1
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Lee CSK, Weiβ M, Hamperl S. Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes. Nucleus 2023; 14:2229642. [PMID: 37469113 PMCID: PMC10361152 DOI: 10.1080/19491034.2023.2229642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
In eukaryotic genomes, hundreds to thousands of potential start sites of DNA replication named origins are dispersed across each of the linear chromosomes. During S-phase, only a subset of origins is selected in a stochastic manner to assemble bidirectional replication forks and initiate DNA synthesis. Despite substantial progress in our understanding of this complex process, a comprehensive 'identity code' that defines origins based on specific nucleotide sequences, DNA structural features, the local chromatin environment, or 3D genome architecture is still missing. In this article, we review the genetic and epigenetic features of replication origins in yeast and metazoan chromosomes and highlight recent insights into how this flexibility in origin usage contributes to nuclear organization, cell growth, differentiation, and genome stability.
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Affiliation(s)
- Clare S K Lee
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Matthias Weiβ
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
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2
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Gutierrez C. A Journey to the Core of the Plant Cell Cycle. Int J Mol Sci 2022; 23:8154. [PMID: 35897730 PMCID: PMC9330084 DOI: 10.3390/ijms23158154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/16/2022] [Accepted: 07/21/2022] [Indexed: 02/04/2023] Open
Abstract
Production of new cells as a result of progression through the cell division cycle is a fundamental biological process for the perpetuation of both unicellular and multicellular organisms. In the case of plants, their developmental strategies and their largely sessile nature has imposed a series of evolutionary trends. Studies of the plant cell division cycle began with cytological and physiological approaches in the 1950s and 1960s. The decade of 1990 marked a turn point with the increasing development of novel cellular and molecular protocols combined with advances in genetics and, later, genomics, leading to an exponential growth of the field. In this article, I review the current status of plant cell cycle studies but also discuss early studies and the relevance of a multidisciplinary background as a source of innovative questions and answers. In addition to advances in a deeper understanding of the plant cell cycle machinery, current studies focus on the intimate interaction of cell cycle components with almost every aspect of plant biology.
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Affiliation(s)
- Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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3
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A DNA replication-independent function of pre-replication complex genes during cell invasion in C. elegans. PLoS Biol 2022; 20:e3001317. [PMID: 35192608 PMCID: PMC8863262 DOI: 10.1371/journal.pbio.3001317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/01/2021] [Indexed: 11/19/2022] Open
Abstract
Cell invasion is an initiating event during tumor cell metastasis and an essential process during development. A screen of C. elegans orthologs of genes overexpressed in invasive human melanoma cells has identified several components of the conserved DNA pre-replication complex (pre-RC) as positive regulators of anchor cell (AC) invasion. The pre-RC genes function cell-autonomously in the G1-arrested AC to promote invasion, independently of their role in licensing DNA replication origins in proliferating cells. While the helicase activity of the pre-RC is necessary for AC invasion, the downstream acting DNA replication initiation factors are not required. The pre-RC promotes the invasive fate by regulating the expression of extracellular matrix genes and components of the PI3K signaling pathway. Increasing PI3K pathway activity partially suppressed the AC invasion defects caused by pre-RC depletion, suggesting that the PI3K pathway is one critical pre-RC target. We propose that the pre-RC, or a part of it, acts in the postmitotic AC as a transcriptional regulator that facilitates the switch to an invasive phenotype.
