1
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Distinct features of nucleolus-associated domains in mouse embryonic stem cells. Chromosoma 2020; 129:121-139. [PMID: 32219510 DOI: 10.1007/s00412-020-00734-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 10/24/2022]
Abstract
Heterochromatin in eukaryotic interphase cells frequently localizes to the nucleolar periphery (nucleolus-associated domains (NADs)) and the nuclear lamina (lamina-associated domains (LADs)). Gene expression in somatic cell NADs is generally low, but NADs have not been characterized in mammalian stem cells. Here, we generated the first genome-wide map of NADs in mouse embryonic stem cells (mESCs) via deep sequencing of chromatin associated with biochemically purified nucleoli. As we had observed in mouse embryonic fibroblasts (MEFs), the large type I subset of NADs overlaps with constitutive LADs and is enriched for features of constitutive heterochromatin, including late replication timing and low gene density and expression levels. Conversely, the type II NAD subset overlaps with loci that are not lamina-associated, but in mESCs, type II NADs are much less abundant than in MEFs. mESC NADs are also much less enriched in H3K27me3 modified regions than are NADs in MEFs. Additionally, comparision of MEF and mESC NADs revealed enrichment of developmentally regulated genes in cell-type-specific NADs. Together, these data indicate that NADs are a developmentally dynamic component of heterochromatin. These studies implicate association with the nucleolar periphery as a mechanism for developmentally regulated gene expression and will facilitate future studies of NADs during mESC differentiation.
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2
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Regulation of ectopic heterochromatin-mediated epigenetic diversification by the JmjC family protein Epe1. PLoS Genet 2019; 15:e1008129. [PMID: 31206516 PMCID: PMC6576747 DOI: 10.1371/journal.pgen.1008129] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 04/09/2019] [Indexed: 01/28/2023] Open
Abstract
H3K9 methylation (H3K9me) is a conserved marker of heterochromatin, a transcriptionally silent chromatin structure. Knowledge of the mechanisms for regulating heterochromatin distribution is limited. The fission yeast JmjC domain-containing protein Epe1 localizes to heterochromatin mainly through its interaction with Swi6, a homologue of heterochromatin protein 1 (HP1), and directs JmjC-mediated H3K9me demethylation in vivo. Here, we found that loss of epe1 (epe1Δ) induced a red-white variegated phenotype in a red-pigment accumulation background that generated uniform red colonies. Analysis of isolated red and white colonies revealed that silencing of genes involved in pigment accumulation by stochastic ectopic heterochromatin formation led to white colony formation. In addition, genome-wide analysis of red- and white-isolated clones revealed that epe1Δ resulted in a heterogeneous heterochromatin distribution among clones. We found that Epe1 had an N-terminal domain distinct from its JmjC domain, which activated transcription in both fission and budding yeasts. The N-terminal transcriptional activation (NTA) domain was involved in suppression of ectopic heterochromatin-mediated red-white variegation. We introduced a single copy of Epe1 into epe1Δ clones harboring ectopic heterochromatin, and found that Epe1 could reduce H3K9me from ectopic heterochromatin but some of the heterochromatin persisted. This persistence was due to a latent H3K9me source embedded in ectopic heterochromatin. Epe1H297A, a canonical JmjC mutant, suppressed red-white variegation, but entirely failed to remove already-established ectopic heterochromatin, suggesting that Epe1 prevented stochastic de novo deposition of ectopic H3K9me in an NTA-dependent but JmjC-independent manner, while its JmjC domain mediated removal of H3K9me from established ectopic heterochromatin. Our results suggest that Epe1 not only limits the distribution of heterochromatin but also controls the balance between suppression and retention of heterochromatin-mediated epigenetic diversification. Suppression of unscheduled epigenetic alterations is important for maintenance of homogeneity among clones, while emergence of epigenetic differences is also important for adaptation or differentiation. The mechanisms that balance both processes warrant further investigation. Epe1, a fission yeast JmjC domain-containing protein, is thought to be an H3K9me demethylase that targets ectopic heterochromatin via its JmjC-dependent demethylation function. Here we found that loss of epe1 induced stochastic ectopic heterochromatin formation genome-wide, suggesting that the fission yeast genome had multiple potential heterochromatin formation sites, which were protected by Epe1. We found that Epe1 prevented deposition of ectopic H3K9me independently of its JmjC-mediated demethylation before heterochromatin establishment. By contrast, Epe1 could attack already-established ectopic heterochromatin via its JmjC domain, but demethylation was not 100% effective, which provided a basis for epigenetic variation. Together, our findings indicate that Epe1 is involved in both maintenance and alteration of heterochromatin distribution, and shed light on the mechanisms controlling individual-specific epigenome profiles.
