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The extrachromosomal elements of the Naegleria genus: How little we know. Plasmid 2021; 115:102567. [PMID: 33617907 DOI: 10.1016/j.plasmid.2021.102567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 11/20/2022]
Abstract
There are currently 47 characterized species in the Naegleria genus of free-living amoebae. Each amoeba has thousands of extrachromosomal elements that are closed circular structures comprised of a single ribosomal DNA (rDNA) copy and a large non-rDNA sequence. Despite the presence of putative open reading frames and introns, ribosomal RNA is the only established transcript. A single origin of DNA replication (ori) has been mapped within the non-rDNA sequence for one species (N. gruberi), a finding that strongly indicates that these episomes replicate independently of the cell's chromosomal DNA component. This article reviews that which has been published about these interesting DNA elements and by analyzing available sequence data, discusses the possibility that different phylogenetically related clusters of Naegleria species individually conserve ori structures and suggests where the rRNA promoter and termination sites may be located.
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Mocquard-Bucher E, Galvani A, Thiriet C. Histone H4 acetylation links nucleosome turnover and nucleosome assembly: lessons from the slime moldPhysarum polycephalum. FRONTIERS IN LIFE SCIENCE 2013. [DOI: 10.1080/21553769.2013.848241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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3
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Elliott GO, Murphy KJ, Hayes JJ, Thiriet C. Replication-independent nucleosome exchange is enhanced by local and specific acetylation of histone H4. Nucleic Acids Res 2013; 41:2228-38. [PMID: 23303778 PMCID: PMC3575802 DOI: 10.1093/nar/gks1451] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We used a novel single-cell strategy to examine the fate of histones during G2-phase. Consistent with previous results, we find that in G2-phase, the majority of nuclear histones are assembled into chromatin, whereas a small fraction comprises an unassembled pool. Small increases in the amount of histones within the free pool affect the extent of exchange, suggesting that the free pool is in dynamic equilibrium with chromatin proteins. Unexpectedly, acetylated H4 is preferentially partitioned to the unassembled pool. Although an increase in global histone acetylation did not affect overall nucleosome dynamics, an H4 containing lysine to glutamine substitutions as mimics of acetylation significantly increased the rate of exchange, but did not affect the acetylation state of neighbouring nucleosomes. Interestingly, transcribed regions are particularly predisposed to exchange on incorporation of H4 acetylation mimics compared with surrounding regions. Our results support a model whereby histone acetylation on K8 and K16 specifically marks nucleosomes for eviction, with histones being rapidly deacetylated on reassembly.
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Affiliation(s)
- Giles O Elliott
- UFIP (FRE-CNRS 3478), Université de Nantes, 2 rue de la Houssinière, 44322 Nantes Cedex 3, France
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Cayrou C, Coulombe P, Vigneron A, Stanojcic S, Ganier O, Peiffer I, Rivals E, Puy A, Laurent-Chabalier S, Desprat R, Méchali M. Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res 2011; 21:1438-49. [PMID: 21750104 DOI: 10.1101/gr.121830.111] [Citation(s) in RCA: 247] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In metazoans, thousands of DNA replication origins (Oris) are activated at each cell cycle. Their genomic organization and their genetic nature remain elusive. Here, we characterized Oris by nascent strand (NS) purification and a genome-wide analysis in Drosophila and mouse cells. We show that in both species most CpG islands (CGI) contain Oris, although methylation is nearly absent in Drosophila, indicating that this epigenetic mark is not crucial for defining the activated origin. Initiation of DNA synthesis starts at the borders of CGI, resulting in a striking bimodal distribution of NS, suggestive of a dual initiation event. Oris contain a unique nucleotide skew around NS peaks, characterized by G/T and C/A overrepresentation at the 5' and 3' of Ori sites, respectively. Repeated GC-rich elements were detected, which are good predictors of Oris, suggesting that common sequence features are part of metazoan Oris. In the heterochromatic chromosome 4 of Drosophila, Oris correlated with HP1 binding sites. At the chromosome level, regions rich in Oris are early replicating, whereas Ori-poor regions are late replicating. The genome-wide analysis was coupled with a DNA combing analysis to unravel the organization of Oris. The results indicate that Oris are in a large excess, but their activation does not occur at random. They are organized in groups of site-specific but flexible origins that define replicons, where a single origin is activated in each replicon. This organization provides both site specificity and Ori firing flexibility in each replicon, allowing possible adaptation to environmental cues and cell fates.