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4
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Ocaña-Pallarès E, Vergara Z, Desvoyes B, Tejada-Jimenez M, Romero-Jurado A, Galván A, Fernández E, Ruiz-Trillo I, Gutierrez C. Origin Recognition Complex (ORC) Evolution Is Influenced by Global Gene Duplication/Loss Patterns in Eukaryotic Genomes. Genome Biol Evol 2020; 12:3878-3889. [PMID: 31990293 PMCID: PMC7058166 DOI: 10.1093/gbe/evaa011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 12/29/2022] Open
Abstract
The conservation of orthologs of most subunits of the origin recognition complex (ORC) has served to propose that the whole complex is common to all eukaryotes. However, various uncertainties have arisen concerning ORC subunit composition in a variety of lineages. Also, it is unclear whether the ancestral diversification of ORC in eukaryotes was accompanied by the neofunctionalization of some subunits, for example, role of ORC1 in centriole homeostasis. We have addressed these questions by reconstructing the distribution and evolutionary history of ORC1-5/CDC6 in a taxon-rich eukaryotic data set. First, we identified ORC subunits previously undetected in divergent lineages, which allowed us to propose a series of parsimonious scenarios for the origin of this multiprotein complex. Contrary to previous expectations, we found a global tendency in eukaryotes to increase or decrease the number of subunits as a consequence of genome duplications or streamlining, respectively. Interestingly, parasites show significantly lower number of subunits than free-living eukaryotes, especially those with the lowest genome size and gene content metrics. We also investigated the evolutionary origin of the ORC1 role in centriole homeostasis mediated by the PACT region in human cells. In particular, we tested the consequences of reducing ORC1 levels in the centriole-containing green alga Chlamydomonas reinhardtii. We found that the proportion of centrioles to flagella and nuclei was not dramatically affected. This, together with the PACT region not being significantly more conserved in centriole-bearing eukaryotes, supports the notion that this neofunctionalization of ORC1 would be a recent acquisition rather than an ancestral eukaryotic feature.
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Affiliation(s)
| | - Zaida Vergara
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, Spain
| | - Bénédicte Desvoyes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, Spain
| | - Manuel Tejada-Jimenez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Córdoba, Córdoba, Spain
| | - Ainoa Romero-Jurado
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Córdoba, Córdoba, Spain
| | - Aurora Galván
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Córdoba, Córdoba, Spain
| | - Emilio Fernández
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Córdoba, Córdoba, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, Spain
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5
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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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6
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Akerman I, Kasaai B, Bazarova A, Sang PB, Peiffer I, Artufel M, Derelle R, Smith G, Rodriguez-Martinez M, Romano M, Kinet S, Tino P, Theillet C, Taylor N, Ballester B, Méchali M. A predictable conserved DNA base composition signature defines human core DNA replication origins. Nat Commun 2020; 11:4826. [PMID: 32958757 PMCID: PMC7506530 DOI: 10.1038/s41467-020-18527-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023] Open
Abstract
DNA replication initiates from multiple genomic locations called replication origins. In metazoa, DNA sequence elements involved in origin specification remain elusive. Here, we examine pluripotent, primary, differentiating, and immortalized human cells, and demonstrate that a class of origins, termed core origins, is shared by different cell types and host ~80% of all DNA replication initiation events in any cell population. We detect a shared G-rich DNA sequence signature that coincides with most core origins in both human and mouse genomes. Transcription and G-rich elements can independently associate with replication origin activity. Computational algorithms show that core origins can be predicted, based solely on DNA sequence patterns but not on consensus motifs. Our results demonstrate that, despite an attributed stochasticity, core origins are chosen from a limited pool of genomic regions. Immortalization through oncogenic gene expression, but not normal cellular differentiation, results in increased stochastic firing from heterochromatin and decreased origin density at TAD borders. In metazoan the DNA sequence elements characterizing origin specification are unknown. By generating and analysing 19 SNS-seq datasets from different human cell types, the authors reveal a class and features of Core origins of replication which can be predicted by an algorithm.
