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Wu S, Chen J, Teo BHD, Wee SYK, Wong MHM, Cui J, Chen J, Leong KP, Lu J. The axis of complement C1 and nucleolus in antinuclear autoimmunity. Front Immunol 2023; 14:1196544. [PMID: 37359557 PMCID: PMC10288996 DOI: 10.3389/fimmu.2023.1196544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Antinuclear autoantibodies (ANA) are heterogeneous self-reactive antibodies that target the chromatin network, the speckled, the nucleoli, and other nuclear regions. The immunological aberration for ANA production remains partially understood, but ANA are known to be pathogenic, especially, in systemic lupus erythematosus (SLE). Most SLE patients exhibit a highly polygenic disease involving multiple organs, but in rare complement C1q, C1r, or C1s deficiencies, the disease can become largely monogenic. Increasing evidence point to intrinsic autoimmunogenicity of the nuclei. Necrotic cells release fragmented chromatins as nucleosomes and the alarmin HMGB1 is associated with the nucleosomes to activate TLRs and confer anti-chromatin autoimmunogenecity. In speckled regions, the major ANA targets Sm/RNP and SSA/Ro contain snRNAs that confer autoimmunogenecity to Sm/RNP and SSA/Ro antigens. Recently, three GAR/RGG-containing alarmins have been identified in the nucleolus that helps explain its high autoimmunogenicity. Interestingly, C1q binds to the nucleoli exposed by necrotic cells to cause protease C1r and C1s activation. C1s cleaves HMGB1 to inactive its alarmin activity. C1 proteases also degrade many nucleolar autoantigens including nucleolin, a major GAR/RGG-containing autoantigen and alarmin. It appears that the different nuclear regions are intrinsically autoimmunogenic by containing autoantigens and alarmins. However, the extracellular complement C1 complex function to dampen nuclear autoimmunogenecity by degrading these nuclear proteins.
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Affiliation(s)
- Shan Wu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Junjie Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Boon Heng Dennis Teo
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Seng Yin Kelly Wee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ming Hui Millie Wong
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jianzhou Cui
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jinmiao Chen
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Khai Pang Leong
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Jinhua Lu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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2
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Humenyuk YA, Kotrla M, Netočný K, Slanina F. Separation of dense colloidal suspensions in narrow channels: A stochastic model. Phys Rev E 2020; 101:032608. [PMID: 32289907 DOI: 10.1103/physreve.101.032608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/06/2020] [Indexed: 06/11/2023]
Abstract
The flow of a colloidal suspension in a narrow channel of periodically varying width is described by the one-dimensional generalized asymmetric exclusion process. Each site admits multiple particle occupancy. We consider particles of two different sizes. The sites available to particles form a comblike geometry: entropic traps due to variation of channel width are modeled by dead ends, or pockets, attached individually to each site of a one-dimensional chain. This geometry, combined with periodically alternating external driving, leads to a ratchet effect which is very sensitive to particle size, thus enabling particle sorting. A typical behavior is reversal of the current orientation when we change the density of small and big particles. In an optimal situation, the two types of particles move in opposite directions, and particle separation is in principle perfect. We show that in the simplest situation with one type of particles only, this model is exactly soluble. In the general case we use enhanced mean-field approximation as well as direct numerical simulations.
