1
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Guo Y, Zhang X. Unveiling intracellular phase separation: advances in optical imaging of biomolecular condensates. Trends Biochem Sci 2024:S0968-0004(24)00163-4. [PMID: 39034215 DOI: 10.1016/j.tibs.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
Intracellular biomolecular condensates, which form via phase separation, display a highly organized ultrastructure and complex properties. Recent advances in optical imaging techniques, including super-resolution microscopy and innovative microscopic methods that leverage the intrinsic properties of the molecules observed, have transcended the limitations of conventional microscopies. These advances facilitate the exploration of condensates at finer scales and in greater detail. The deployment of these emerging but sophisticated imaging tools allows for precise observations of the multiphasic organization and physicochemical properties of these condensates, shedding light on their functions in cellular processes. In this review, we highlight recent progress in methodological innovations and their profound implications for understanding the organization and dynamics of intracellular biomolecular condensates.
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Affiliation(s)
- Yinfeng Guo
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, PR China
| | - Xin Zhang
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, PR China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, PR China.
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2
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Su Z, Ho JWK, Yau RCH, Lam YL, Shek TWH, Yeung MCF, Chen H, Oreffo ROC, Cheah KSE, Cheung KSC. A single-cell atlas of conventional central chondrosarcoma reveals the role of endoplasmic reticulum stress in malignant transformation. Commun Biol 2024; 7:124. [PMID: 38267611 PMCID: PMC10808239 DOI: 10.1038/s42003-024-05790-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
The transformation of benign lesions to malignant tumours is a crucial aspect of understanding chondrosarcomas, which are malignant cartilage tumours that could develop from benign chondroid lesions. However, the process of malignant transformation for chondroid lesions remains poorly understood, and no reliable markers are available to aid clinical decision-making. To address this issue, we conducted a study analysing 11 primary cartilage tumours and controls using single-cell RNA sequencing. By creating a single-cell atlas, we were able to identify the role of endoplasmic reticulum (ER) stress in the malignant transformation of conventional central chondrosarcomas (CCCS). Our research revealed that lower levels of ER stress promote chondrosarcoma growth in a patient-derived xenograft mouse model, while intensive ER stress reduces primary chondrosarcoma cell viability. Furthermore, we discovered that the NF-κB pathway alleviates ER stress-induced apoptosis during chondrosarcoma progression. Our single-cell signatures and large public data support the use of key ER stress regulators, such as DNA Damage Inducible Transcript 3 (DDIT3; also known as CHOP), as malignant markers for overall patient survival. Ultimately, our study highlights the significant role that ER stress plays in the malignant transformation of cartilaginous tumours and provides a valuable resource for future diagnostic markers and therapeutic strategies.
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Affiliation(s)
- Zezhuo Su
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, New Territories, Hong Kong SAR, China
| | - Joshua Wing Kei Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, New Territories, Hong Kong SAR, China
| | - Raymond Ching Hing Yau
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Ying Lee Lam
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tony Wai Hung Shek
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Maximus Chun Fai Yeung
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hongtai Chen
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Richard O C Oreffo
- Bone and Joint Research Group, Centre for Human Development, Stem Cells and Regeneration, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6HW, United Kingdom
| | - Kathryn Song Eng Cheah
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kelvin Sin Chi Cheung
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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3
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Daiß JL, Griesenbeck J, Tschochner H, Engel C. Synthesis of the ribosomal RNA precursor in human cells: mechanisms, factors and regulation. Biol Chem 2023; 404:1003-1023. [PMID: 37454246 DOI: 10.1515/hsz-2023-0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
The ribosomal RNA precursor (pre-rRNA) comprises three of the four ribosomal RNAs and is synthesized by RNA polymerase (Pol) I. Here, we describe the mechanisms of Pol I transcription in human cells with a focus on recent insights gained from structure-function analyses. The comparison of Pol I-specific structural and functional features with those of other Pols and with the excessively studied yeast system distinguishes organism-specific from general traits. We explain the organization of the genomic rDNA loci in human cells, describe the Pol I transcription cycle regarding structural changes in the enzyme and the roles of human Pol I subunits, and depict human rDNA transcription factors and their function on a mechanistic level. We disentangle information gained by direct investigation from what had apparently been deduced from studies of the yeast enzymes. Finally, we provide information about how Pol I mutations may contribute to developmental diseases, and why Pol I is a target for new cancer treatment strategies, since increased rRNA synthesis was correlated with rapidly expanding cell populations.
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Affiliation(s)
- Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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4
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Riback JA, Eeftens JM, Lee DSW, Quinodoz SA, Donlic A, Orlovsky N, Wiesner L, Beckers L, Becker LA, Strom AR, Rana U, Tolbert M, Purse BW, Kleiner R, Kriwacki R, Brangwynne CP. Viscoelasticity and advective flow of RNA underlies nucleolar form and function. Mol Cell 2023; 83:3095-3107.e9. [PMID: 37683610 PMCID: PMC11089468 DOI: 10.1016/j.molcel.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 04/20/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
The nucleolus is the largest biomolecular condensate and facilitates transcription, processing, and assembly of ribosomal RNA (rRNA). Although nucleolar function is thought to require multiphase liquid-like properties, nucleolar fluidity and its connection to the highly coordinated transport and biogenesis of ribosomal subunits are poorly understood. Here, we use quantitative imaging, mathematical modeling, and pulse-chase nucleotide labeling to examine nucleolar material properties and rRNA dynamics. The mobility of rRNA is several orders of magnitude slower than that of nucleolar proteins, with rRNA steadily moving away from the transcriptional sites in a slow (∼1 Å/s), radially directed fashion. This constrained but directional mobility, together with polymer physics-based calculations, suggests that nascent rRNA forms an entangled gel, whose constant production drives outward flow. We propose a model in which progressive maturation of nascent rRNA reduces its initial entanglement, fluidizing the nucleolar periphery to facilitate the release of assembled pre-ribosomal particles.
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Affiliation(s)
- Joshua A Riback
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Jorine M Eeftens
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Daniel S W Lee
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Sofia A Quinodoz
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Anita Donlic
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Natalia Orlovsky
- Department of Molecular Biology, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Lennard Wiesner
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Lien Beckers
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Lindsay A Becker
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Amy R Strom
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Ushnish Rana
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Michele Tolbert
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Byron W Purse
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Ralph Kleiner
- Department of Chemistry, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Richard Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, Princeton, NJ 08544, USA; Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA.