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Affiliation(s)
- Ildem Akerman
- Institute of Human Genetics, CNRS - University of Montpellier, Montpellier, France. .,Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK.
| | - Bahar Kasaai
- Institute of Human Genetics, CNRS - University of Montpellier, Montpellier, France
| | - Alina Bazarova
- Centre for Computational Biology (CCB), University of Birmingham, Birmingham, UK.,Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - Pau Biak Sang
- Institute of Human Genetics, CNRS - University of Montpellier, Montpellier, France
| | - Isabelle Peiffer
- Institute of Human Genetics, CNRS - University of Montpellier, Montpellier, France
| | - Marie Artufel
- Aix-Marseille University, INSERM, TAGC, UMR S1090, Marseille, France
| | - Romain Derelle
- Life and Environmental Sciences (LES), University of Birmingham, Birmingham, UK
| | - Gabrielle Smith
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK
| | | | - Manuela Romano
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Sandrina Kinet
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Peter Tino
- Centre for Computational Biology (CCB), University of Birmingham, Birmingham, UK
| | - Charles Theillet
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Montpellier, France
| | - Naomi Taylor
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France.,Pediatric Oncology Branch, NCI, CCR, NIH, Bethesda, MD, USA
| | - Benoit Ballester
- Aix-Marseille University, INSERM, TAGC, UMR S1090, Marseille, France
| | - Marcel Méchali
- Institute of Human Genetics, CNRS - University of Montpellier, Montpellier, France.
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7
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Mamun MA, Albergante L, J Blow J, Newman TJ. 3 tera-basepairs as a fundamental limit for robust DNA replication. Phys Biol 2020; 17:046002. [PMID: 32320972 DOI: 10.1088/1478-3975/ab8c2f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In order to maintain functional robustness and species integrity, organisms must ensure high fidelity of the genome duplication process. This is particularly true during early development, where cell division is often occurring both rapidly and coherently. By studying the extreme limits of suppressing DNA replication failure due to double fork stall errors, we uncover a fundamental constant that describes a trade-off between genome size and architectural complexity of the developing organism. This constant has the approximate value N U ≈ 3 × 1012 basepairs, and depends only on two highly conserved molecular properties of DNA biology. We show that our theory is successful in interpreting a diverse range of data across the Eukaryota.
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Affiliation(s)
- M Al Mamun
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom. CIB-CSIC, Madrid 28040, Spain
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8
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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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9
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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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10
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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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11
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Prorok P, Artufel M, Aze A, Coulombe P, Peiffer I, Lacroix L, Guédin A, Mergny JL, Damaschke J, Schepers A, Cayrou C, Teulade-Fichou MP, Ballester B, Méchali M. Involvement of G-quadruplex regions in mammalian replication origin activity. Nat Commun 2019; 10:3274. [PMID: 31332171 PMCID: PMC6646384 DOI: 10.1038/s41467-019-11104-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/08/2019] [Indexed: 12/11/2022] Open
Abstract
Genome-wide studies of DNA replication origins revealed that origins preferentially associate with an Origin G-rich Repeated Element (OGRE), potentially forming G-quadruplexes (G4). Here, we functionally address their requirements for DNA replication initiation in a series of independent approaches. Deletion of the OGRE/G4 sequence strongly decreased the corresponding origin activity. Conversely, the insertion of an OGRE/G4 element created a new replication origin. This element also promoted replication of episomal EBV vectors lacking the viral origin, but not if the OGRE/G4 sequence was deleted. A potent G4 ligand, PhenDC3, stabilized G4s but did not alter the global origin activity. However, a set of new, G4-associated origins was created, whereas suppressed origins were largely G4-free. In vitro Xenopus laevis replication systems showed that OGRE/G4 sequences are involved in the activation of DNA replication, but not in the pre-replication complex formation. Altogether, these results converge to the functional importance of OGRE/G4 elements in DNA replication initiation.
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Affiliation(s)
- Paulina Prorok
- Institute of Human Genetics, CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | | | - Antoine Aze
- Institute of Human Genetics, CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Philippe Coulombe
- Institute of Human Genetics, CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Isabelle Peiffer
- Institute of Human Genetics, CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Laurent Lacroix
- Balasubramanian group, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Aurore Guédin
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), Pessac, 33607, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), Pessac, 33607, France.,Institut Curie, CNRS UMR9187, Inserm U1196, Universite Paris Saclay, Orsay, France
| | - Julia Damaschke
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Marchioninistraße 25, 81377, Munich, Germany
| | - Aloys Schepers
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Marchioninistraße 25, 81377, Munich, Germany.,Monoclonal Antibody Core Facility & Research Group, Institute for Diabetes and Obesity, Helmholtz Zentrum München, Ingolstädter Landstrasse, 85764, Neuherberg, Germany
| | - Christelle Cayrou
- Institute of Human Genetics, CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France.,Centre de Recherche en Cancérologie de Marseille 27 Boulevard Lei Roure, 13273, Marseille, France
| | | | | | - Marcel Méchali
- Institute of Human Genetics, CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France.