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3
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Iarovaia OV, Minina EP, Sheval EV, Onichtchouk D, Dokudovskaya S, Razin SV, Vassetzky YS. Nucleolus: A Central Hub for Nuclear Functions. Trends Cell Biol 2019; 29:647-659. [PMID: 31176528 DOI: 10.1016/j.tcb.2019.04.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/19/2022]
Abstract
The nucleolus is the largest and most studied nuclear body, but its role in nuclear function is far from being comprehensively understood. Much work on the nucleolus has focused on its role in regulating RNA polymerase I (RNA Pol I) transcription and ribosome biogenesis; however, emerging evidence points to the nucleolus as an organizing hub for many nuclear functions, accomplished via the shuttling of proteins and nucleic acids between the nucleolus and nucleoplasm. Here, we discuss the cellular mechanisms affected by shuttling of nucleolar components, including the 3D organization of the genome, stress response, DNA repair and recombination, transcription regulation, telomere maintenance, and other essential cellular functions.
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Affiliation(s)
- Olga V Iarovaia
- Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France
| | - Elizaveta P Minina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugene V Sheval
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Daria Onichtchouk
- Developmental Biology Unit, Department of Biology I, University of Freiburg, Hauptstrasse 1, D-79104 Freiburg, Germany
| | - Svetlana Dokudovskaya
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France; UMR8126, Université Paris-Sud, CNRS, Institut Gustave Roussy, 94805 Villejuif, France
| | - Sergey V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France; Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Yegor S Vassetzky
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France; Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; UMR8126, Université Paris-Sud, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.
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4
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Abstract
The nucleolus as site of ribosome biogenesis holds a pivotal role in cell metabolism. It is composed of ribosomal DNA (rDNA), which is present as tandem arrays located in nucleolus organizer regions (NORs). In interphase cells, rDNA can be found inside and adjacent to nucleoli and the location is indicative for transcriptional activity of ribosomal genes-inactive rDNA (outside) versus active one (inside). Moreover, the nucleolus itself acts as a spatial organizer of non-nucleolar chromatin. Microscopy-based approaches offer the possibility to explore the spatially distinct localization of the different DNA populations in relation to the nucleolar structure. Recent technical developments in microscopy and preparatory methods may further our understanding of the functional architecture of nucleoli. This review will attempt to summarize the current understanding of mammalian nucleolar chromatin organization as seen from a microscopist's perspective.
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Affiliation(s)
- Christian Schöfer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria.
| | - Klara Weipoltshammer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria
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5
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Pichugin A, Iarovaia OV, Gavrilov A, Sklyar I, Barinova N, Barinov A, Ivashkin E, Caron G, Aoufouchi S, Razin SV, Fest T, Lipinski M, Vassetzky YS. The IGH locus relocalizes to a "recombination compartment" in the perinucleolar region of differentiating B-lymphocytes. Oncotarget 2018; 8:40079-40089. [PMID: 28445143 PMCID: PMC5522243 DOI: 10.18632/oncotarget.16941] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 03/29/2017] [Indexed: 12/22/2022] Open
Abstract
The immunoglobulin heavy chain (IGH) gene loci are subject to specific recombination events during B-cell differentiation including somatic hypermutation and class switch recombination which mark the end of immunoglobulin gene maturation in germinal centers of secondary lymph nodes. These two events rely on the activity of activation-induced cytidine deaminase (AID) which requires DNA double strand breaks be created, a potential danger to the cell. Applying 3D-fluorescence in situ hybridization coupled with immunofluorescence staining to a previously described experimental system recapitulating normal B-cell differentiation ex vivo, we have kinetically analyzed the radial positioning of the two IGH gene loci as well as their proximity with the nucleolus, heterochromatin and γH2AX foci. Our observations are consistent with the proposal that these IGH gene rearrangements take place in a specific perinucleolar “recombination compartment” where AID could be sequestered thus limiting the extent of its potentially deleterious off-target effects.