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5
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Dash S, Lamb MC, Lange JJ, McKinney MC, Tsuchiya D, Guo F, Zhao X, Corbin TJ, Kirkman M, Delventhal K, Moore EL, McKinney S, Shiang R, Trainor PA. rRNA transcription is integral to phase separation and maintenance of nucleolar structure. PLoS Genet 2023; 19:e1010854. [PMID: 37639467 PMCID: PMC10513380 DOI: 10.1371/journal.pgen.1010854] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/21/2023] [Accepted: 07/03/2023] [Indexed: 08/31/2023] Open
Abstract
Transcription of ribosomal RNA (rRNA) by RNA Polymerase (Pol) I in the nucleolus is necessary for ribosome biogenesis, which is intimately tied to cell growth and proliferation. Perturbation of ribosome biogenesis results in tissue specific disorders termed ribosomopathies in association with alterations in nucleolar structure. However, how rRNA transcription and ribosome biogenesis regulate nucleolar structure during normal development and in the pathogenesis of disease remains poorly understood. Here we show that homozygous null mutations in Pol I subunits required for rRNA transcription and ribosome biogenesis lead to preimplantation lethality. Moreover, we discovered that Polr1a-/-, Polr1b-/-, Polr1c-/- and Polr1d-/- mutants exhibit defects in the structure of their nucleoli, as evidenced by a decrease in number of nucleolar precursor bodies and a concomitant increase in nucleolar volume, which results in a single condensed nucleolus. Pharmacological inhibition of Pol I in preimplantation and midgestation embryos, as well as in hiPSCs, similarly results in a single condensed nucleolus or fragmented nucleoli. We find that when Pol I function and rRNA transcription is inhibited, the viscosity of the granular compartment of the nucleolus increases, which disrupts its phase separation properties, leading to a single condensed nucleolus. However, if a cell progresses through mitosis, the absence of rRNA transcription prevents reassembly of the nucleolus and manifests as fragmented nucleoli. Taken together, our data suggests that Pol I function and rRNA transcription are required for maintaining nucleolar structure and integrity during development and in the pathogenesis of disease.
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Affiliation(s)
- Soma Dash
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Maureen C. Lamb
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Mary C. McKinney
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Fengli Guo
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Xia Zhao
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Timothy J. Corbin
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - MaryEllen Kirkman
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Kym Delventhal
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Emma L. Moore
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Rita Shiang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
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6
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Islas-Morales PF, Cárdenas A, Mosqueira MJ, Jiménez-García LF, Voolstra CR. Ultrastructural and proteomic evidence for the presence of a putative nucleolus in an Archaeon. Front Microbiol 2023; 14:1075071. [PMID: 36819014 PMCID: PMC9932318 DOI: 10.3389/fmicb.2023.1075071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/02/2023] [Indexed: 02/05/2023] Open
Abstract
Nucleoli are subcellular compartments where transcription and maturation of pre-ribosomal RNAs occur. While the transcription of ribosomal RNAs is common to all living cells, the presence and ultrastructure of nucleoli has been only documented in eukaryotes. Asgard-Archaea, the closest prokaryotic relatives of eukaryotes, and their near relatives TACK-Archaea have homologs of nucleolar proteins and RNAs in their genome, but the cellular organization of both is largely unexplored. Here we provide ultrastructural and molecular evidence for the presence of putative nucleolus-like subcellular domains in the TACK crenarchaeon Saccharolobus solfataricus (formerly known as Sulfolobus solfataricus). Transmission electron microscopy (TEM) revealed consistent electron-dense fibro-granular compartments, also positive to the specific silver staining for nucleolar organizer regions (AgNOR). TEM also confirmed that ribosomal DNA (rDNA) is spatially distributed in non-random, clustered arrays underlying fine structures, as observed by ultrastructural in situ hybridization (UISH). To further explore these observations, proteomic sequencing of isolated bands from AgNOR-stained protein gels was conducted and compared against a compiled inventory of putative nucleolar homologs from the S. solfataricus P1 genome. Sequenced AgNOR-sensitive peptides encoded homologs of eukaryotic nucleoli proteins, enriched for nucleolus-related functions. Our results provide first evidence that subcellular domains of nucleolar-like nature are not exclusive to eukaryotes. Based on our data, we propose a model for a putative nucleolus in S. solfataricus. Whereas technical limitations and further aspects remain a matter for future functional studies, our data supports the origin of nucleoli within the common ancestor of Eukarya and TACK-Archaea, based on a two-domain tree of life.
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Affiliation(s)
- Parsifal F. Islas-Morales
- Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, UNAM, Mexico City, Mexico,UNESCO Chair on Science Diplomacy and Scientific Heritage, Instituto de Biología, UNAM, Mexico City, Mexico,Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anny Cárdenas
- Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia,Department of Biology, University of Konstanz, Konstanz, Germany,Department of Biology, American University, Washington, DC, United States
| | - María J. Mosqueira
- Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia,NEOM, Saudi Arabia
| | - Luis Felipe Jiménez-García
- Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, UNAM, Mexico City, Mexico,Department of Cell Biology, Faculty of Sciences, UNAM, Mexico City, Mexico,*Correspondence: Luis Felipe Jiménez-García, ✉
| | - Christian R. Voolstra
- Red Sea Research Center (RSRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia,Department of Biology, University of Konstanz, Konstanz, Germany,Christian R. Voolstra, ✉
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7
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NAT10 regulates mitotic cell fate by acetylating Eg5 to control bipolar spindle assembly and chromosome segregation. Cell Death Differ 2022; 29:846-860. [PMID: 35210604 PMCID: PMC8989979 DOI: 10.1038/s41418-021-00899-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 02/07/2023] Open
Abstract
Cell fate of mitotic cell is controlled by spindle assembly. Deficient spindle assembly results in mitotic catastrophe leading to cell death to maintain cellular homeostasis. Therefore, inducing mitotic catastrophe provides a strategy for tumor therapy. Nucleolar acetyltransferase NAT10 has been found to regulate various cellular processes to maintain cell homeostasis. Here we report that NAT10 regulates mitotic cell fate by acetylating Eg5. NAT10 depletion results in multinuclear giant cells, which is the hallmark of mitotic catastrophe. Live-cell imaging showed that knockdown of NAT10 dramatically prolongs the mitotic time and induces defective chromosome segregation including chromosome misalignment, bridge and lagging. NAT10 binds and co-localizes with Eg5 in the centrosome during mitosis. Depletion of NAT10 reduces the centrosome loading of Eg5 and impairs the poleward movement of centrosome, leading to monopolar and asymmetrical spindle formation. Furthermore, NAT10 stabilizes Eg5 through its acetyltransferase function. NAT10 acetylates Eg5 at K771 to control Eg5 stabilization. We generated K771-Ac specific antibody and showed that Eg5 K771-Ac specifically localizes in the centrosome during mitosis. Additionally, K771 acetylation is required for the motor function of Eg5. The hyper-acetylation mimic Flag-Eg5 K771Q but not Flag-Eg5 rescued the NAT10 depletion-induced defective spindle formation and mitotic catastrophe, demonstrating that NAT10 controls mitosis through acetylating Eg5 K771. Collectively, we identify Eg5 as an important substrate of NAT10 in the control of mitosis and provide K771 as an essential acetylation site in the stabilization and motor function of Eg5. Our findings reveal that targeting the NAT10-mediated Eg5 K771 acetylation provides a potential strategy for tumor therapy.