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Eukaryotic DNA replication origins: many choices for appropriate answers. Nat Rev Mol Cell Biol 2010; 11:728-38. [DOI: 10.1038/nrm2976] [Citation(s) in RCA: 310] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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RNase-dependent discontinuities associated with the crossovers of spontaneously formed joint DNA molecules in Physarum polycephalum. Chromosoma 2010; 119:601-11. [DOI: 10.1007/s00412-010-0281-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 06/07/2010] [Accepted: 06/11/2010] [Indexed: 11/27/2022]
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Maric C, Prioleau MN. Interplay between DNA replication and gene expression: a harmonious coexistence. Curr Opin Cell Biol 2010; 22:277-83. [PMID: 20363609 DOI: 10.1016/j.ceb.2010.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/11/2010] [Accepted: 03/12/2010] [Indexed: 01/01/2023]
Abstract
Multicellular organisms have evolved highly sophisticated machinery to that their genomes are accurately duplicated and that the various gene expression programs are established correctly. Recent large-scale studies have shed light on how these fundamental processes interact. Although the machinery mediating these processes share similar cis-regulatory elements, they are not strictly coregulated. Furthermore, studies of the replisome show that highly transcribed genes present a major obstacle to its operation. Further studies will be needed to identify key regulators of the spatio-temporal program of DNA replication, for the elucidation of the complex interplay between replication and transcription.
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Affiliation(s)
- Chrystelle Maric
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris 7, Paris, France
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Thiriet C, Hayes JJ. Linker histone phosphorylation regulates global timing of replication origin firing. J Biol Chem 2008; 284:2823-2829. [PMID: 19015270 DOI: 10.1074/jbc.m805617200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Despite the presence of linker histone in all eukaryotes, the primary function(s) of this histone have been difficult to clarify. Knock-out experiments indicate that H1s play a role in regulation of only a small subset of genes but are an essential component in mouse development. Here, we show that linker histone (H1) is involved in the global regulation of DNA replication in Physarum polycephalum. We find that genomic DNA of H1 knock-down cells is more rapidly replicated, an effect due at least in part to disruption of the native timing of replication fork firing. Immunoprecipitation experiments demonstrate that H1 is transiently lost from replicating chromatin via a process facilitated by phosphorylation. Our results suggest that linker histones generate a chromatin environment refractory to replication and that their transient removal via protein phosphorylation during S phase is a critical step in the epigenetic regulation of replication timing.
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Affiliation(s)
- Christophe Thiriet
- 1UMR-CNRS 6204 U3B, Université de Nantes, Dynamique de la Chromatine et Épigénétique, 44322 Nantes, France.
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642.
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Bénard M, Maric C, Pierron G. Low rate of replication fork progression lengthens the replication timing of a locus containing an early firing origin. Nucleic Acids Res 2007; 35:5763-74. [PMID: 17717000 PMCID: PMC2034475 DOI: 10.1093/nar/gkm586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Invariance of temporal order of genome replication in eukaryotic cells and its correlation with gene activity has been well-documented. However, recent data suggest a relax control of replication timing. To evaluate replication schedule accuracy, we detailed the replicational organization of the developmentally regulated php locus that we previously found to be lately replicated, even though php gene is highly transcribed in naturally synchronous plasmodia of Physarum. Unexpectedly, bi-dimensional agarose gel electrophoreses of DNA samples prepared at specific time points of S phase showed that replication of the locus actually begins at the onset of S phase but it proceeds through the first half of S phase, so that complete replication of php-containing DNA fragments occurs in late S phase. Origin mapping located replication initiation upstream php coding region. This proximity and rapid fork progression through the coding region result in an early replication of php gene. We demonstrated that afterwards an unusually low fork rate and unidirectional fork pausing prolong complete replication of php locus, and we excluded random replication timing. Importantly, we evidenced that the origin linked to php gene in plasmodium is not fired in amoebae when php expression dramatically reduced, further illustrating replication-transcription coupling in Physarum.
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Affiliation(s)
- Marianne Bénard
- CNRS-FRE 2937, Institut André Lwoff, BP8, 94800 Villejuif, France.