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Affiliation(s)
- Andrey Pichugin
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Olga V Iarovaia
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France
| | - Alexey Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France
| | - Ilya Sklyar
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France
| | - Natalja Barinova
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France
| | - Aleksandr Barinov
- LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France
| | - Evgeny Ivashkin
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France.,Department of Experimental Neurocytology, Research Center of Neurology, Branch of Brain Research, Moscow, Russia
| | - Gersende Caron
- INSERM U1236, CHU de Rennes, Université Rennes 1, Rennes, France
| | - Said Aoufouchi
- UMR8200 CNRS, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France.,Moscow State University, Moscow, Russia
| | - Thierry Fest
- INSERM U1236, CHU de Rennes, Université Rennes 1, Rennes, France
| | - Marc Lipinski
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France
| | - Yegor S Vassetzky
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France.,Moscow State University, Moscow, Russia
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6
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Jahn LJ, Mason B, Brøgger P, Toteva T, Nielsen DK, Thon G. Dependency of Heterochromatin Domains on Replication Factors. G3 (BETHESDA, MD.) 2018; 8:477-489. [PMID: 29187422 PMCID: PMC5919735 DOI: 10.1534/g3.117.300341] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/20/2017] [Indexed: 01/26/2023]
Abstract
Chromatin structure regulates both genome expression and dynamics in eukaryotes, where large heterochromatic regions are epigenetically silenced through the methylation of histone H3K9, histone deacetylation, and the assembly of repressive complexes. Previous genetic screens with the fission yeast Schizosaccharomyces pombe have led to the identification of key enzymatic activities and structural constituents of heterochromatin. We report here on additional factors discovered by screening a library of deletion mutants for silencing defects at the edge of a heterochromatic domain bound by its natural boundary-the IR-R+ element-or by ectopic boundaries. We found that several components of the DNA replication progression complex (RPC), including Mrc1/Claspin, Mcl1/Ctf4, Swi1/Timeless, Swi3/Tipin, and the FACT subunit Pob3, are essential for robust heterochromatic silencing, as are the ubiquitin ligase components Pof3 and Def1, which have been implicated in the removal of stalled DNA and RNA polymerases from chromatin. Moreover, the search identified the cohesin release factor Wpl1 and the forkhead protein Fkh2, both likely to function through genome organization, the Ssz1 chaperone, the Fkbp39 proline cis-trans isomerase, which acts on histone H3P30 and P38 in Saccharomyces cerevisiae, and the chromatin remodeler Fft3. In addition to their effects in the mating-type region, to varying extents, these factors take part in heterochromatic silencing in pericentromeric regions and telomeres, revealing for many a general effect in heterochromatin. This list of factors provides precious new clues with which to study the spatiotemporal organization and dynamics of heterochromatic regions in connection with DNA replication.
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Affiliation(s)
| | - Bethany Mason
- Department of Biology, University of Copenhagen, BioCenter, 2200, Denmark
| | - Peter Brøgger
- Department of Biology, University of Copenhagen, BioCenter, 2200, Denmark
| | - Tea Toteva
- Department of Biology, University of Copenhagen, BioCenter, 2200, Denmark
| | - Dennis Kim Nielsen
- Department of Biology, University of Copenhagen, BioCenter, 2200, Denmark
| | - Genevieve Thon
- Department of Biology, University of Copenhagen, BioCenter, 2200, Denmark
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7
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Gadaleta MC, Noguchi E. Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome. Genes (Basel) 2017; 8:genes8030098. [PMID: 28272375 PMCID: PMC5368702 DOI: 10.3390/genes8030098] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/03/2017] [Indexed: 02/07/2023] Open
Abstract
All living organisms need to duplicate their genetic information while protecting it from unwanted mutations, which can lead to genetic disorders and cancer development. Inaccuracies during DNA replication are the major cause of genomic instability, as replication forks are prone to stalling and collapse, resulting in DNA damage. The presence of exogenous DNA damaging agents as well as endogenous difficult-to-replicate DNA regions containing DNA–protein complexes, repetitive DNA, secondary DNA structures, or transcribing RNA polymerases, increases the risk of genomic instability and thus threatens cell survival. Therefore, understanding the cellular mechanisms required to preserve the genetic information during S phase is of paramount importance. In this review, we will discuss our current understanding of how cells cope with these natural impediments in order to prevent DNA damage and genomic instability during DNA replication.