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12
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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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13
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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 DOI: 10.1080/15384101.2019.1618641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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
- a 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
- a 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
- a 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
- a 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
- a 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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Gaboriaud J, Wu PYJ. Insights into the Link between the Organization of DNA Replication and the Mutational Landscape. Genes (Basel) 2019; 10:genes10040252. [PMID: 30934791 PMCID: PMC6523204 DOI: 10.3390/genes10040252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 12/17/2022] Open
Abstract
The generation of a complete and accurate copy of the genetic material during each cell cycle is integral to cell growth and proliferation. However, genetic diversity is essential for adaptation and evolution, and the process of DNA replication is a fundamental source of mutations. Genome alterations do not accumulate randomly, with variations in the types and frequencies of mutations that arise in different genomic regions. Intriguingly, recent studies revealed a striking link between the mutational landscape of a genome and the spatial and temporal organization of DNA replication, referred to as the replication program. In our review, we discuss how this program may contribute to shaping the profile and spectrum of genetic alterations, with implications for genome dynamics and organismal evolution in natural and pathological contexts.
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Affiliation(s)
- Julia Gaboriaud
- CNRS, University of Rennes, Institute of Genetics and Development of Rennes, 35043 Rennes, France.
| | - Pei-Yun Jenny Wu
- CNRS, University of Rennes, Institute of Genetics and Development of Rennes, 35043 Rennes, France.
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15
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Sequeira-Mendes J, Vergara Z, Peiró R, Morata J, Aragüez I, Costas C, Mendez-Giraldez R, Casacuberta JM, Bastolla U, Gutierrez C. Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins. Genome Res 2019; 29:784-797. [PMID: 30846531 PMCID: PMC6499314 DOI: 10.1101/gr.240986.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 02/25/2019] [Indexed: 12/20/2022]
Abstract
Eukaryotic genome replication depends on thousands of DNA replication origins (ORIs). A major challenge is to learn ORI biology in multicellular organisms in the context of growing organs to understand their developmental plasticity. We have identified a set of ORIs of Arabidopsis thaliana and their chromatin landscape at two stages of post-embryonic development. ORIs associate with multiple chromatin signatures including transcription start sites (TSS) but also proximal and distal regulatory regions and heterochromatin, where ORIs colocalize with retrotransposons. In addition, quantitative analysis of ORI activity led us to conclude that strong ORIs have high GC content and clusters of GGN trinucleotides. Development primarily influences ORI firing strength rather than ORI location. ORIs that preferentially fire at early developmental stages colocalize with GC-rich heterochromatin, but at later stages with transcribed genes, perhaps as a consequence of changes in chromatin features associated with developmental processes. Our study provides the set of ORIs active in an organism at the post-embryo stage that should allow us to study ORI biology in response to development, environment, and mutations with a quantitative approach. In a wider scope, the computational strategies developed here can be transferred to other eukaryotic systems.
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Affiliation(s)
- Joana Sequeira-Mendes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Zaida Vergara
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Ramon Peiró
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Jordi Morata
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus Universitat Autónoma de Barcelona, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Irene Aragüez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Celina Costas
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Raul Mendez-Giraldez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus Universitat Autónoma de Barcelona, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Ugo Bastolla
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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16
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Linking the organization of DNA replication with genome maintenance. Curr Genet 2019; 65:677-683. [PMID: 30600398 DOI: 10.1007/s00294-018-0923-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 12/11/2022]
Abstract
The spatial and temporal organization of genome duplication, also referred to as the replication program, is defined by the distribution and the activities of the sites of replication initiation across the genome. Alterations to the replication profile are associated with cell fate changes during development and in pathologies, but the importance of undergoing S phase with distinct and specific programs remains largely unexplored. We have recently addressed this question, focusing on the interplay between the replication program and genome maintenance. In particular, we demonstrated that when cells encounter challenges to DNA synthesis, the organization of DNA replication drives the response to replication stress that is mediated by the ATR/Rad3 checkpoint pathway, thus shaping the pattern of genome instability along the chromosomes. In this review, we present the major findings of our study and discuss how they may bring new perspectives to our understanding of the biological importance of the replication program.