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Aladjem MI. Replication in context: dynamic regulation of DNA replication patterns in metazoans. Nat Rev Genet 2007; 8:588-600. [PMID: 17621316 DOI: 10.1038/nrg2143] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Replication in eukaryotes initiates from discrete genomic regions according to a strict, often tissue-specific temporal programme. However, the locations of initiation events within initiation regions vary, show sequence disparity and are affected by interactions with distal elements. Increasing evidence suggests that specification of replication sites and the timing of replication are dynamic processes that are regulated by tissue-specific and developmental cues, and are responsive to epigenetic modifications. Dynamic specification of replication patterns might serve to prevent or resolve possible spatial and/or temporal conflicts between replication, transcription and chromatin assembly, and facilitate subtle or extensive changes of gene expression during differentiation and development.
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Affiliation(s)
- Mirit I Aladjem
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Building 37, Room 5056, 37 Convent Drive, Bethesda, Maryland 20892-4255, USA.
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Norio P. DNA replication: the unbearable lightness of origins. EMBO Rep 2006; 7:779-81. [PMID: 16880822 PMCID: PMC1525147 DOI: 10.1038/sj.embor.7400766] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Accepted: 06/29/2006] [Indexed: 11/08/2022] Open
Affiliation(s)
- Paolo Norio
- Department of Cell Biology, CH416, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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Dazy S, Gandrillon O, Hyrien O, Prioleau MN. Broadening of DNA replication origin usage during metazoan cell differentiation. EMBO Rep 2006; 7:806-11. [PMID: 16799461 PMCID: PMC1525144 DOI: 10.1038/sj.embor.7400736] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 05/15/2006] [Accepted: 05/15/2006] [Indexed: 01/11/2023] Open
Abstract
We have examined whether replication of the chicken beta-globin locus changes during differentiation of primary erythroid progenitors into erythrocytes. In undifferentiated progenitors, four principal initiation sites and a replication fork pausing region (RFP) were observed. Forty-eight hours after induction of differentiation, the principal sites were maintained, even in the activated beta(A)-globin gene, some minor sites were enhanced, three new sites appeared and the RFP disappeared. One of the activated origins showed increased histone H3 K9K14 diacetylation, but the others did not. These results demonstrate a broadening of DNA replication origin usage during differentiation of untransformed metazoan cells and indicate that histone H3 diacetylation, other histone modifications so far reported and transcription are not crucial determinants of origin selection in this system.
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Affiliation(s)
- Sébastien Dazy
- Centre de Génétique Moléculaire et Cellulaire, Université Claude Bernard-Lyon I, 16 rue Dubois, 69622 Villeurbanne Cedex, France
| | - Olivier Gandrillon
- Centre de Génétique Moléculaire et Cellulaire, Université Claude Bernard-Lyon I, 16 rue Dubois, 69622 Villeurbanne Cedex, France
| | - Olivier Hyrien
- Laboratoire de Génétique Moléculaire, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France
| | - Marie-Noëlle Prioleau
- Laboratoire de Génétique Moléculaire, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France
- Laboratoire de Biologie des génomes, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
- Tel: +33 (1) 44 27 40 93; Fax: +33 (1) 44 27 57 16; E-mail:
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Abstract
Replication origins should no longer be thought of as housekeeping elements that function similarly in all cell types. provide the most authoritative evidence to date that mammalian replication origins can be dynamically regulated during differentiation.
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Affiliation(s)
- David M Gilbert
- Department of Biochemistry and Molecular Biology, The State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210, USA
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Thiriet C, Hayes JJ. Replication-independent core histone dynamics at transcriptionally active loci in vivo. Genes Dev 2005; 19:677-82. [PMID: 15769942 PMCID: PMC1065721 DOI: 10.1101/gad.1265205] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We used a novel labeling technique in the naturally synchronous organism Physarum polycephalum to examine the fate of core histones in G2 phase. We find rapid exchange of H2A/H2B dimers with free pools that is greatly diminished by treatment of the cells with alpha-amanitin. This exchange is enhanced in pol II-coding sequences compared with extragenic regions or inactive loci. In contrast, H3/H4 tetramers exhibit far lower levels of exchange in the pol II-transcribed genes tested, suggesting that tetramer exchange occurs via a distinct mechanism. However, we find that transcribed regions of the ribosomal RNA gene loci exhibit rapid exchange of H3/H4 tetramers. Thus, our data show that the majority of the pol II transcription-dependent histone exchange is due to elongation in vivo rather than promoter remodeling or other pol II-dependent alterations in promoter structure and, in contrast to pol I, pol II transcription through nucleosomes in vivo causes facile exchange of both H2A/H2B dimers while allowing conservation of epigenetic "marks" and other post-translational modifications on H3 and H4.