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8
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Gilloteaux J, Bouchat J, Brion JP, Nicaise C. The osmotic demyelination syndrome: the resilience of thalamic neurons is verified with transmission electron microscopy. Ultrastruct Pathol 2021; 44:450-480. [DOI: 10.1080/01913123.2020.1853865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jacques Gilloteaux
- Unit of Research in Molecular Physiology (Urphym- NARILIS), Department of Medicine, Université de Namur, Namur, Belgium
- Department of Anatomical Sciences, St George’s University School of Medicine, KB Taylor Global Scholar’s Program at UNN, School of Health and Life Sciences, Newcastle upon Tyne, UK
| | - Joanna Bouchat
- Unit of Research in Molecular Physiology (Urphym- NARILIS), Department of Medicine, Université de Namur, Namur, Belgium
| | - Jean-Pierre Brion
- Laboratory of Histology, Neuroanatomy and Neuropathology, Faculté de Médecine Université Libre de Bruxelles, Brussels, Belgium
| | - Charles Nicaise
- Unit of Research in Molecular Physiology (Urphym- NARILIS), Department of Medicine, Université de Namur, Namur, Belgium
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9
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Corbet GA, Parker R. RNP Granule Formation: Lessons from P-Bodies and Stress Granules. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:203-215. [PMID: 32482896 DOI: 10.1101/sqb.2019.84.040329] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
It is now clear that cells form a wide collection of large RNA-protein assemblies, referred to as RNP granules. RNP granules exist in bacterial cells and can be found in both the cytosol and nucleus of eukaryotic cells. Recent approaches have begun to define the RNA and protein composition of a number of RNP granules. Herein, we review the composition and assembly of RNP granules, as well as how RNPs are targeted to RNP granules using stress granules and P-bodies as model systems. Taken together, these reveal that RNP granules form through the summative effects of a combination of protein-protein, protein-RNA, and RNA-RNA interactions. Similarly, the partitioning of individual RNPs into stress granules is determined by the combinatorial effects of multiple elements. Thus, RNP granules are assemblies generally dominated by combinatorial effects, thereby providing rich opportunities for biological regulation.
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Affiliation(s)
- Giulia Ada Corbet
- Department of Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
- Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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10
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Bouchat J, Gilloteaux J, Suain V, Van Vlaender D, Brion JP, Nicaise C. Ultrastructural Analysis of Thalamus Damages in a Mouse Model of Osmotic-Induced Demyelination. Neurotox Res 2019; 36:144-162. [DOI: 10.1007/s12640-019-00041-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 03/25/2019] [Accepted: 04/04/2019] [Indexed: 12/31/2022]
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11
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Abstract
Eukaryotic cells contain a large number of RNA-protein assemblies, generically referred to as ribonucleoprotein (RNP) granules. Such RNP granules include stress granules and P-bodies in the cytosol and the nucleolus, Cajal bodies, and paraspeckles in the nucleus. A variety of imaging approaches have been used to reveal different components, structural features, and dynamics of RNP granules. In this review, we discuss imaging approaches that have been used to study stress granules and the insights gained from these experiments. A general theme is that these approaches can be transferred to other RNP granules to examine similar aspects of their composition, ultrastructure, dynamics and control.
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Affiliation(s)
- Briana Van Treeck
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
| | - Roy Parker
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
- Howard Hughes Medical Institute, Boulder, Colorado 80303
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12
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Abstract
The nucleolus is a prominent subnuclear compartment, where ribosome biosynthesis takes place. Recently, the nucleolus has gained attention for its novel role in the regulation of cellular stress. Nucleolar stress is emerging as a new concept, which is characterized by diverse cellular insult-induced abnormalities in nucleolar structure and function, ultimately leading to activation of p53 or other stress signaling pathways and alterations in cell behavior. Despite a number of comprehensive reviews on this concept, straightforward and clear-cut way criteria for a nucleolar stress state, regarding the factors that elicit this state, the morphological and functional alterations as well as the rationale for p53 activation are still missing. Based on literature of the past two decades, we herein summarize the evolution of the concept and provide hallmarks of nucleolar stress. Along with updated information and thorough discussion of existing confusions in the field, we pay particular attention to the current understanding of the sensing mechanisms, i.e., how stress is integrated by p53. In addition, we propose our own emphasis regarding the role of nucleolar protein NPM1 in the hallmarks of nucleolar stress and sensing mechanisms. Finally, the links of nucleolar stress to human diseases are briefly and selectively introduced.
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Affiliation(s)
- Kai Yang
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.,Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases with Integrated Chinese-Western Medicine, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, China
| | - Jie Yang
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Jing Yi
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
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13
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Chen L, Jiao Y, Guan X, Li X, Feng Y, Jiao M. Investigation of cell cycle-associated structural reorganization in nucleolar FC/DFCs from mouse MFC cells by electron microscopy. Microscopy (Oxf) 2018; 67:4994513. [PMID: 29750255 DOI: 10.1093/jmicro/dfy020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/08/2018] [Indexed: 11/14/2022] Open
Abstract
Nucleolus structure alters as the cell cycle is progressing. It is established in telophase, maintained throughout the entire interphase and disassembled in metaphase. Fibrillar centers (FCs), dense fibrillar components (DFCs) and granular components (GCs) are essential nucleolar organizations where rRNA transcription and processing and ribosome assembly take place. Hitherto, little is known about the cell cycle-dependent reorganization of these structures. In this study, we followed the nucleolus structure during the cell cycle by electron microscopy (EM). We found the nucleolus experienced multiple rounds of structural reorganization within a single cell cycle: (1) when nucleoli are formed during the transition from late M to G1 phase, FCs, DFCs and GCs are constructed, leading to the establishment of tripartite nucleolus; (2) as FC/DFCs are disrupted at mid-G1, tripartite nucleolus is gradually changed into a bipartite organization; (3) at late G1, the reassembly of FC/DFCs results in a structural transition from bipartite nucleolus towards tripartite nucleolus; (4) as cells enter S phase, FC/DFCs are disassembled again and tripartite nucleolus is thus changed into a bipartite organization. Of note, FC/DFCs were not observed until late S phase; (5) FC/DFCs experience structural disruption and restoration during G2 and (6) when cells are at mitotic stage, FC/DFCs disappear before nucleolus structure is disassembled. These results also suggest that bipartite nucleolus can exist in higher eukaryotes at certain period of the cell cycle. As structures are the fundamental basis of diverse cell activities, unveiling the structural reorganization of nucleolar FCs and DFCs may bring insights into the spatial-temporal compartmentalization of relevant cellular functions.
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Affiliation(s)
- Lingling Chen
- School of Life Sciences, Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Yang Jiao
- School of Physical Education, Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Xin Guan
- School of Life Sciences, Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Xiliang Li
- School of Life Sciences, Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Yunpeng Feng
- School of Life Sciences, Northeast Normal University, Changchun, Jilin Province 130024, China
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin Province 130024, China
| | - Mingda Jiao
- School of Life Sciences, Northeast Normal University, Changchun, Jilin Province 130024, China
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14
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Yu S, Lemos B. The long-range interaction map of ribosomal DNA arrays. PLoS Genet 2018; 14:e1007258. [PMID: 29570716 PMCID: PMC5865718 DOI: 10.1371/journal.pgen.1007258] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 02/15/2018] [Indexed: 11/28/2022] Open
Abstract
The repeated rDNA array gives rise to the nucleolus, an organelle that is central to cellular processes as varied as stress response, cell cycle regulation, RNA modification, cell metabolism, and genome stability. The rDNA array is also responsible for the production of more than 70% of all cellular RNAs (the ribosomal RNAs). The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1 while the 45S rDNA arrays reside on the short arm of five human acrocentric chromosomes. These critical genome elements have remained unassembled and have been excluded from all Hi-C analyses to date. Here we built the first high resolution map of 5S and 45S rDNA array contacts with the rest of the genome combining over 15 billion Hi-C reads from several experiments. The data enabled sufficiently high coverage to map rDNA-genome interactions with 1MB resolution and identify rDNA-gene contacts. The map showed that the 5S and 45S arrays display preferential contact at common sites along the genome but are not themselves sufficiently close to yield 5S-45S Hi-C contacts. Ribosomal DNA contacts are enriched in segments of closed, repressed, and late replicating chromatin, as well as CTCF binding sites. Finally, we identified functional categories whose dispersed genes coalesced in proximity to the rDNA arrays or instead avoided proximity with the rDNA arrays. The observations further our understanding of the spatial localization of rDNA arrays and their contribution to the architecture of the cell nucleus.