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17
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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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18
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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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19
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Singh B, Wu PYJ. Regulation of the program of DNA replication by CDK: new findings and perspectives. Curr Genet 2018; 65:79-85. [PMID: 29926159 DOI: 10.1007/s00294-018-0860-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 12/18/2022]
Abstract
Progression through the cell cycle is driven by the activities of the cyclin-dependent kinase (CDK) family of enzymes, which establish an ordered passage through the cell cycle phases. CDK activity is crucial for the cellular transitions from G1 to S and G2 to M, which are highly controlled to promote the faithful duplication of the genetic material and the transmission of the genome into daughter cells, respectively. While oscillations in CDK activity are essential for cell division, how its specific dynamics may shape cellular processes remains an open question. Recently, we have investigated the potential role of CDK in establishing the profile of replication initiation along the chromosomes, also referred to as the replication program. Our results demonstrated that the timing and level of CDK activity at G1/S provide two critical and independent inputs that modulate the pattern of origin usage. In this review, we will present the conclusions of our study and discuss the implications of our findings for cellular function and physiology.
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Affiliation(s)
- Balveer Singh
- CNRS, Institute of Genetics and Development of Rennes, University of Rennes, UMR 6290, 2 avenue du Pr. Léon Bernard, 35043, Rennes, France
| | - Pei-Yun Jenny Wu
- CNRS, Institute of Genetics and Development of Rennes, University of Rennes, UMR 6290, 2 avenue du Pr. Léon Bernard, 35043, Rennes, France.
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20
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Chromatin conformation regulates the coordination between DNA replication and transcription. Nat Commun 2018; 9:1590. [PMID: 29686321 PMCID: PMC5913246 DOI: 10.1038/s41467-018-03539-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 02/21/2018] [Indexed: 12/26/2022] Open
Abstract
Chromatin is the template for the basic processes of replication and transcription, making the maintenance of chromosomal integrity critical for cell viability. To elucidate how dividing cells respond to alterations in chromatin structure, here we analyse the replication programme of primary cells with altered chromatin configuration caused by the genetic ablation of the HMGB1 gene, or three histone H1 genes. We find that loss of chromatin compaction in H1-depleted cells triggers the accumulation of stalled forks and DNA damage as a consequence of transcription–replication conflicts. In contrast, reductions in nucleosome occupancy due to the lack of HMGB1 cause faster fork progression without impacting the initiation landscape or fork stability. Thus, perturbations in chromatin integrity elicit a range of responses in the dynamics of DNA replication and transcription, with different consequences on replicative stress. These findings have broad implications for our understanding of how defects in chromatin structure contribute to genomic instability. The maintenance of chromatin integrity during replication is critical for cell viability. Here the authors study how dividing cells respond to alterations in chromatin structure and find that these elicit a range of responses in the dynamics of DNA replication and consequences on replicative stress.