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Affiliation(s)
- Mariana C Gadaleta
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
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8
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Toteva T, Mason B, Kanoh Y, Brøgger P, Green D, Verhein-Hansen J, Masai H, Thon G. Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast. Proc Natl Acad Sci U S A 2017; 114:1093-1098. [PMID: 28096402 PMCID: PMC5293076 DOI: 10.1073/pnas.1614837114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Shelterin component Rif1 has emerged as a global regulator of the replication-timing program in all eukaryotes examined to date, possibly by modulating the 3D-organization of the genome. In fission yeast a second Shelterin component, Taz1, might share similar functions. Here, we identified unexpected properties for Rif1 and Taz1 by conducting high-throughput genetic screens designed to identify cis- and trans-acting factors capable of creating heterochromatin-euchromatin boundaries in fission yeast. The preponderance of cis-acting elements identified in the screens originated from genomic loci bound by Taz1 and associated with origins of replication whose firing is repressed by Taz1 and Rif1. Boundary formation and gene silencing by these elements required Taz1 and Rif1 and coincided with altered replication timing in the region. Thus, small chromosomal elements sensitive to Taz1 and Rif1 (STAR) could simultaneously regulate gene expression and DNA replication over a large domain, at the edge of which they established a heterochromatin-euchromatin boundary. Taz1, Rif1, and Rif1-associated protein phosphatases Sds21 and Dis2 were each sufficient to establish a boundary when tethered to DNA. Moreover, efficient boundary formation required the amino-terminal domain of the Mcm4 replicative helicase onto which the antagonistic activities of the replication-promoting Dbf4-dependent kinase and Rif1-recruited phosphatases are believed to converge to control replication origin firing. Altogether these observations provide an insight into a coordinated control of DNA replication and organization of the genome into expression domains.
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Affiliation(s)
- Tea Toteva
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Bethany Mason
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Yutaka Kanoh
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamkitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Peter Brøgger
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Daniel Green
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Janne Verhein-Hansen
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Hisao Masai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamkitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Geneviève Thon
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark;
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9
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Belagal P, Normand C, Shukla A, Wang R, Léger-Silvestre I, Dez C, Bhargava P, Gadal O. Decoding the principles underlying the frequency of association with nucleoli for RNA polymerase III-transcribed genes in budding yeast. Mol Biol Cell 2016; 27:3164-3177. [PMID: 27559135 PMCID: PMC5063623 DOI: 10.1091/mbc.e16-03-0145] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 08/18/2016] [Indexed: 01/09/2023] Open
Abstract
In budding yeast, RNA polymerase III–transcribed genes preferentially associate with the nucleolar and nuclear periphery when permitted by the Rabl-like orientation of interphase chromosomes. The association of RNA polymerase III (Pol III)–transcribed genes with nucleoli seems to be an evolutionarily conserved property of the spatial organization of eukaryotic genomes. However, recent studies of global chromosome architecture in budding yeast have challenged this view. We used live-cell imaging to determine the intranuclear positions of 13 Pol III–transcribed genes. The frequency of association with nucleolus and nuclear periphery depends on linear genomic distance from the tethering elements—centromeres or telomeres. Releasing the hold of the tethering elements by inactivating centromere attachment to the spindle pole body or changing the position of ribosomal DNA arrays resulted in the association of Pol III–transcribed genes with nucleoli. Conversely, ectopic insertion of a Pol III–transcribed gene in the vicinity of a centromere prevented its association with nucleolus. Pol III–dependent transcription was independent of the intranuclear position of the gene, but the nucleolar recruitment of Pol III–transcribed genes required active transcription. We conclude that the association of Pol III–transcribed genes with the nucleolus, when permitted by global chromosome architecture, provides nucleolar and/or nuclear peripheral anchoring points contributing locally to intranuclear chromosome organization.
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Affiliation(s)
- Praveen Belagal
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Christophe Normand
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Ashutosh Shukla
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad 500007, India
| | - Renjie Wang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Isabelle Léger-Silvestre
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Christophe Dez
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Purnima Bhargava
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad 500007, India
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
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10
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Abstract
Nucleoli are formed on the basis of ribosomal genes coding for RNAs of ribosomal particles, but also include a great variety of other DNA regions. In this article, we discuss the characteristics of ribosomal DNA: the structure of the rDNA locus, complex organization and functions of the intergenic spacer, multiplicity of gene copies in one cell, selective silencing of genes and whole gene clusters, relation to components of nucleolar ultrastructure, specific problems associated with replication. We also review current data on the role of non-ribosomal DNA in the organization and function of nucleoli. Finally, we discuss probable causes preventing efficient visualization of DNA in nucleoli.
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11
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Mizuguchi T, Barrowman J, Grewal SIS. Chromosome domain architecture and dynamic organization of the fission yeast genome. FEBS Lett 2015; 589:2975-86. [PMID: 26096785 PMCID: PMC4598268 DOI: 10.1016/j.febslet.2015.06.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 12/20/2022]
Abstract
Advanced techniques including the chromosome conformation capture (3C) methodology and its derivatives are complementing microscopy approaches to study genome organization, and are revealing new details of three-dimensional (3D) genome architecture at increasing resolution. The fission yeast Schizosaccharomyces pombe (S. pombe) comprises a small genome featuring organizational elements of more complex eukaryotic systems, including conserved heterochromatin assembly machinery. Here we review key insights into genome organization revealed in this model system through a variety of techniques. We discuss the predominant role of Rabl-like configuration for interphase chromosome organization and the dynamic changes that occur during mitosis and meiosis. High resolution Hi-C studies have also revealed the presence of locally crumpled chromatin regions called "globules" along chromosome arms, and implicated a critical role for pericentromeric heterochromatin in imposing fundamental constraints on the genome to maintain chromosome territoriality and stability. These findings have shed new light on the connections between genome organization and function. It is likely that insights gained from the S. pombe system will also broadly apply to higher eukaryotes.