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Affiliation(s)
- Shoukai Yu
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, United States of America
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, United States of America
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15
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Fernández-Ponce C, Durán-Ruiz MC, Narbona-Sánchez I, Muñoz-Miranda JP, Arbulo-Echevarria MM, Serna-Sanz A, Baumann C, Litrán R, Aguado E, Bloch W, García-Cozar F. Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells. Front Microbiol 2018; 8:2595. [PMID: 29354102 PMCID: PMC5758585 DOI: 10.3389/fmicb.2017.02595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 12/12/2017] [Indexed: 12/24/2022] Open
Abstract
Hepatitis C virus core protein is a highly basic viral protein that multimerizes with itself to form the viral capsid. When expressed in CD4+ T lymphocytes, it can induce modifications in several essential cellular and biological networks. To shed light on the mechanisms underlying the alterations caused by the viral protein, we have analyzed HCV-core subcellular localization and its associations with host proteins in Jurkat T cells. In order to investigate the intracellular localization of Hepatitis C virus core protein, we have used a lentiviral system to transduce Jurkat T cells and subsequently localize the protein using immunoelectron microscopy techniques. We found that in Jurkat T cells, Hepatitis C virus core protein mostly localizes in the nucleus and specifically in the nucleolus. In addition, we performed pull-down assays combined with Mass Spectrometry Analysis, to identify proteins that associate with Hepatitis C virus core in Jurkat T cells. We found proteins such as NOLC1, PP1γ, ILF3, and C1QBP implicated in localization and/or traffic to the nucleolus. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4+ T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. Thus, in the current work, we show the ultrastructural localization of Hepatitis C virus core and the first profile of HCV core associated proteins in T cells, and we discuss the functions and interconnections of these proteins in molecular networks where relevant biological modifications have been described upon the expression of Hepatitis C virus core protein. Thereby, the current work constitutes a necessary step toward understanding the mechanisms underlying HCV core mediated alterations that had been described in relevant biological processes in CD4+ T cells.
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Affiliation(s)
- Cecilia Fernández-Ponce
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Maria C Durán-Ruiz
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Isaac Narbona-Sánchez
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Juan P Muñoz-Miranda
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Mikel M Arbulo-Echevarria
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | | | | | - Rocío Litrán
- Department of Condensed Matter Physics, University of Cádiz, Puerto Real, Spain
| | - Enrique Aguado
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
| | - Wilhelm Bloch
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiovascular Research and Sport Medicine, German Sport University Cologne, Cologne, Germany
| | - Francisco García-Cozar
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz and Institute of Biomedical Research Cádiz (INIBICA), Cadiz, Spain
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16
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Guan X, Jiao Y, Chen L, Li X, Shang G, Wang F, Feng Y, Jiao M. Disruption and restoration of nucleolar FC and DFC during S phase in HeLa cells. Cell Biol Int 2017; 41:258-266. [DOI: 10.1002/cbin.10719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/17/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Xin Guan
- School of Life Sciences; Northeast Normal University; Changchun Jilin Province 130024 China
| | - Yang Jiao
- School of Life Sciences; Northeast Normal University; Changchun Jilin Province 130024 China
| | - Lingling Chen
- School of Life Sciences; Northeast Normal University; Changchun Jilin Province 130024 China
| | - Xiliang Li
- School of Life Sciences; Northeast Normal University; Changchun Jilin Province 130024 China
| | - Guangbin Shang
- Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Ministry of Education; Jiangxi University of Traditional Chinese Medicine; Nanchang Jiangxi Province 330004 China
| | - Fengcai Wang
- Jiu Jiang University; Jiangxi Province 332000 China
| | - Yunpeng Feng
- School of Life Sciences; Northeast Normal University; Changchun Jilin Province 130024 China
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE); Northeast Normal University; Changchun Jilin Province 130024 China
| | - Mingda Jiao
- School of Life Sciences; Northeast Normal University; Changchun Jilin Province 130024 China
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17
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Yu S, Lemos B. A Portrait of Ribosomal DNA Contacts with Hi-C Reveals 5S and 45S rDNA Anchoring Points in the Folded Human Genome. Genome Biol Evol 2016; 8:3545-3558. [PMID: 27797956 PMCID: PMC5203791 DOI: 10.1093/gbe/evw257] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Ribosomal RNAs (rRNAs) account for >60% of all RNAs in eukaryotic cells and are encoded in the ribosomal DNA (rDNA) arrays. The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1, whereas the 45S rDNA array resides on the short arm of five human acrocentric chromosomes. The 45S rDNA gives origin to the nucleolus, the nuclear organelle that is the site of ribosome biogenesis. Intriguingly, 5S and 45S rDNA arrays exhibit correlated copy number variation in lymphoblastoid cells (LCLs). Here we examined the genomic architecture and repeat content of the 5S and 45S rDNA arrays in multiple human genome assemblies (including PacBio MHAP assembly) and ascertained contacts between the rDNA arrays and the rest of the genome using Hi-C datasets from two human cell lines (erythroleukemia K562 and lymphoblastoid cells). Our analyses revealed that 5S and 45S arrays each have thousands of contacts in the folded genome, with rDNA-associated regions and genes dispersed across all chromosomes. The rDNA contact map displayed conserved and disparate features between two cell lines, and pointed to specific chromosomes, genomic regions, and genes with evidence of spatial proximity to the rDNA arrays; the data also showed a lack of direct physical interaction between the 5S and 45S rDNA arrays. Finally, the analysis identified an intriguing organization in the 5S array with Alu and 5S elements adjacent to one another and organized in opposite orientation along the array. Portraits of genome folding centered on the ribosomal DNA array could help understand the emergence of concerted variation, the control of 5S and 45S expression, as well as provide insights into an organelle that contributes to the spatial localization of human chromosomes during interphase.
