of Montpellier, Montpellier 34293, France
| | - Etienne Schwob
- Institut of Molecular Genetics, CNRS UMR5535 and University of Montpellier, Montpellier 34293, France
| | - Giuseppe Baldacci
- Institut Jacques Monod, UMR7592, CNRS and University Paris-Diderot, 15 Rue Hélène Brion, Paris, Cedex 13 75205, France
| | - Christophe Cazaux
- 1] Equipe Labellisée Ligue contre le Cancer 2013 INSERM Unit 1037; CNRS ERL 5294; CRCT (Cancer Research Center of Toulouse), BP3028, CHU Purpan, Toulouse 31024, France [2] Université Paul Sabatier, University of Toulouse III, Toulouse F-31062, France
| | - Jean-Sébastien Hoffmann
- 1] Equipe Labellisée Ligue contre le Cancer 2013 INSERM Unit 1037; CNRS ERL 5294; CRCT (Cancer Research Center of Toulouse), BP3028, CHU Purpan, Toulouse 31024, France [2] Université Paul Sabatier, University of Toulouse III, Toulouse F-31062, France
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24
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Smith OK, Aladjem MI. Chromatin structure and replication origins: determinants of chromosome replication and nuclear organization. J Mol Biol 2014; 426:3330-41. [PMID: 24905010 DOI: 10.1016/j.jmb.2014.05.027] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/22/2014] [Accepted: 05/24/2014] [Indexed: 12/29/2022]
Abstract
The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes on chromatin is illustrated by two recent sets of discoveries. First, chromatin-associated proteins that are not part of the core replication machinery were shown to affect the timing of DNA replication. These chromatin-associated proteins could be working in concert, or perhaps in competition, with the transcriptional machinery and with chromatin modifiers to determine the spatial and temporal organization of replication initiation events. Second, epigenetic interactions are mediated by DNA sequences that determine chromosomal replication. In this review, we summarize recent findings and current models linking spatial and temporal regulation of the replication program with epigenetic signaling. We discuss these issues in the context of the genome's three-dimensional structure with an emphasis on events occurring during the initiation of DNA replication.
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Affiliation(s)
- Owen K Smith
- DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Mirit I Aladjem
- DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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25
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The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells. PLoS Genet 2014; 10:e1004282. [PMID: 24785686 PMCID: PMC4006723 DOI: 10.1371/journal.pgen.1004282] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 02/18/2014] [Indexed: 11/19/2022] Open
Abstract
The duplication of mammalian genomes is under the control of a spatiotemporal program that orchestrates the positioning and the timing of firing of replication origins. The molecular mechanisms coordinating the activation of about predicted origins remain poorly understood, partly due to the intrinsic rarity of replication bubbles, making it difficult to purify short nascent strands (SNS). The precise identification of origins based on the high-throughput sequencing of SNS constitutes a new methodological challenge. We propose a new statistical method with a controlled resolution, adapted to the detection of replication origins from SNS data. We detected an average of 80,000 replication origins in different cell lines. To evaluate the consistency between different protocols, we compared SNS detections with bubble trapping detections. This comparison demonstrated a good agreement between genome-wide methods, with 65% of SNS-detected origins validated by bubble trapping, and 44% of bubble trapping origins validated by SNS origins, when compared at the same resolution. We investigated the interplay between the spatial and the temporal programs of replication at fine scales. We show that most of the origins detected in regions replicated in early S phase are shared by all the cell lines investigated whereas cell-type-specific origins tend to be replicated in late S phase. We shed a new light on the key role of CpG islands, by showing that 80% of the origins associated with CGIs are constitutive. Our results further show that at least 76% of CGIs are origins of replication. The analysis of associations with chromatin marks at different timing of cell division revealed new potential epigenetic regulators driving the spatiotemporal activity of replication origins. We highlight the potential role of H4K20me1 and H3K27me3, the coupling of which is correlated with increased efficiency of replication origins, clearly identifying those marks as potential key regulators of replication origins. Replication is the mechanism by which genomes are duplicated into two exact copies. Genomic stability is under the control of a spatiotemporal program that orchestrates both the positioning and the timing of firing of about 50,000 replication starting points, also called replication origins. Replication bubbles found at origins have been very difficult to map due to their short lifespan. Moreover, with the flood of data characterizing new sequencing technologies, the precise statistical analysis of replication data has become an additional challenge. We propose a new method to map replication origins on the human genome, and we assess the reliability of our finding using experimental validation and comparison with origins maps obtained by bubble trapping. This fine mapping then allowed us to identify potential regulators of the replication dynamics. Our study highlights the key role of CpG Islands and identifies new potential epigenetic regulators (methylation of lysine 4 on histone H4, and tri-methylation of lysine 27 on histone H3) whose coupling is correlated with an increase in the efficiency of replication origins, suggesting those marks as potential key regulators of replication. Overall, our study defines new potentially important pathways that might regulate the sequential firing of origins during genome duplication.