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Affiliation(s)
- Yosyp A Humenyuk
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, CZ-18221 Praha, Czech Republic
- Institute for Condensed Matter Physics of the National Academy of Sciences of Ukraine, 1 Svientsitskii St, UA-79011 Lviv, Ukraine
| | - Miroslav Kotrla
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, CZ-18221 Praha, Czech Republic
| | - Karel Netočný
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, CZ-18221 Praha, Czech Republic
| | - František Slanina
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, CZ-18221 Praha, Czech Republic
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3
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Dvořáčková M, Fajkus J. Visualization of the Nucleolus Using Ethynyl Uridine. FRONTIERS IN PLANT SCIENCE 2018; 9:177. [PMID: 29503656 PMCID: PMC5820300 DOI: 10.3389/fpls.2018.00177] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/30/2018] [Indexed: 05/04/2023]
Abstract
Thanks to recent innovative methodologies, key cellular processes such as replication or transcription can be visualized directly in situ in intact tissues. Many studies use so-called click iT chemistry where nascent DNA can be tracked by 5-ethynyl-2'-deoxyuridine (EdU), and nascent RNA by 5-ethynyl uridine (EU). While the labeling of replicating DNA by EdU has already been well established and further exploited in plants, the use of EU to reveal nascent RNA has not been developed to such an extent. In this article, we present a protocol for labeling of nucleolar RNA transcripts using EU and show that EU effectively highlights the nucleolus. The method is advantageous, because the need to prepare transgenic plants expressing fluorescently tagged nucleolar components when the nucleolus has to be visualized can be avoided.
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Affiliation(s)
- Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- *Correspondence: Martina Dvořáčková, Jiří Fajkus, ;
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- *Correspondence: Martina Dvořáčková, Jiří Fajkus, ;
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4
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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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The nucleolus—guardian of cellular homeostasis and genome integrity. Chromosoma 2014; 122:487-97. [PMID: 24022641 DOI: 10.1007/s00412-013-0430-0] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/05/2013] [Indexed: 01/25/2023]
Abstract
All organisms sense and respond to conditions that stress their homeostasis by downregulating the synthesis of rRNA and ribosome biogenesis, thus designating the nucleolus as the central hub in coordinating the cellular stress response. One of the most intriguing roles of the nucleolus, long regarded as a mere ribosome-producing factory, is its participation in monitoring cellular stress signals and transmitting them to the RNA polymerase I (Pol I) transcription machinery. As rRNA synthesis is a most energy-consuming process, switching off transcription of rRNA genes is an effective way of saving the energy required to maintain cellular homeostasis during acute stress. The Pol I transcription machinery is the key convergence point that collects and integrates a vast array of information from cellular signaling cascades to regulate ribosome production which, in turn, guides cell growth and proliferation. This review focuses on the mechanisms that link cell physiology to rDNA silencing, a prerequisite for nucleolar integrity and cell survival.
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Alevi KCC, Mendonça PP, Pereira NP, da Rosa JA, de Azeredo-Oliveira MTV. Is there post-meiotic transcriptional activity during hemipteran spermiogenesis? INVERTEBR REPROD DEV 2014. [DOI: 10.1080/07924259.2014.889767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Slanina F. Interacting molecular motors: efficiency and work fluctuations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:061135. [PMID: 20365146 DOI: 10.1103/physreve.80.061135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Revised: 11/05/2009] [Indexed: 05/29/2023]
Abstract
We investigate the model of "reversible ratchet" with interacting particles, presented by us earlier [F. Slanina, EPL 84, 50009 (2008)]. We further clarify the effect of efficiency enhancement due to interaction and show that it is of energetic origin, rather than a consequence of reduced fluctuations. We also show complicated structures emerging in the interaction and density dependence of the current and response function. The fluctuation properties of the work and input energy indicate in detail the far-from-equilibrium nature of the dynamics.
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Affiliation(s)
- Frantisek Slanina
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Praha, Czech Republic.