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21
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Bellush JM, Whitehouse I. DNA replication through a chromatin environment. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0287. [PMID: 28847824 DOI: 10.1098/rstb.2016.0287] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2017] [Indexed: 01/03/2023] Open
Abstract
Compaction of the genome into the nuclear space is achieved by wrapping DNA around octameric assemblies of histone proteins to form nucleosomes, the fundamental repeating unit of chromatin. Aside from providing a means by which to fit larger genomes into the cell, chromatinization of DNA is a crucial means by which the cell regulates access to the genome. While the complex role that chromatin plays in gene transcription has been appreciated for a long time, it is now also apparent that crucial aspects of DNA replication are linked to the biology of chromatin. This review will focus on recent advances in our understanding of how the chromatin environment influences key aspects of DNA replication.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- James M Bellush
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.,BCMB Graduate Program, Weill Cornell Medical College, 1300 York Avenue, New York, NY, USA
| | - Iestyn Whitehouse
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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22
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Murray JI. Systems biology of embryonic development: Prospects for a complete understanding of the Caenorhabditis elegans embryo. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 7:e314. [PMID: 29369536 DOI: 10.1002/wdev.314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/01/2017] [Accepted: 12/12/2017] [Indexed: 01/07/2023]
Abstract
The convergence of developmental biology and modern genomics tools brings the potential for a comprehensive understanding of developmental systems. This is especially true for the Caenorhabditis elegans embryo because its small size, invariant developmental lineage, and powerful genetic and genomic tools provide the prospect of a cellular resolution understanding of messenger RNA (mRNA) expression and regulation across the organism. We describe here how a systems biology framework might allow large-scale determination of the embryonic regulatory relationships encoded in the C. elegans genome. This framework consists of two broad steps: (a) defining the "parts list"-all genes expressed in all cells at each time during development and (b) iterative steps of computational modeling and refinement of these models by experimental perturbation. Substantial progress has been made towards defining the parts list through imaging methods such as large-scale green fluorescent protein (GFP) reporter analysis. Imaging results are now being augmented by high-resolution transcriptome methods such as single-cell RNA sequencing, and it is likely the complete expression patterns of all genes across the embryo will be known within the next few years. In contrast, the modeling and perturbation experiments performed so far have focused largely on individual cell types or genes, and improved methods will be needed to expand them to the full genome and organism. This emerging comprehensive map of embryonic expression and regulatory function will provide a powerful resource for developmental biologists, and would also allow scientists to ask questions not accessible without a comprehensive picture. This article is categorized under: Invertebrate Organogenesis > Worms Technologies > Analysis of the Transcriptome Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics.
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Affiliation(s)
- John Isaac Murray
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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23
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Vergara Z, Sequeira-Mendes J, Morata J, Peiró R, Hénaff E, Costas C, Casacuberta JM, Gutierrez C. Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin. Nucleic Acids Res 2017; 45:8358-8368. [PMID: 28605523 PMCID: PMC5737333 DOI: 10.1093/nar/gkx524] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/05/2017] [Indexed: 12/28/2022] Open
Abstract
Genomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands of DNA replication origins (ORIs) scattered throughout the genome. The DNA and chromatin features determining ORI specification are not presently known. We have generated a high-resolution genome-wide map of 3230 ORIs in cultured Arabidopsis thaliana cells. Here, we focused on defining the features associated with ORIs in heterochromatin. In pericentromeric gene-poor domains ORIs associate almost exclusively with the retrotransposon class of transposable elements (TEs), in particular of the Gypsy family. ORI activity in retrotransposons occurs independently of TE expression and while maintaining high levels of H3K9me2 and H3K27me1, typical marks of repressed heterochromatin. ORI-TEs largely colocalize with chromatin signatures defining GC-rich heterochromatin. Importantly, TEs with active ORIs contain a local GC content higher than the TEs lacking them. Our results lead us to conclude that ORI colocalization with retrotransposons is determined by their transposition mechanism based on transcription, and a specific chromatin landscape. Our detailed analysis of ORIs responsible for heterochromatin replication has implications on the mechanisms of ORI specification in other multicellular organisms in which retrotransposons are major components of heterochromatin and of the entire genome.
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Affiliation(s)
- Zaida Vergara
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Joana Sequeira-Mendes
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Jordi Morata
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus Universitat Autónoma de Barcelona, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Ramón Peiró
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Elizabeth Hénaff
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus Universitat Autónoma de Barcelona, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Celina Costas
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus Universitat Autónoma de Barcelona, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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