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26
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Valton AL, Hassan-Zadeh V, Lema I, Boggetto N, Alberti P, Saintomé C, Riou JF, Prioleau MN. G4 motifs affect origin positioning and efficiency in two vertebrate replicators. EMBO J 2014; 33:732-46. [PMID: 24521668 DOI: 10.1002/embj.201387506] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA replication ensures the accurate duplication of the genome at each cell cycle. It begins at specific sites called replication origins. Genome-wide studies in vertebrates have recently identified a consensus G-rich motif potentially able to form G-quadruplexes (G4) in most replication origins. However, there is no experimental evidence to demonstrate that G4 are actually required for replication initiation. We show here, with two model origins, that G4 motifs are required for replication initiation. Two G4 motifs cooperate in one of our model origins. The other contains only one critical G4, and its orientation determines the precise position of the replication start site. Point mutations affecting the stability of this G4 in vitro also impair origin function. Finally, this G4 is not sufficient for origin activity and must cooperate with a 200-bp cis-regulatory element. In conclusion, our study strongly supports the predicted essential role of G4 in replication initiation.
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Affiliation(s)
- Anne-Laure Valton
- Institut Jacques Monod, CNRS UMR7592 Université Paris Diderot Equipe Labellisée Ligue contre le cancer, Paris, France
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27
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Comoglio F, Paro R. Combinatorial modeling of chromatin features quantitatively predicts DNA replication timing in Drosophila. PLoS Comput Biol 2014; 10:e1003419. [PMID: 24465194 PMCID: PMC3900380 DOI: 10.1371/journal.pcbi.1003419] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 11/18/2013] [Indexed: 01/14/2023] Open
Abstract
In metazoans, each cell type follows a characteristic, spatio-temporally regulated DNA replication program. Histone modifications (HMs) and chromatin binding proteins (CBPs) are fundamental for a faithful progression and completion of this process. However, no individual HM is strictly indispensable for origin function, suggesting that HMs may act combinatorially in analogy to the histone code hypothesis for transcriptional regulation. In contrast to gene expression however, the relationship between combinations of chromatin features and DNA replication timing has not yet been demonstrated. Here, by exploiting a comprehensive data collection consisting of 95 CBPs and HMs we investigated their combinatorial potential for the prediction of DNA replication timing in Drosophila using quantitative statistical models. We found that while combinations of CBPs exhibit moderate predictive power for replication timing, pairwise interactions between HMs lead to accurate predictions genome-wide that can be locally further improved by CBPs. Independent feature importance and model analyses led us to derive a simplified, biologically interpretable model of the relationship between chromatin landscape and replication timing reaching 80% of the full model accuracy using six model terms. Finally, we show that pairwise combinations of HMs are able to predict differential DNA replication timing across different cell types. All in all, our work provides support to the existence of combinatorial HM patterns for DNA replication and reveal cell-type independent key elements thereof, whose experimental investigation might contribute to elucidate the regulatory mode of this fundamental cellular process.
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Affiliation(s)
- Federico Comoglio
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
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28
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Abstract
Patterns of replication within eukaryotic genomes correlate with gene expression, chromatin structure, and genome evolution. Recent advances in genome-scale mapping of replication kinetics have allowed these correlations to be explored in many species, cell types, and growth conditions, and these large data sets have allowed quantitative and computational analyses. One striking new correlation to emerge from these analyses is between replication timing and the three-dimensional structure of chromosomes. This correlation, which is significantly stronger than with any single histone modification or chromosome-binding protein, suggests that replication timing is controlled at the level of chromosomal domains. This conclusion dovetails with parallel work on the heterogeneity of origin firing and the competition between origins for limiting activators to suggest a model in which the stochastic probability of individual origin firing is modulated by chromosomal domain structure to produce patterns of replication. Whether these patterns have inherent biological functions or simply reflect higher-order genome structure is an open question.