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8
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Dynamic changes of nucleolar DNA configuration and distribution during the cell cycle in Allium sativum cells. Micron 2009; 40:449-54. [DOI: 10.1016/j.micron.2009.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Revised: 01/14/2009] [Accepted: 01/15/2009] [Indexed: 12/17/2022]
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9
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Morielle-Souza A, de Azeredo-Oliveira MTV. Study of the nucleolar cycle and ribosomal RNA distribution during meiosis in triatomines (Triatominae, Heteroptera). Micron 2008; 39:1020-6. [DOI: 10.1016/j.micron.2007.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 09/06/2007] [Accepted: 09/07/2007] [Indexed: 11/26/2022]
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10
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[Localization of nucleolar DNA and transcription sites of rRNA genes in situ in wheat cells]. YI CHUAN = HEREDITAS 2008; 30:231-6. [PMID: 18244931 DOI: 10.3724/sp.j.1005.2008.00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
By using the conventional electron microscopic technique and DNA specific cytochemical staining method (NAMA-Ur), we directly observed the arrangement and location of intranucleolar DNA in situ in wheat (Triticum aestivum L.) cells. The results showed that nucleolar DNA was found in Fibrillar Centers (FC), Dense Fibrillar Component (DFC) and the transitional region between FC and DFC. Moreover, the nucleolar DNA was distributed along the periphery of FC and by surrounding FC. We employed RNP preference staining (Bernhard staining) method to visualize the distribution and position of RNP in situ in nucleoli of wheat cells. The results directly showed that RNP mainly located in the transitional region between FC and DFC, in DFC and in Granular Component (GC). Moreover, RNP was irregularly distributed around FC. By employing anti-RNA/DNA hybrid antibodies, we directly and selectively labeled transcription sites of rRNA genes and testified that localization of transcription sites was not only in the transitional region between DFC and FC but also in DFC of nucleoli in wheat cells.
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12
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Tripathi T, Chowdhury D. Interacting RNA polymerase motors on a DNA track: effects of traffic congestion and intrinsic noise on RNA synthesis. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:011921. [PMID: 18351890 DOI: 10.1103/physreve.77.011921] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Indexed: 05/26/2023]
Abstract
RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input to move along the track formed by DNA. In many circumstances, which are described in this paper, a large number of RNAPs move simultaneously along the same track; we refer to such collective movements of the RNAPs as RNAP traffic. Here we develop a theoretical model for RNAP traffic by incorporating the steric interactions between RNAPs as well as the mechanochemical cycle of individual RNAPs during the elongation of the mRNA. By a combination of analytical and numerical techniques, we calculate the rates of mRNA synthesis and the average density profile of the RNAPs on the DNA track. We also introduce, and compute, two different measures of fluctuations in the synthesis of RNA. Analyzing these fluctuations, we show how the level of intrinsic noise in mRNA synthesis depends on the concentrations of the RNAPs as well as on those of some of the reactants and the products of the enzymatic reactions catalyzed by RNAP. We suggest appropriate experimental systems and techniques for testing our theoretical predictions.
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Affiliation(s)
- Tripti Tripathi
- Physics Department, Indian Institute of Technology, Kanpur 208016, India
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Raska I, Shaw PJ, Cmarko D. Structure and function of the nucleolus in the spotlight. Curr Opin Cell Biol 2006; 18:325-34. [PMID: 16687244 DOI: 10.1016/j.ceb.2006.04.008] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Accepted: 04/07/2006] [Indexed: 10/24/2022]
Abstract
The nucleolus is the most obvious and clearly differentiated nuclear sub-compartment. It is where ribosome biogenesis takes place, but it is becoming clear that the nucleolus also has non-ribosomal functions. In this review we discuss recent progress in our understanding of how both ribosome biosynthesis and some non-ribosomal functions relate to observable nucleolar structure. We still do not have detailed enough information about the in situ organization of the various processes taking place in the nucleolus. However, the present power of light and electron microscopy techniques means that a description of the organization of nucleolar processes at the molecular level is now achievable, and the time is ripe for such an effort.
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Affiliation(s)
- Ivan Raska
- Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Czech Republic.