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Affiliation(s)
- Shoukai Yu
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
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18
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Li Y, Hu Y, Che L, Jia J, Chen M. Nucleolar localization of Small G protein RhoA is associated with active RNA synthesis in human carcinoma HEp-2 cells. Oncol Lett 2016; 11:3605-3610. [PMID: 27313679 PMCID: PMC4888017 DOI: 10.3892/ol.2016.4450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 03/01/2016] [Indexed: 01/09/2023] Open
Abstract
Previous studies have demonstrated that the nuclear localization of ras homolog family member A (RhoA), with prominent concentration in the nucleolus, is a common feature in human cancer tissues and cancer cell lines. Although a previous study has demonstrated that the nuclear translocation of RhoA occurs via active transport, a process that occurs through importin α in a nuclear factor-κB-dependent manner, the mechanism, biological function and pathological meaning of the nucleolar residency of RhoA remain to be elucidated. As the cell nucleolus is the site of ribosome biosynthesis, the aim of the present study was to investigate the association between RNA synthesis and the nucleolar localization of RhoA, as well as the molecular mechanisms underlying the residency of RhoA in the nucleolus of HEp-2 (human larynx epithelial carcinoma) cells. Indirect immunofluorescence microscopy was used to evaluate the subcellular distribution of nuclear RhoA, and immunoblotting analysis was used to determine the total cellular protein level of RhoA. Consistent with the results of previous studies, untreated HEp-2 cells exhibited bright nucleolar staining, indicating an increased concentration of RhoA in the nucleoli. Treatment with actinomycin D for the inhibition of RNA synthesis caused a redistribution of RhoA from the nucleoli to the nucleoplasm with a speckled staining pattern. Immunoblotting revealed that neither the total cellular amount of RhoA nor the integrity of RhoA was affected by treatment with actinomycin D. In cells that were treated at a decreased concentration (0.05 mg/l) of actinomycin D, the redistribution of RhoA was reversible following the removal of the drug from the culture medium. However, this reversal was not observed at an increased drug concentration (1 mg/l). Overall, to the best of our knowledge, the results of the present study provide the first in situ evidence that the inhibition of RNA synthesis induces a redistribution of nucleolar RhoA to the nucleoplasm, and additionally suggest that the nucleolar residency of RhoA in HEp-2 cells may be associated with active RNA synthesis.
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Affiliation(s)
- Yueying Li
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Yong Hu
- Department of Neonatology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, P.R. China
| | - Lilong Che
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Junhai Jia
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Min Chen
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
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19
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Todd MAM, Huh MS, Picketts DJ. The sub-nucleolar localization of PHF6 defines its role in rDNA transcription and early processing events. Eur J Hum Genet 2016; 24:1453-9. [PMID: 27165002 PMCID: PMC5027685 DOI: 10.1038/ejhg.2016.40] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/30/2016] [Accepted: 04/12/2016] [Indexed: 12/20/2022] Open
Abstract
Ribosomal RNA synthesis occurs in the nucleolus and is a tightly regulated process that is targeted in some developmental diseases and hyperactivated in multiple cancers. Subcellular localization and immunoprecipitation coupled mass spectrometry demonstrated that a proportion of plant homeodomain (PHD) finger protein 6 (PHF6) protein is localized within the nucleolus and interacts with proteins involved in ribosomal processing. PHF6 sequence variants cause Börjeson–Forssman–Lehmann syndrome (BFLS, MIM#301900) and are also associated with a female-specific phenotype overlapping with Coffin–Siris syndrome (MIM#135900), T-cell acute lymphoblastic leukemia (MIM#613065), and acute myeloid leukemia (MIM#601626); however, very little is known about its cellular function, including its nucleolar role. HEK 293T cells were treated with RNase A, DNase I, actinomycin D, or 5,6-dichloro-β-D-ribofuranosylbenzimadole, followed by immunocytochemistry to determine PHF6 sub-nucleolar localization. We observed RNA-dependent localization of PHF6 to the sub-nucleolar fibrillar center (FC) and dense fibrillar component (DFC), at whose interface rRNA transcription occurs. Subsequent ChIP-qPCR analysis revealed strong enrichment of PHF6 across the entire rDNA-coding sequence but not along the intergenic spacer (IGS) region. When rRNA levels were quantified in a PHF6 gain-of-function model, we observed an overall decrease in rRNA transcription, accompanied by a modest increase in repressive promoter-associated RNA (pRNA) and a significant increase in the expression levels of the non-coding IGS36RNA and IGS39RNA transcripts. Collectively, our results demonstrate a role for PHF6 in carefully mediating the overall levels of ribosome biogenesis within a cell.
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Affiliation(s)
- Matthew A M Todd
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael S Huh
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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20
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A Cold-Inducible DEAD-Box RNA Helicase from Arabidopsis thaliana Regulates Plant Growth and Development under Low Temperature. PLoS One 2016; 11:e0154040. [PMID: 27116354 PMCID: PMC4846089 DOI: 10.1371/journal.pone.0154040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/07/2016] [Indexed: 01/29/2023] Open
Abstract
DEAD-box RNA helicases comprise a large family and are involved in a range of RNA processing events. Here, we identified one of the Arabidopsis thaliana DEAD-box RNA helicases, AtRH7, as an interactor of Arabidopsis COLD SHOCK DOMAIN PROTEIN 3 (AtCSP3), which is an RNA chaperone involved in cold adaptation. Promoter:GUS transgenic plants revealed that AtRH7 is expressed ubiquitously and that its levels of the expression are higher in rapidly growing tissues. Knockout mutant lines displayed several morphological alterations such as disturbed vein pattern, pointed first true leaves, and short roots, which resemble ribosome-related mutants of Arabidopsis. In addition, aberrant floral development was also observed in rh7 mutants. When the mutants were germinated at low temperature (12°C), both radicle and first leaf emergence were severely delayed; after exposure of seedlings to a long period of cold, the mutants developed aberrant, fewer, and smaller leaves. RNA blots and circular RT-PCR revealed that 35S and 18S rRNA precursors accumulated to higher levels in the mutants than in WT under both normal and cold conditions, suggesting the mutants are partially impaired in pre-rRNA processing. Taken together, the results suggest that AtRH7 affects rRNA biogenesis and plays an important role in plant growth under cold.
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21
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Wang H, Luo X, You W, Dong Y, Ke C. Cytogenetic analysis and chromosomal characteristics of the polymorphic 18S rDNA of Haliotis discus hannai from Fujian, China. PLoS One 2015; 10:e0113816. [PMID: 25699679 PMCID: PMC4336138 DOI: 10.1371/journal.pone.0113816] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 10/31/2014] [Indexed: 11/27/2022] Open
Abstract
We report on novel chromosomal characteristics of Haliotis discus hannai from a breeding population at Fujian, China. The karyotypes of H. discus hannai we obtained from an abalone farm include a common type 2n = 36 = 10M + 8SM (82%) and two rare types 2n = 36 = 11M + 7SM (14%) and 2n = 36 = 10M + 7SM + 1ST (4%). The results of silver staining showed that the NORs of H. discus hannai were usually located terminally on the long arms of chromosome pairs 14 and 17, NORs were also sometimes located terminally on the short arms of other chromosomes, either metacentric or submetacentric pairs. The number of Ag-nucleoli ranged from 2 to 8, and the mean number was 3.61 ± 0.93. Among the scored interphase cells, 41% had 3 detectable nucleoli and 37% had 4 nucleoli. The 18S rDNA FISH result is the first report of the location of 18S rDNA genes in H. discus hannai. The 18S rDNA locations were highly polymorphic in this species. Copies of the gene were observed in the terminal of long or/and short arms of submetacentric or/and metacentric chromosomes. Using FISH with probe for vertebrate-like telomeric sequences (CCCTAA)3 displayed positive green FITC signals at telomere regions of all analyzed chromosome types. We found about 7% of chromosomes had breaks in prophase. A special form of nucleolus not previously described from H. discus hannai was observed in some interphase cells. It consists of many small silver-stained nucleoli gathered together to form a larger nucleolus and may correspond to prenucleolar bodies.