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Affiliation(s)
- Nicholas Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
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29
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Abstract
The size of a eukaryotic genome presents a unique challenge to the cell: package and organize the DNA to fit within the confines of the nucleus while at the same time ensuring sufficient dynamics to allow access to specific sequences and features such as genes and regulatory elements. This is achieved via the dynamic nucleoprotein organization of eukaryotic DNA into chromatin. The basic unit of chromatin, the nucleosome, comprises a core particle with 147 bp of DNA wrapped 1.7 times around an octamer of histones. The nucleosome is a highly versatile and modular structure, both in its composition, with the existence of various histone variants, and through the addition of a series of posttranslational modifications on the histones. This versatility allows for both short-term regulatory responses to external signaling, as well as the long-term and multigenerational definition of large functional chromosomal domains within the nucleus, such as the centromere. Chromatin organization and its dynamics participate in essentially all DNA-templated processes, including transcription, replication, recombination, and repair. Here we will focus mainly on nucleosomal organization and describe the pathways and mechanisms that contribute to assembly of this organization and the role of chromatin in regulating the DNA replication program.
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Affiliation(s)
- David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, USA.
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30
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Pope BD, Gilbert DM. The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture. J Mol Biol 2013; 425:4690-5. [PMID: 23603017 DOI: 10.1016/j.jmb.2013.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/09/2013] [Accepted: 04/15/2013] [Indexed: 01/12/2023]
Abstract
The "Replicon Theory" of Jacob, Brenner, and Cuzin has reliably served as the paradigm for regulating the sites where individual replicons initiate replication. Concurrent with the replicon model was Taylor's demonstration that plant and animal chromosomes replicate segmentally in a defined temporal sequence, via cytologically defined units too large to be accounted for by a single replicon. Instead, there seemed to be a program to choreograph when chromosome units replicate during S phase, executed by initiation at clusters of individual replicons within each segment. Here, we summarize recent molecular evidence for the existence of such units, now known as "replication domains", and discuss how the organization of large chromosomes into structural units has added additional layers of regulation to the original replicon model.
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Affiliation(s)
- Benjamin D Pope
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
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31
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Méchali M, Yoshida K, Coulombe P, Pasero P. Genetic and epigenetic determinants of DNA replication origins, position and activation. Curr Opin Genet Dev 2013; 23:124-31. [PMID: 23541525 DOI: 10.1016/j.gde.2013.02.010] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 11/28/2022]
Abstract
In the genome of eukaryotic cells, DNA synthesis is initiated at multiple sites called origins of DNA replication. Origins must fire only once per cell cycle and how this is achieved is now well understood. However, little is known about the mechanisms that determine when and where replication initiates in a given cell. A large body of evidence indicates that origins are not equal in terms of efficiency and timing of activation. Origin usage also changes concomitantly with the different cell differentiation programs. As DNA replication occurs in the context of chromatin, initiation could be influenced by multiple parameters, such as nucleosome positioning, histone modifications, and three-dimensional (3D) organization of the nucleus. This view is supported by recent genome-wide studies showing that DNA replication profiles are shaped by genetic and epigenetic processes that act both at the local and global levels to regulate origin function in eukaryotic cells.
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Affiliation(s)
- Marcel Méchali
- Institute of Human Genetics, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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32
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Lo Sardo F, Lanzuolo C, Comoglio F, De Bardi M, Paro R, Orlando V. PcG-mediated higher-order chromatin structures modulate replication programs at the Drosophila BX-C. PLoS Genet 2013; 9:e1003283. [PMID: 23437006 PMCID: PMC3578750 DOI: 10.1371/journal.pgen.1003283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 12/14/2012] [Indexed: 12/03/2022] Open
Abstract
Polycomb group proteins (PcG) exert conserved epigenetic functions that convey maintenance of repressed transcriptional states, via post-translational histone modifications and high order structure formation. During S-phase, in order to preserve cell identity, in addition to DNA information, PcG-chromatin-mediated epigenetic signatures need to be duplicated requiring a tight coordination between PcG proteins and replication programs. However, the interconnection between replication timing control and PcG functions remains unknown. Using Drosophila embryonic cell lines, we find that, while presence of specific PcG complexes and underlying transcription state are not the sole determinants of cellular replication timing, PcG-mediated higher-order structures appear to dictate the timing of replication and maintenance of the silenced state. Using published datasets we show that PRC1, PRC2, and PhoRC complexes differently correlate with replication timing of their targets. In the fully repressed BX-C, loss of function experiments revealed a synergistic role for PcG proteins in the maintenance of replication programs through the mediation of higher-order structures. Accordingly, replication timing analysis performed on two Drosophila cell lines differing for BX-C gene expression states, PcG distribution, and chromatin domain conformation revealed a cell-type-specific replication program that mirrors lineage-specific BX-C higher-order structures. Our work suggests that PcG complexes, by regulating higher-order chromatin structure at their target sites, contribute to the definition and the maintenance of genomic structural domains where genes showing the same epigenetic state replicate at the same time. DNA replication is a tightly orchestrated process that precisely duplicates the entire genome during cell division to ensure that daughter cells inherit the same genetic information. The genome is replicated following a specific temporal program, where different segments replicate in distinct moments of the S phase correlating with active (early) and repressed (late) transcriptional state of resident genes. Moreover, replicating chromosomal domains are organized in the nuclear space, perhaps to guarantee the conservation of the same topological order in daughter cells. Epigenetic mechanisms, acting via chromatin organization, determine transcriptional states and must be maintained through cell division. Here, we analyzed in detail the link between Polycomb Group (PcG) proteins, higher-order chromatin structure, and replication timing in Drosophila. By using bioinformatic analyses combined with functional experiments, we show that Polycomb Repressive Complex 1 (PRC1), PRC2, and PhoRC differently correlate with replication timing of their targets and that transcription per se does not determine replication timing. Strikingly, by analyzing the PcG-regulated Bithorax Complex, where PRC1, PRC2, and PhoRC complexes are bound to repressed targets, we provide evidence for a synergistic role of PcG proteins in the modulation and maintenance of replication timing through the definition of specific, topologically distinct genomic domains.