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14
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Pliss A, Koberna K, Vecerová J, Malínský J, Masata M, Fialová M, Raska I, Berezney R. Spatio-temporal dynamics at rDNA foci: Global switching between DNA replication and transcription. J Cell Biochem 2004; 94:554-65. [PMID: 15543556 DOI: 10.1002/jcb.20317] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We have investigated the in situ organization of ribosomal gene (rDNA) transcription and replication in HeLa cells. Fluorescence in situ hybridization (FISH) revealed numerous rDNA foci in the nucleolus. Each rDNA focus corresponds to a higher order chromatin domain containing multiple ribosomal genes. Multi-channel labeling experiments indicated that, in the majority of cells, all the rDNA foci were active in transcription as demonstrated by co-localization with signals to transcription and fibrillarin, a protein involved in ribosomal RNA processing. In some cells, however, a small portion of the rDNA foci did not overlap with signals to transcription and fibrillarin. Labeling for DNA replication revealed that those rDNA foci inactive in transcription were restricted to the S-phase of the cell cycle and were replicated predominantly from mid to late S-phase. Electron microscopic analysis localized the nucleolar transcription, replication, and fibrillarin signals to the dense fibrillar components of the nucleolus and at the borders of the fibrillar centers. We propose that the rDNA foci are the functional units for coordinating replication and transcription of the rRNA genes in space and time. This involves a global switching mechanism, active from mid to late S-phase, for turning off transcription and turning on replication at individual rDNA foci. Once all the rRNA genes at individual foci are replicated, these higher order chromatin domains are reprogrammed for transcription.
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Affiliation(s)
- Artem Pliss
- Department of Cell Biology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Albertov 4, CZ-12800 Prague 2, Czech Republic
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15
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Wei T, Baiqu H, Chunxiang L, Zhonghe Z. In situ visualization of rDNA arrangement and its relationship with subnucleolar structural regions in Allium sativum cell nucleolus. J Cell Sci 2003; 116:1117-25. [PMID: 12584254 DOI: 10.1242/jcs.00323] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We used a DNA-specific staining technique to show the two states of DNA component distributed in the nucleolar region of Allium sativum cells. One state is the extended DNA fiber, and the other is the condensed DNA clump. In situ hybridization demonstrated that the extended DNA fiber was an rRNA gene. Anti-fibrillarin antibody immunolabeling revealed that these rRNA genes were located in the dense fibrillar component near the fibrillar center, including at the periphery of the fibrillar center. None was in the dense fibrillar component far away from the fibrillar center. The condensed DNA clump was located in the fibrillar center. Further observations showed that the rRNA genes in the nucleolus were all arranged around the fibrillar center and associated with the DNA clumps in the fibrillar center. Results of statistical analysis showed that the distribution region of rRNA genes occupied about one-third of the total dense fibrillar component region. Ag-NOR protein showed a similar distribution pattern to that of rDNA. Immunolabeling of an anti-RNA/DNA hybrid antibody demonstrated that the transcription sites of rRNA were located at the periphery of the fibrillar center and in the dense fibrillar component near the fibrillar center, and these sites were consistent with the location and arrangement of rDNA shown in situ. These results demonstrated that transcription of rRNA takes place around the fibrillar center and at the periphery, whereas the dense fibrillar component that was far away from fibrillar center was the non-transcription region. The DNA clumps within the fibrillar center were probably the anchoring sites for rDNA arrangement.
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Affiliation(s)
- Tao Wei
- Department of Cell Biology, School of Life Sciences, Peking University, 100871, China.
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Dundr M, Hoffmann-Rohrer U, Hu Q, Grummt I, Rothblum LI, Phair RD, Misteli T. A kinetic framework for a mammalian RNA polymerase in vivo. Science 2002; 298:1623-6. [PMID: 12446911 DOI: 10.1126/science.1076164] [Citation(s) in RCA: 350] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We have analyzed the kinetics of assembly and elongation of the mammalian RNA polymerase I complex on endogenous ribosomal genes in the nuclei of living cells with the use of in vivo microscopy. We show that components of the RNA polymerase I machinery are brought to ribosomal genes as distinct subunits and that assembly occurs via metastable intermediates. With the use of computational modeling of imaging data, we have determined the in vivo elongation time of the polymerase, and measurements of recruitment and incorporation frequencies show that incorporation of components into the assembling polymerase is inefficient. Our data provide a kinetic and mechanistic framework for the function of a mammalian RNA polymerase in living cells.