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Affiliation(s)
- Takeshi Mizuguchi
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jemima Barrowman
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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12
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Padeken J, Heun P. Nucleolus and nuclear periphery: velcro for heterochromatin. Curr Opin Cell Biol 2014; 28:54-60. [PMID: 24690547 DOI: 10.1016/j.ceb.2014.03.001] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 03/06/2014] [Accepted: 03/08/2014] [Indexed: 01/09/2023]
Abstract
Heterochromatin was first defined by Emil Heitz in 1928 by light microscopy. In the 1950s electron microscopy studies revealed that heterochromatin preferentially localizes to the nuclear periphery and around the nucleolus. While the use of genomic approaches led to the genome wide identification of lamina-associated and nucleolus-associated chromatin domains (LADs, NADs), recent studies now shed light on the processes mediating this topology and its dynamics. The identification of different factors on all regulatory levels, such as transcription factors, histone modifications, chromatin proteins, DNA sequences and non-coding RNAs, suggests the involvement of multiple distinct tethering pathways. Positioning at these nuclear sub-compartments is often but not always associated with transcriptional silencing, underlining the importance of the pre-existing chromatin context.
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Affiliation(s)
- Jan Padeken
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse, 66, 4058 Basel, Switzerland
| | - Patrick Heun
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
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13
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Durut N, Abou-Ellail M, Pontvianne F, Das S, Kojima H, Ukai S, de Bures A, Comella P, Nidelet S, Rialle S, Merret R, Echeverria M, Bouvet P, Nakamura K, Sáez-Vásquez J. A duplicated NUCLEOLIN gene with antagonistic activity is required for chromatin organization of silent 45S rDNA in Arabidopsis. THE PLANT CELL 2014; 26:1330-44. [PMID: 24668745 PMCID: PMC4001387 DOI: 10.1105/tpc.114.123893] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 02/24/2014] [Accepted: 03/10/2014] [Indexed: 05/19/2023]
Abstract
In plants as well as in animals, hundreds to thousands of 45S rRNA gene copies localize in Nucleolus Organizer Regions (NORs), and the activation or repression of specific sets of rDNA depends on epigenetic mechanisms. Previously, we reported that the Arabidopsis thaliana nucleolin protein NUC1, an abundant and evolutionarily conserved nucleolar protein in eukaryotic organisms, is required for maintaining DNA methylation levels and for controlling the expression of specific rDNA variants in Arabidopsis. Interestingly, in contrast with animal or yeast cells, plants contain a second nucleolin gene. Here, we report that Arabidopsis NUC1 and NUC2 nucleolin genes are both required for plant growth and survival and that NUC2 disruption represses flowering. However, these genes seem to be functionally antagonistic. In contrast with NUC1, disruption of NUC2 induces CG hypermethylation of rDNA and NOR association with the nucleolus. Moreover, NUC2 loss of function triggers major changes in rDNA spatial organization, expression, and transgenerational stability. Our analyses indicate that silencing of specific rRNA genes is mostly determined by the active or repressed state of the NORs and that nucleolin proteins play a key role in the developmental control of this process.
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Affiliation(s)
- Nathalie Durut
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | - Mohamed Abou-Ellail
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | - Sadhan Das
- École Normale Supérieure Lyon, CNRS,
Unité de Service et de Recherche 3010, Lyon 69364, France
| | - Hisae Kojima
- Graduate School of Bioagricultural Sciences, Nagoya
University, Nagoya 464-8601, Japan
| | - Seiko Ukai
- Graduate School of Bioagricultural Sciences, Nagoya
University, Nagoya 464-8601, Japan
| | - Anne de Bures
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | - Pascale Comella
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | | | | | - Remy Merret
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | - Manuel Echeverria
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
| | - Philippe Bouvet
- École Normale Supérieure Lyon, CNRS,
Unité de Service et de Recherche 3010, Lyon 69364, France
| | - Kenzo Nakamura
- Graduate School of Bioagricultural Sciences, Nagoya
University, Nagoya 464-8601, Japan
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement
des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire
Génome et Développement des Plantes, Unité Mixte de Recherche
5096, F-66860 Perpignan, France
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