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Affiliation(s)
- Federica Lo Sardo
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Chiara Lanzuolo
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
- CNR Institute of Cellular Biology and Neurobiology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Federico Comoglio
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zürich, Basel, Switzerland
| | - Marco De Bardi
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Renato Paro
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zürich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Valerio Orlando
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
- * E-mail:
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Demczuk A, Gauthier MG, Veras I, Kosiyatrakul S, Schildkraut CL, Busslinger M, Bechhoefer J, Norio P. Regulation of DNA replication within the immunoglobulin heavy-chain locus during B cell commitment. PLoS Biol 2012; 10:e1001360. [PMID: 22807655 PMCID: PMC3393677 DOI: 10.1371/journal.pbio.1001360] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 05/30/2012] [Indexed: 12/03/2022] Open
Abstract
The temporal order of replication of mammalian chromosomes appears to be linked to their functional organization, but the process that establishes and modifies this order during cell differentiation remains largely unknown. Here, we studied how the replication of the Igh locus initiates, progresses, and terminates in bone marrow pro-B cells undergoing B cell commitment. We show that many aspects of DNA replication can be quantitatively explained by a mechanism involving the stochastic firing of origins (across the S phase and the Igh locus) and extensive variations in their firing rate (along the locus). The firing rate of origins shows a high degree of coordination across Igh domains that span tens to hundreds of kilobases, a phenomenon not observed in simple eukaryotes. Differences in domain sizes and firing rates determine the temporal order of replication. During B cell commitment, the expression of the B-cell-specific factor Pax5 sharply alters the temporal order of replication by modifying the rate of origin firing within various Igh domains (particularly those containing Pax5 binding sites). We propose that, within the Igh CH-3′RR domain, Pax5 is responsible for both establishing and maintaining high rates of origin firing, mostly by controlling events downstream of the assembly of pre-replication complexes. Each time a mammalian cell duplicates its genome in preparation for cell division it activates thousands of so called “DNA origins of replication.” The timely and complete duplication of the genome depends on careful orchestration of origin activation, which is modified when cells differentiate to perform a specific function. We currently lack a universally accepted model of origin regulation that can explain the replication dynamics in complex eukaryotes. Here, we studied the mouse immunoglobulin heavy-chain locus, one of the antibody-encoding portions of the genome, where origins change activity when antibody-producing B cells differentiate in the bone marrow. We show that multiple aspects of DNA replication initiation, progression, and termination can be explained mathematically by the interplay between randomly firing origins and two independent variables: the speed of progression of replication forks and the firing rate of origins along the locus. The rate of origin firing varies extensively along the locus during B cell differentiation and, thus, is a dominant factor in establishing the temporal order of replication. A differentiation factor called Pax5 can alter the temporal order of replication by modifying the rate of origin firing across various parts of the locus.
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Affiliation(s)
- Agnieszka Demczuk
- Department of Oncology, Montefiore Medical Center, Moses Division, Bronx, New York, United States of America
| | | | - Ingrid Veras
- Department of Oncology, Montefiore Medical Center, Moses Division, Bronx, New York, United States of America
| | - Settapong Kosiyatrakul
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Carl L. Schildkraut
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - John Bechhoefer
- Department of Physics, Simon Fraser University, Burnaby, Canada
| | - Paolo Norio
- Department of Oncology, Montefiore Medical Center, Moses Division, Bronx, New York, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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