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Affiliation(s)
- Miroslav Dundr
- National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD 20892, USA
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17
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Koberna K, Malínský J, Pliss A, Masata M, Vecerova J, Fialová M, Bednár J, Raska I. Ribosomal genes in focus: new transcripts label the dense fibrillar components and form clusters indicative of "Christmas trees" in situ. J Cell Biol 2002; 157:743-8. [PMID: 12034768 PMCID: PMC2173423 DOI: 10.1083/jcb.200202007] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
T he organization of transcriptionally active ribosomal genes in animal cell nucleoli is investigated in this study in order to address the long-standing controversy with regard to the intranucleolar localization of these genes. Detailed analyses of HeLa cell nucleoli include direct localization of ribosomal genes by in situ hybridization and their indirect localization via nascent ribosomal transcript mappings. On the light microscopy (LM) level, ribosomal genes map in 10-40 fluorescence foci per nucleus, and transcription activity is associated with most foci. We demonstrate that each nucleolar focus observed by LM corresponds, on the EM level, to an individual fibrillar center (FC) and surrounding dense fibrillar components (DFCs). The EM data identify the DFC as the nucleolar subcompartment in which rRNA synthesis takes place, consistent with detection of rDNA within the DFC. The highly sensitive method for mapping nascent transcripts in permeabilized cells on ultrastructural level provides intense and unambiguous clustered immunogold signal over the DFC, whereas very little to no label is detected over the FC. This signal is strongly indicative of nascent "Christmas trees" of rRNA associated with individual rDNA genes, sampled on the surface of thin sections. Stereological analysis of the clustered transcription signal further suggests that these Christmas trees may be contorted in space and exhibit a DNA compaction ratio on the order of 4-5.5.
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Affiliation(s)
- Karel Koberna
- Department of Cell Biology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic
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González-Melendi P, Wells B, Beven AF, Shaw PJ. Single ribosomal transcription units are linear, compacted Christmas trees in plant nucleoli. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2001; 27:223-233. [PMID: 11532168 DOI: 10.1046/j.1365-313x.2001.01091.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The rDNA transcription units are enormous macromolecular structures located in the nucleolus and containing 50-100 RNA polymerases together with the nascent pre-rRNA attached to the rDNA. It has not previously been possible to visualize nucleolar transcription units directly in intact nucleoli, although highly spread preparations in the electron microscope have been imaged as "Christmas trees" 2-3 microm long. Here we determine the relative conformation of individual transcription units in Pisum sativum plant nucleoli using a novel labelling technique. Nascent transcripts were detected by a highly sensitive silver-enhanced 1 nm gold procedure, followed by 3D electron microscopy of entire nucleoli. Individual transcription units are seen as conical, elongated clusters approximately 300 nm in length and 130 nm in width at the thickest end. We further show that there were approximately 300 active ribosomal genes in the nucleoli examined. The underlying chromatin structure of the transcribing rDNA was directly visualized by applying a novel limited extraction procedure to fixed specimens in order to wash out the proteins and RNA, thus specifically revealing DNA strands after uranyl acetate staining. Using this technique, followed by post-embedding in situ hybridization, we observed that the nucleolar rDNA fibres are not extended but show a coiled, thread-like appearance. Our results show for the first time that native rDNA transcription units are linear, compacted Christmas trees.
