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Sirri V, Urcuqui-Inchima S, Roussel P, Hernandez-Verdun D. Nucleolus: the fascinating nuclear body. Histochem Cell Biol 2007; 129:13-31. [PMID: 18046571 PMCID: PMC2137947 DOI: 10.1007/s00418-007-0359-6] [Citation(s) in RCA: 295] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2007] [Indexed: 11/30/2022]
Abstract
Nucleoli are the prominent contrasted structures of the cell nucleus. In the nucleolus, ribosomal RNAs are synthesized, processed and assembled with ribosomal proteins. RNA polymerase I synthesizes the ribosomal RNAs and this activity is cell cycle regulated. The nucleolus reveals the functional organization of the nucleus in which the compartmentation of the different steps of ribosome biogenesis is observed whereas the nucleolar machineries are in permanent exchange with the nucleoplasm and other nuclear bodies. After mitosis, nucleolar assembly is a time and space regulated process controlled by the cell cycle. In addition, by generating a large volume in the nucleus with apparently no RNA polymerase II activity, the nucleolus creates a domain of retention/sequestration of molecules normally active outside the nucleolus. Viruses interact with the nucleolus and recruit nucleolar proteins to facilitate virus replication. The nucleolus is also a sensor of stress due to the redistribution of the ribosomal proteins in the nucleoplasm by nucleolus disruption. The nucleolus plays several crucial functions in the nucleus: in addition to its function as ribosome factory of the cells it is a multifunctional nuclear domain, and nucleolar activity is linked with several pathologies. Perspectives on the evolution of this research area are proposed.
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Affiliation(s)
- Valentina Sirri
- Nuclei and Cell Cycle, CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
| | - Silvio Urcuqui-Inchima
- Nuclei and Cell Cycle, CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
- Grupo de Inmunovirología, Biogénesis, Universidad de Antioquia, Calle 62 No. 52-59, Medellin, Colombia
| | - Pascal Roussel
- Nuclei and Cell Cycle, CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
| | - Danièle Hernandez-Verdun
- Nuclei and Cell Cycle, CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
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Hannan KM, Hannan RD, Smith SD, Jefferson LS, Lun M, Rothblum LI. Rb and p130 regulate RNA polymerase I transcription: Rb disrupts the interaction between UBF and SL-1. Oncogene 2000; 19:4988-99. [PMID: 11042686 DOI: 10.1038/sj.onc.1203875] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have previously demonstrated that the protein encoded by the retinoblastoma susceptibility gene (Rb) functions as a regulator of transcription by RNA polymerase I (rDNA transcription) by inhibiting UBF-mediated transcription. In the present study, we have examined the mechanism by which Rb represses UBF-dependent rDNA transcription and determined if other Rb-like proteins have similar effects. We demonstrate that authentic or recombinant UBF and Rb interact directly and this requires a functional A/B pocket. DNase footprinting and band-shift assays demonstrated that the interaction between Rb and UBF does not inhibit the binding of UBF to DNA. However, the formation of an UBF/Rb complex does block the interaction of UBF with SL-1, as indicated by using the 48 kDa subunit as a marker for SL-1. Additional evidence is presented that another pocket protein, p130 but not p107, can be found in a complex with UBF. Interestingly, the cellular content of p130 inversely correlated with the rate of rDNA transcription in two physiological systems, and overexpression of p130 inhibited rDNA transcription. These results suggest that p130 may regulate rDNA transcription in a similar manner to Rb.
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Affiliation(s)
- K M Hannan
- Henry Hood Research Program, Weis Center for Research, Geisinger Clinic, 100 N. Academy Ave., Danville, Pennsylvania, PA 17822 USA
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Reeder RH. Regulation of RNA polymerase I transcription in yeast and vertebrates. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1999; 62:293-327. [PMID: 9932458 DOI: 10.1016/s0079-6603(08)60511-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
This article focuses on what is currently known about the regulation of transcription by RNA polymerase I (pol I) in eukaryotic organisms at opposite ends of the evolutionary spectrum--a yeast, Saccharomyces cerevisiae, and vertebrates, including mice, frogs, and man. Contemporary studies that have defined the DNA sequence elements are described, as well as the majority of the basal transcription factors essential for pol I transcription. Situations in which pol I transcription is known to be regulated are reviewed and possible regulatory mechanisms are critically discussed. Some aspects of basal pol I transcription machinery appear to have been conserved from fungi to vertebrates, but other aspects have evolved, perhaps to meet the needs of a metazoan organism. Different parts of the pol I transcription machinery are regulatory targets depending on different physiological stimuli. This suggests that multiple signaling pathways may also be involved. The involvement of ribosomal genes and their transcripts in events such as mitosis, cancer, and aging is discussed.