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Affiliation(s)
- Christophe Thiriet
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
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16
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Abstract
Eukaryotic DNA replication begins at numerous but often poorly characterized sequences called origins, which are distributed fairly regularly along chromosomes. The elusive and idiosyncratic nature of origins in higher eukaryotes is now understood as resulting from a strong epigenetic influence on their specification, which provides flexibility in origin selection and allows for tailoring the dynamics of chromosome replication to the specific needs of cells. By contrast, the factors that assemble in trans to make these origins competent for replication and the kinases that trigger initiation are well conserved. Genome-wide and single-molecule approaches are being developed to elucidate the dynamics of chromosome replication. The notion that a well-coordinated progression of replication forks is crucial for many aspects of the chromosome cycle besides simply duplication begins to be appreciated.
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Affiliation(s)
- Etienne Schwob
- Institute of Molecular Genetics, CNRS UMR5535 and University Montpellier 2, 1919, route de Mende, 34293 Montpellier, France
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Abstract
After 40 years of searching for the eukaryotic replicator sequence, it is time to abandon the concept of 'the' replicator as a single genetic entity. Here I propose a 'relaxed replicon model' in which a positive initiator-replicator interaction is facilitated by a combination of several complex features of chromatin. An important question for the future is whether the positions of replication origins are simply a passive result of local chromatin structure or are actively localized to coordinate replication with other chromosomal activities.
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Affiliation(s)
- David M Gilbert
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NewYork 13210, USA.
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Antequera F. Genomic specification and epigenetic regulation of eukaryotic DNA replication origins. EMBO J 2004; 23:4365-70. [PMID: 15510221 PMCID: PMC526466 DOI: 10.1038/sj.emboj.7600450] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Accepted: 09/24/2004] [Indexed: 11/09/2022] Open
Abstract
Identification of DNA replication origins (ORIs) at a genome-wide level in eukaryotes has proved to be difficult due to the high degree of degeneracy of their sequences. Recent structural and functional approaches, however, have circumvented this limitation and have provided reliable predictions of their genomic distribution in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, and they have also significantly increased the number of characterized ORIs in animals. This article reviews recent evidence on how ORIs are specified and maintained in these systems and on their regulation and sensitivity to epigenetic signals. It also discusses the possible additional involvement of ORIs in processes other than DNA replication.
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Affiliation(s)
- Francisco Antequera
- Instituto de Microbiología Bioquímica, CSIC/Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Microbiología Bioquímica, CSIC/Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain. Tel.: +34 923 121778; Fax: +34 923 224876; E-mail:
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Danis E, Brodolin K, Menut S, Maiorano D, Girard-Reydet C, Méchali M. Specification of a DNA replication origin by a transcription complex. Nat Cell Biol 2004; 6:721-30. [PMID: 15247921 DOI: 10.1038/ncb1149] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Accepted: 06/14/2004] [Indexed: 11/08/2022]
Abstract
In early Xenopus development, transcription is repressed and DNA replication initiates at non-specific sites. Here, we show that a site-specific DNA replication origin can be induced in this context by the assembly of a transcription domain. Deletion of the promoter element abolishes site-specific initiation, and its relocalization to an ectopic site induces a new origin of replication. This process does not require active transcription, and specification of the origin occurs mainly through a decrease in non-specific initiation at sites distant from the promoter. Finally, chromatin immunoprecipitation experiments suggest that site-specific acetylation of histones favours the selection of the active DNA replication origin. We propose that the specification of active DNA replication origins occurs by secondary epigenetic events and that the programming of chromatin for transcription during development contributes to this selection in higher eukaryotes.
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Affiliation(s)
- Etienne Danis
- Institute of Human Genetics, CNRS, Genome Dynamics and Development, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
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