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Affiliation(s)
- P González-Melendi
- Department of Cell Biology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
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Abstract
An understanding of the functional organization of nucleoli, the sites of ribosome biosynthesis, is limited by the present uncertainty about the topological arrangement of the transcribing rRNA genes. Since studies with “standard” nucleoli from somatic cells produced conflicting results, we have examined the amplified nucleoli of Xenopus oocytes. These nucleoli are unique in that they contain high copy numbers of rRNA genes, are not attached to chromosomes, lack non-ribosomal DNA and can be examined in light microscopic spread preparations of nuclear contents. By immunostaining and confocal microscopy we show that in growing stage IV oocytes the sites of rDNA are surrounded by the dense fibrillar component. The rDNA is actively transcribed as revealed by BrUTP injection into oocytes and localization of components of the nucleolar transcription machinery (RNA polymerase I and the transcription factor UBF). At the ultrastructural level, the rDNA sites correlate with the fibrillar centers of amplified nucleoli fixed in situ. The results provide clear evidence that the transcriptionally active rRNA genes are confined to the fibrillar centers of the oocyte nucleoli and open the possibility to analyze the protein composition of almost native, transcriptionally highly active nucleolar chromatin by immunofluorescence microscopy.
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Affiliation(s)
- C Mais
- Department of Cell and Developmental Biology, Biocenter of the University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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Demirtas H, Candemir Z, Cücer N, Imamoglu N, Dönmez H, Bökesoy I. Essay on the nucleoli survey by the alpha- and beta-satellite DNA probes of the acrocentric chromosomes in mitogen-stimulated human lymphocytes. ANNALES DE GENETIQUE 2000; 43:61-8. [PMID: 10998446 DOI: 10.1016/s0003-3995(00)01014-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The two constitutive heterochromatin (alpha- and beta-satellite DNA) probes of human acrocentric chromosomes were assayed separately to label the nucleoli in the phytohemagglutinin (PHA)-stimulated human lymphocytes. Fluorescent in situ hybridisation (FISH) results have shown that: a) whole (100%) signal-nucleoli overlapping was obtained with both heterochromatin probes in maximally activated nuclei (MANs); b) partial overlapping was observed in non-activated or slightly activated nuclei; c) random signal-nucleolus overlapping (background level) was found to be approximately 6% by the NOR-irrelevant euchromatic probe (D5S23); d) Yq-nucleolus association in the MANs was found to be approximately 97% without the subtraction of the background level. We concluded that: a) acrocentric alpha- or beta-satellite DNA probes may be used as nucleolar markers only in the MANs and not in slightly activated or non-activated nuclei; b) the distances between rDNA loci and alpha-/beta-satellite DNA on human acrocentrics are short enough to permit their observation on the same nucleolus.
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Affiliation(s)
- H Demirtas
- Medical Biology and Genetics Department, Medical Faculty, Erciyes University, 38039, Kayseri, Turkey.
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Thiry M. Ultrastructural methods for nucleic acid detection by immunocytology. PROGRESS IN HISTOCHEMISTRY AND CYTOCHEMISTRY 1999; 34:87-159. [PMID: 10546283 DOI: 10.1016/s0079-6336(99)80008-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In the present review are summarized recent developments in immunocytochemical detection of nucleic acids in biological materials at the ultrastructural level. Not only the approaches using antibodies to natural nucleic acids are described but also the techniques involving the use of antibodies raised against various nucleotide analogs incorporated beforehand into nucleic acids. Special emphasis is placed on each method's potential and limitations. These methods, combined or not with molecular biotechnology, are powerful tools for studying the structure and function of nucleic acids. They can be used to investigate the distribution and topological organization of DNA and RNA molecules or of specialized within these molecules in the cells.
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Affiliation(s)
- M Thiry
- Laboratory of Cell and Tissue Biology, Institute of Histology, University of Liège, Belgium.
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Abstract
The activity of the ribosomal RNA genes generates a distinct subnuclear structure, the nucleolus, which is the site of ribosome biogenesis. The signals that target proteins and snoRNAs (small nucleolar RNAs) to the nucleolus, the nuclear import of ribosomal proteins, the export of the completed ribosomal subunits and the molecular organization of the nucleolus have been the subject of intense research during the past year. Evidence is accumulating that nucleoli functionally interact with coiled bodies and are also involved in the maturation of non-ribosomal RNA species.
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Affiliation(s)
- U Scheer
- Department of Cell and Developmental Biology, Biocenter University of Würzburg, Am Hubland, D-97074, Würzburg, Germany.
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