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Affiliation(s)
- R H Reeder
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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Liu Z, Zhao A, Chen L, Pape L. Activated levels of rRNA synthesis in fission yeast are driven by an intergenic rDNA region positioned over 2500 nucleotides upstream of the initiation site. Nucleic Acids Res 1997; 25:659-67. [PMID: 9016610 PMCID: PMC146475 DOI: 10.1093/nar/25.3.659] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
RNA polymerase I-catalyzed synthesis of the Schizosaccharomyces pombe approximately 37S pre-rRNAs was shown to be sensitive to regulatory sequences located several kilobases upstream of the initiation site for the rRNA gene. An in vitro transcription system for RNA polymerase I-catalyzed RNA synthesis was established that supports correct and activated transcription from templates bearing a full S. pombe rRNA gene promoter. A 780 bp region starting at -2560 significantly stimulates transcription of ac is-located rDNA promoter and competes with an rDNA promoter in trans, thus displaying some of the activities of rDNA transcriptional enhancers in vitro. Deletion of a 30 bp enhancer-homologous domain in this 780 bp far upstream region blocked its cis-stimulatory effect. The sequence of the S. pombe 3.5 kb intergenic spacer was determined and its organization differs from that of vertebrate, Drosophila, Acanthamoeba and plant intergenic rDNA spacers: it does not contain multiple, imperfect copies of the rRNA gene promoter nor repetitive elements of 140 bp, as are found in vertebrate rDNA enhancers.
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Affiliation(s)
- Z Liu
- Department of Chemistry, New York University, New York, NY 10003, USA
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Hannan RD, Stefanovsky V, Taylor L, Moss T, Rothblum LI. Overexpression of the transcription factor UBF1 is sufficient to increase ribosomal DNA transcription in neonatal cardiomyocytes: implications for cardiac hypertrophy. Proc Natl Acad Sci U S A 1996; 93:8750-5. [PMID: 8710943 PMCID: PMC38745 DOI: 10.1073/pnas.93.16.8750] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The accelerated protein accumulation characteristic of cardiomyocyte hypertrophy results from increased cellular protein synthetic capacity (elevated ribosome content). The rate limiting step in ribosome accumulation is transcription of the rRNA genes. During neonatal cardiomyocyte hypertrophy induced by norepinephrine or spontaneous contraction, changes in the expression of a ribosomal DNA transcription factor, UBF, correlated with increased rates of ribosome biogenesis. We hypothesized that elevated expression of UBF was part of the mechanism by which these hypertrophic stimuli effected increases in the rate of transcription from the rDNA promoter. In this study, we have examined directly the effect of overexpressing UBF on rDNA transcription in neonatal cardiomyocytes in culture. In control experiments, a novel reporter construct for rDNA transcription (pSMECAT) showed similar increases in activity in response to hypertrophic stimuli (10(-4) M phenylephrine, 10(-7) M endothelin, and spontaneous contraction) as did the endogenous rRNA genes. When contraction-arrested cardiomyocytes were cotransfected with pSMECAT and increasing amounts of a UBF1 expression vector; a dose-dependent (3-5 fold) increase in rDNA transcription was observed. Western blot analysis confirmed that the overexpressed, FLAG-tagged UBF accumulated in the cardiomyocyte nuclei. The observation that overexpression of UBF1 is sufficient to increase rDNA transcription in neonatal cardiomyocytes provides evidence in support of the hypothesis that the regulation of UBF is a key component of the increased ribosome biogenesis and protein accumulation associated with cardiomyocyte hypertrophy.