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Affiliation(s)
- Haishan Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Colleges of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Colleges of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Colleges of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yunwei Dong
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Colleges of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Colleges of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- * E-mail:
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22
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Pickard AJ, Bierbach U. The cell's nucleolus: an emerging target for chemotherapeutic intervention. ChemMedChem 2013; 8:1441-9. [PMID: 23881648 PMCID: PMC3893319 DOI: 10.1002/cmdc.201300262] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Indexed: 01/01/2023]
Abstract
The transient nucleolus plays a central role in the up-regulated synthesis of ribosomal RNA (rRNA) to sustain ribosome biogenesis, a hallmark of aberrant cell growth. This function, in conjunction with its unique pathohistological features in malignant cells and its ability to mediate apoptosis, renders this sub-nuclear structure a potential target for chemotherapeutic agents. In this Minireview, structurally and functionally diverse small molecules are discussed that have been reported to either interact with the nucleolus directly or perturb its function indirectly by acting on its dynamic components. These molecules include all major classes of nucleic-acid-targeted agents, antimetabolites, kinase inhibitors, anti-inflammatory drugs, natural product antibiotics, oligopeptides, as well as nanoparticles. Together, these molecules are invaluable probes of structure and function of the nucleolus. They also provide a unique opportunity to develop novel strategies for more selective and therefore better-tolerated chemotherapeutic intervention. In this regard, inhibition of RNA polymerase-I-mediated rRNA synthesis appears to be a promising mechanism for killing cancer cells. The recent development of molecules targeted at G-quadruplex-forming rRNA gene sequences, which are currently undergoing clinical trials, seems to attest to the success of this approach.
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Affiliation(s)
- Amanda J. Pickard
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109 (USA)
| | - Ulrich Bierbach
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109 (USA)
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23
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Sakai D, Dixon J, Dixon MJ, Trainor PA. Mammalian neurogenesis requires Treacle-Plk1 for precise control of spindle orientation, mitotic progression, and maintenance of neural progenitor cells. PLoS Genet 2012; 8:e1002566. [PMID: 22479190 PMCID: PMC3315461 DOI: 10.1371/journal.pgen.1002566] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 01/16/2012] [Indexed: 11/18/2022] Open
Abstract
The cerebral cortex is a specialized region of the brain that processes cognitive, motor, somatosensory, auditory, and visual functions. Its characteristic architecture and size is dependent upon the number of neurons generated during embryogenesis and has been postulated to be governed by symmetric versus asymmetric cell divisions, which mediate the balance between progenitor cell maintenance and neuron differentiation, respectively. The mechanistic importance of spindle orientation remains controversial, hence there is considerable interest in understanding how neural progenitor cell mitosis is controlled during neurogenesis. We discovered that Treacle, which is encoded by the Tcof1 gene, is a novel centrosome- and kinetochore-associated protein that is critical for spindle fidelity and mitotic progression. Tcof1/Treacle loss-of-function disrupts spindle orientation and cell cycle progression, which perturbs the maintenance, proliferation, and localization of neural progenitors during cortical neurogenesis. Consistent with this, Tcof1(+/-) mice exhibit reduced brain size as a consequence of defects in neural progenitor maintenance. We determined that Treacle elicits its effect via a direct interaction with Polo-like kinase1 (Plk1), and furthermore we discovered novel in vivo roles for Plk1 in governing mitotic progression and spindle orientation in the developing mammalian cortex. Increased asymmetric cell division, however, did not promote increased neuronal differentiation. Collectively our research has therefore identified Treacle and Plk1 as novel in vivo regulators of spindle fidelity, mitotic progression, and proliferation in the maintenance and localization of neural progenitor cells. Together, Treacle and Plk1 are critically required for proper cortical neurogenesis, which has important implications in the regulation of mammalian brain size and the pathogenesis of congenital neurodevelopmental disorders such as microcephaly.
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Affiliation(s)
- Daisuke Sakai
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Jill Dixon
- Faculty of Medical and Human Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
| | - Michael J. Dixon
- Faculty of Medical and Human Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
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Localization and expression of peptidylarginine deiminase 4 (PAD4) in mammalian oocytes and preimplantation embryos. ZYGOTE 2011; 21:314-24. [PMID: 22126893 DOI: 10.1017/s0967199411000633] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Post-translational modifications generally involve the addition or removal of various functional groups to or from the protein residues. However, citrullination, which is catalyzed by the peptidylarginine deiminases (PADs), involves conversion of one kind of amino acid residue into another. One of five isoforms, PAD4 is a nuclear enzyme known to play a role in development, differentiation and apoptosis through gene regulation. To investigate the possible role of PAD4 in mammalian preimplantation embryonic development, we first studied localization and expression of PAD4 and citrullinated proteins in pig and mouse oocytes, and parthenogenetic or in vitro fertilized (IVF) embryos. Immunofluorescence study revealed that PAD4 primarily localizes in the cytoplasm in pig oocytes and parthenogenetic embryos. However, the nuclear translocation of PAD4 was observed in late germinal vesicle (GV) stage oocytes prior to GV breakdown and was localized around the metaphase (M)I and II spindle. Nucleus localized PAD4 was noticed partially again in blastocysts. In mouse IVF embryos, nuclear translocation started from the 2-cell stage and gradually increased up to blastocyst. Western blot studies confirmed that PAD4 was expressed in oocytes, and parthenogenetic embryos of pig. Citrullinated proteins were detected in granular form on the chromatin in GV, MI and MII oocytes and nuclei in all the stages of the embryos studied. It was found that the target of citrullination was histone protein (H3), not B23. Therefore the presence of PAD4 and citrullinated histone H3 in oocytes and embryos suggested a possible role for PAD4 in preimplantation embryonic development.
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25
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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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26
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Localization of Nopp140 within mammalian cells during interphase and mitosis. Histochem Cell Biol 2009; 132:129-40. [PMID: 19381672 DOI: 10.1007/s00418-009-0599-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2009] [Indexed: 10/20/2022]
Abstract
We investigated distribution of the nucleolar phosphoprotein Nopp140 within mammalian cells, using immunofluorescence confocal microscopy and immunoelectron microscopy. During interphase, three-dimensional image reconstructions of confocal sections revealed that nucleolar labelling appeared as several tiny spheres organized in necklaces. Moreover, after an immunogold labelling procedure, gold particles were detected not only over the dense fibrillar component but also over the fibrillar centres of nucleoli in untreated and actinomycin D-treated cells. Labelling was also consistently present in Cajal bodies. After pulse-chase experiments with BrUTP, colocalization was more prominent after a 10- to 15-min chase than after a 5-min chase. During mitosis, confocal analysis indicated that Nopp140 organization was lost. The protein dispersed between and around the chromosomes in prophase. From prometaphase to telophase, it was also detected in numerous cytoplasmic nucleolus-derived foci. During telophase, it reappeared in the reforming nucleoli of daughter nuclei. This strongly suggests that Nopp140 could be a component implicated in the early steps of pre-rRNA processing.
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27
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Tsai YT, Lin CI, Chen HK, Lee KM, Hsu CY, Yang SJ, Yeh NH. Chromatin tethering effects of hNopp140 are involved in the spatial organization of nucleolus and the rRNA gene transcription. J Biomed Sci 2008; 15:471-86. [PMID: 18253863 PMCID: PMC2440943 DOI: 10.1007/s11373-007-9226-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 11/23/2007] [Indexed: 11/29/2022] Open
Abstract
The short arms of five human acrocentric chromosomes contain ribosomal gene (rDNA) clusters where numerous mini-nucleoli arise at the exit of mitosis. These small nucleoli tend to coalesce into one or a few large nucleoli during interphase by unknown mechanisms. Here, we demonstrate that the N- and C-terminal domains of a nucleolar protein, hNopp140, bound respectively to alpha-satellite arrays and rDNA clusters of acrocentric chromosomes for nucleolar formation. The central acidic-and-basic repeated domain of hNopp140, possessing a weak self-self interacting ability, was indispensable for hNopp140 to build up a nucleolar round-shaped structure. The N- or the C-terminally truncated hNopp140 caused nucleolar segregation and was able to alter locations of the rDNA transcription, as mediated by detaching the rDNA repeats from the acrocentric alpha-satellite arrays. Interestingly, an hNopp140 mutant, made by joining the N- and C-terminal domains but excluding the entire central repeated region, induced nucleolar disruption and global chromatin condensation. Furthermore, RNAi knockdown of hNopp140 resulted in dispersion of the rDNA and acrocentric alpha-satellite sequences away from nucleolus that was accompanied by rDNA transcriptional silence. Our findings indicate that hNopp140, a scaffold protein, is involved in the nucleolar assembly, fusion, and maintenance.
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Affiliation(s)
- Yi-Tzang Tsai
- School of Life Science, Institute of Microbiology and Immunology, National Yang-Ming University, 155 Li-Nong Street Sec. 2, Taipei, 112, Taiwan
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Hirano Y, Takahashi H, Kumeta M, Hizume K, Hirai Y, Otsuka S, Yoshimura SH, Takeyasu K. Nuclear architecture and chromatin dynamics revealed by atomic force microscopy in combination with biochemistry and cell biology. Pflugers Arch 2008; 456:139-53. [PMID: 18172599 DOI: 10.1007/s00424-007-0431-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 11/29/2007] [Accepted: 12/10/2007] [Indexed: 10/22/2022]
Abstract
The recent technical development of atomic force microscopy (AFM) has made nano-biology of the nucleus an attractive and promising field. In this paper, we will review our current understanding of nuclear architecture and dynamics from the structural point of view. Especially, special emphases will be given to: (1) How to approach the nuclear architectures by means of new techniques using AFM, (2) the importance of the physical property of DNA in the construction of the higher-order structures, (3) the significance and implication of the linker and core histones and the nuclear matrix/scaffold proteins for the chromatin dynamics, (4) the nuclear proteins that contribute to the formation of the inner nuclear architecture. Spatio-temporal analyses using AFM, in combination with biochemical and cell biological approaches, will play important roles in the nano-biology of the nucleus, as most of nuclear structures and events occur in nanometer, piconewton and millisecond order. The new applications of AFM, such as recognition imaging, fast-scanning imaging, and a variety of modified cantilevers, are expected to be powerful techniques to reveal the nanostructure of the nucleus.
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Affiliation(s)
- Yasuhiro Hirano
- Kyoto University Graduate School of Biostudies, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
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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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Svarcova O, Laurincik J, Avery B, Mlyncek M, Niemann H, Maddox-Hyttel P. Nucleolar development and allocation of key nucleolar proteins require de novo transcription in bovine embryos. Mol Reprod Dev 2007; 74:1428-35. [PMID: 17410544 DOI: 10.1002/mrd.20727] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The goal of the present study was to investigate whether key nucleolar proteins involved in ribosomal RNA (rRNA) transcription and processing are transcribed de novo or from maternally inherited messenger RNAs (mRNA) in bovine embryos, and to which extent de novo transcription of these proteins mRNA is required for the development of functional nucleoli during the major activation of the embryonic genome. Immunofluorescence for localization of key nucleolar proteins, autoradiography for detection of transcriptional activity, and transmission electron microscopy were applied to in vitro produced bovine embryos cultured from the 2-cell stage with or without (control groups) alpha-amanitin, which blocks the RNA polymerases II and III transcription and, thus the synthesis of mRNA. In the control groups, weak autoradiographic labeling was initially observed in the periphery of few nuclei at the 4-cell and the early 8-cell stage, and the entire nucleoplasm as well as nucleolus precursor bodies (NBBs) were prominently labelled in all late 8-cell stages. The NPBs displayed initial transformation into fibrillo-granular nucleoli. In the alpha-amanitin group, lack of autoradiographic labeling was seen at all developmental stages and disintegrated NPBs stage were found at the late 8-cell. Our immunofluorescence data indicate that RNA polymerase I, UBF, topoisomerase I and fibrillarin are transcribed de novo whereas nucleolin and nucleophosmin are maternally inherited as demonstrated by alpha -amanitin inhibition. However, localization of these two proteins to the nucleolar compartments was negatively affected by the alpha-amanitin treatment. Consequently, functional nucleoli were not established.
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Affiliation(s)
- Olga Svarcova
- Department of Basic Animal and Veterinary Sciences, Royal Veterinary and Agricultural University, Frederiksberg C, Denmark.
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31
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Chou CC, Yung BYM, Hsu CY. Involvement of nPKC-MAPK pathway in the decrease of nucleophosmin/B23 during megakaryocytic differentiation of human myelogenous leukemia K562 cells. Life Sci 2007; 80:2051-9. [PMID: 17448503 DOI: 10.1016/j.lfs.2007.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 01/27/2007] [Accepted: 03/07/2007] [Indexed: 11/17/2022]
Abstract
Human myelogenous leukemia K562 cells were induced to undergo megakaryocytic differentiation by long-term treatment with phorbol ester 12-O-tetradecanoyl-phorbol-13-acetate (TPA). The protein level of nucleophosmin/B23 (NPM/B23), a nucleolar protein, was substantially decreased upon TPA treatment. In this study, we found that the proteasome inhibitors blocked the decrease of NPM/B23 protein in response to TPA, suggesting the proteasomes were involved in the downregulation of NPM/B23 upon megakaryocytic differentiation. To investigate the signaling pathway in the downregulation of NPM/B23 during early TPA-induced megakaryocytic differentiation of K562 cells, K562 cells were treated with TPA in the presence of the PKC isozyme-selective inhibitors, GF109203X and Gö 6976, or MEK1 inhibitor, PD98059. The decrease of NPM/B23 protein in the TPA-treated K562 cells was blocked by GF109203X but not by Gö 6976, suggesting the involvement of novel PKCs in the downregulation of NPM/B23 during TPA-induced megakaryocytic differentiation of K562 cells. The application of MEK1 inhibitor PD98059 upon TPA treatment blocked the TPA-induced decrease of NPM/B23 protein and aborted the megakaryocytic differentiation but not to break through the cell growth arrest. Unlike NPM/B23, the degradation of nucleolin in the TPA-treated K562 cells could not be blocked by PD98059 while the TPA-induced megakaryocytic differentiation was abrogated. The decrease of NPM/B23 protein seems to be more correlated with the novel PKC-MAPK-induced megakaryocytic differentiation than another nucleolar protein, nucleolin. Taken together, our results indicated that novel PKC-MAPK pathway was required for the decrease of NPM/B23 during TPA-induced megakaryocytic differentiation.