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Affiliation(s)
- R D Hannan
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, PA 17822, USA
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Moss T, Stefanovsky VY. Promotion and regulation of ribosomal transcription in eukaryotes by RNA polymerase I. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1995; 50:25-66. [PMID: 7754036 DOI: 10.1016/s0079-6603(08)60810-7] [Citation(s) in RCA: 154] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- T Moss
- Cancer Research Centre, Laval University, Hôtel-Dieu de Québec, Canada
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Factor C*, the specific initiation component of the mouse RNA polymerase I holoenzyme, is inactivated early in the transcription process. Mol Cell Biol 1994. [PMID: 8007994 DOI: 10.1128/mcb.14.7.5010] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Factor C* is the component of the RNA polymerase I holoenzyme (factor C) that allows specific transcriptional initiation on a factor D (SL1)- and UBF-activated rRNA gene promoter. The in vitro transcriptional capacity of a preincubated rDNA promoter complex becomes exhausted very rapidly upon initiation of transcription. This is due to the rapid depletion of C* activity. In contrast, C* activity is not unstable in the absence of transcription, even in the presence of nucleoside triphosphates (NTPs). By using 3'dNTPs to specifically halt elongation, C* is seen to remain active through transcription complex assembly, initiation, and the first approximately 37 nucleotides of elongation, but it is inactivated before synthesis proceeds beyond approximately 40 nucleotides. When elongation is halted before this critical distance, the C* remains active and on that template complex, greatly extending the kinetics of transcription and generating manyfold more transcripts than would have been synthesized if elongation had proceeded past the critical distance where C* is inactivated. In complementary in vivo analysis under conditions where C* activity is not replenished, C* activity becomes depleted from cells, but this also occurs only when there is ongoing rDNA transcription. Thus, both in vitro and in vivo, the specific initiation-conferring component of the RNA polymerase I holoenzyme is used stoichiometrically in the transcription process.
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Brun RP, Ryan K, Sollner-Webb B. Factor C*, the specific initiation component of the mouse RNA polymerase I holoenzyme, is inactivated early in the transcription process. Mol Cell Biol 1994; 14:5010-21. [PMID: 8007994 PMCID: PMC358872 DOI: 10.1128/mcb.14.7.5010-5021.1994] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Factor C* is the component of the RNA polymerase I holoenzyme (factor C) that allows specific transcriptional initiation on a factor D (SL1)- and UBF-activated rRNA gene promoter. The in vitro transcriptional capacity of a preincubated rDNA promoter complex becomes exhausted very rapidly upon initiation of transcription. This is due to the rapid depletion of C* activity. In contrast, C* activity is not unstable in the absence of transcription, even in the presence of nucleoside triphosphates (NTPs). By using 3'dNTPs to specifically halt elongation, C* is seen to remain active through transcription complex assembly, initiation, and the first approximately 37 nucleotides of elongation, but it is inactivated before synthesis proceeds beyond approximately 40 nucleotides. When elongation is halted before this critical distance, the C* remains active and on that template complex, greatly extending the kinetics of transcription and generating manyfold more transcripts than would have been synthesized if elongation had proceeded past the critical distance where C* is inactivated. In complementary in vivo analysis under conditions where C* activity is not replenished, C* activity becomes depleted from cells, but this also occurs only when there is ongoing rDNA transcription. Thus, both in vitro and in vivo, the specific initiation-conferring component of the RNA polymerase I holoenzyme is used stoichiometrically in the transcription process.
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Affiliation(s)
- R P Brun
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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Smith SD, O'Mahony DJ, Kinsella BT, Rothblum LI. Transcription from the rat 45S ribosomal DNA promoter does not require the factor UBF. Gene Expr 1993; 3:229-36. [PMID: 8019125 PMCID: PMC6081612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/1993] [Accepted: 09/13/1993] [Indexed: 01/28/2023]
Abstract
For efficient transcription from the rat ribosomal DNA (rDNA) promoter by RNA polymerase I in vitro, at least two transcription factors, rat UBF and rat SL-1, are required. Transcription cannot take place in vitro in the absence of SL-1. On the other hand, there is considerable difference of opinion concerning the necessity for UBF in in vitro transcription mediated by RNA polymerase 1, and the requirement for UBF is not clear. Mammalian cells code for UBF1 and UBF2, two forms of UBF that differ in HMG box-2, one of four HMG boxes or DNA-binding domains. We have used a monospecific antibody raised to recombinant rat UBF to determine whether UBF1 and UBF2 are required for RNA polymerase I-mediated transcription. This antibody can detect as little as 1.35 x 10(-15) moles of UBF1 or UBF2 in an immunoblot. Fractionated extracts that were competent for transcription had no detectable UBF1 or UBF2 when assayed in immunoblots with this antiserum. This evidence supports the hypothesis that UBF is not required for transcription of the rat rDNA promoter in vitro and most likely functions as an auxillary transcription factor. In addition, we have fractionated rat UBF1 from UBF2 and tested each of them in in vitro transcription assays in which the 45S or spacer rDNA promoter template is limiting. UBF1 can activate transcription from either the 45S or spacer promoter under these conditions, whereas UBF2 cannot. This implies that there is a functional difference in the transactivation of RNA polymerase I by UBF1 and UBF2 in vitro.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S D Smith
- Department of Chemistry, Susquehanna University, Selingsgrove, Pennsylvania
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