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Affiliation(s)
- Chih-Chung Chou
- Department and Graduate School of Biotechnology, Fooyin University, 151 Chin-Hsueh, Rd., Ta-Liao Hsiang, Kaohsiung Hsien, 831 Taiwan, ROC
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Hernandez-Verdun D. The nucleolus: a model for the organization of nuclear functions. Histochem Cell Biol 2006; 126:135-48. [PMID: 16835752 DOI: 10.1007/s00418-006-0212-3] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2006] [Indexed: 10/24/2022]
Abstract
Nucleoli are the prominent contrasted structures of the cell nucleus. In the nucleolus, ribosomal RNAs (rRNAs) are synthesized, processed and assembled with ribosomal proteins. The size and organization of the nucleolus are directly related to ribosome production. The organization of the nucleolus reveals the functional compartmentation of the nucleolar machineries that depends on nucleolar activity. When this activity is blocked, disrupted or impossible, the nucleolar proteins have the capacity to interact independently of the processing activity. In addition, nucleoli are dynamic structures in which nucleolar proteins rapidly associate and dissociate with nucleolar components in continuous exchanges with the nucleoplasm. At the time of nucleolar assembly, the processing machineries are recruited in a regulated manner in time and space, controlled by different kinases and form intermediate structures, the prenucleolar bodies. The participation of stable pre-rRNAs in nucleolar assembly was demonstrated after mitosis and during development but this is an intriguing observation since the role of these pre-rRNAs is presently unknown. A brief report on the nucleolus and diseases is proposed as well as of nucleolar functions different from ribosome biogenesis.
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Affiliation(s)
- Danièle Hernandez-Verdun
- Nuclei and Cell Cycle, Institut Jacques Monod, CNRS, Université Paris VI, Université Paris VII, 2 place Jussieu, 75251 Paris Cedex 05, France.
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Díez JL, Vilariño VR, Medina FJ, Morcillo G. Nucleolar localization of a reverse transcriptase related to telomere maintenance in Chironomus (Diptera). Histochem Cell Biol 2006; 126:445-52. [PMID: 16607537 DOI: 10.1007/s00418-006-0179-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
A growing number of cellular processes originally thought not to involve the nucleolus now seem to be associated with this organelle. In recent years, a variety of RNAs and proteins with no apparent function in ribosome genesis have been discovered in this nuclear compartment. This paper reports the presence in the nucleolus of a reverse transcriptase (RT) previously found to be associated with telomeres in Chironomus. Immunofluorescence detection using a specific antibody against conserved domains shared by RTs showed a distinct pattern of staining in the giant nucleoli of polytenized cells. This nucleolar localization was confirmed in a number of larval tissues and embryonic cells of Chironomus thummi and C. pallidivitatus; its distribution showed a definite necklace pattern that did not completely colocalize with fibrillarin or nucleolin and appeared to be different to that of typical nucleolar components. There is evidence that both telomerase RT and RNA template subunits are present in the nucleoli of mammalian and yeast cells. However, chironomids do not have typical telomeres or telomerase. As in other Diptera, telomeres lack the short, simple repeats maintained by telomerase and instead have more complex sequences in the range of hundreds of nucleotides. It has been suggested that the RT associated with these telomeres might be involved in their maintenance, perhaps involving a mechanism similar to that of telomerase retrotranscription and retrotransposition in Drosophila. The present results indicate that the putative Chironomus telomere elongation machinery and telomerase share a nucleolar localization. This reinforces the idea that nucleoli are functionally linked to telomere maintenance irrespective of the differences in their molecular organization and therefore in the strategy adopted for their elongation.
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Affiliation(s)
- José Luis Díez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain.
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34
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Louvet E, Junéra HR, Berthuy I, Hernandez-Verdun D. Compartmentation of the nucleolar processing proteins in the granular component is a CK2-driven process. Mol Biol Cell 2006; 17:2537-46. [PMID: 16540521 PMCID: PMC1474808 DOI: 10.1091/mbc.e05-10-0923] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
To analyze the compartmentation of nucleolar protein complexes, the mechanisms controlling targeting of nucleolar processing proteins onto rRNA transcription sites has been investigated. We studied the reversible disconnection of transcripts and processing proteins using digitonin-permeabilized cells in assays capable of promoting nucleolar reorganization. The assays show that the dynamics of nucleolar reformation is ATP/GTP-dependent, sensitive to temperature, and CK2-driven. We further demonstrate the role of CK2 on the rRNA-processing protein B23. Mutation of the major CK2 site on B23 induces reorganization of nucleolar components that separate from each other. This was confirmed in assays using extracts containing B23 mutated in the CK2-binding sites. We propose that phosphorylation controls the compartmentation of the rRNA-processing proteins and that CK2 is involved in this process.
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Affiliation(s)
- Emilie Louvet
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University Paris VI and Paris VII, 75251 Paris Cedex 05, France
| | - Henriette Roberte Junéra
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University Paris VI and Paris VII, 75251 Paris Cedex 05, France
| | - Isabelle Berthuy
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University Paris VI and Paris VII, 75251 Paris Cedex 05, France
| | - Danièle Hernandez-Verdun
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University Paris VI and Paris VII, 75251 Paris Cedex 05, France
- Address correspondence to: D. Hernandez-Verdun (
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Abstract
The nucleolus, a large nuclear domain, is the ribosome factory of the cells. Ribosomal RNAs are synthesized, processed and assembled with ribosomal proteins in the nucleolus, and the ribosome subunits are then transported to the cytoplasm. In this review, the structural organization of the nucleolus and the dynamics of the nucleolar proteins are discussed in an attempt to link both information. By electron microscopy, three main nucleolar components corresponding to different steps of ribosome biogenesis are identified and the nucleolar organization reflects its activity. Time-lapse videomicroscopy and fluorescent recovery after photobleaching (FRAP) demonstrate that mobility of GFP-tagged nucleolar proteins is slower in the nucleolus than in the nucleoplasm. Fluorescent recovery rates change with inhibition of transcription, decreased temperature and depletion of ATP, indicating that recovery is correlated with cell activity. At the exit of mitosis, the nucleolar processing machinery is first concentrated in prenucleolar bodies (PNBs). The dynamics of the PNBs suggests a steady state favoring residence of processing factors that are then released in a control- and time-dependent manner. Time-lapse analysis of fluorescence resonance energy transfer demonstrates that processing complexes are formed in PNBs. Finally, the nucleolus appears at the center of several trafficking pathways in the nucleus.
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Affiliation(s)
- Danièle Hernandez-Verdun
- Nuclei and Cell Cycle, Institut Jacques Monod, CNRS, Université Paris VI et Paris VII, 2 place Jussieu, 75251, Paris, Cedex 05, France.
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36
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Yang H, Henning D, Valdez BC. Functional interaction between RNA helicase II/Gu(alpha) and ribosomal protein L4. FEBS J 2005; 272:3788-802. [PMID: 16045751 DOI: 10.1111/j.1742-4658.2005.04811.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
RNA helicase II/Gu(alpha) is a multifunctional nucleolar protein involved in ribosomal RNA processing in Xenopus laevis oocytes and mammalian cells. Downregulation of Gu(alpha) using small interfering RNA (siRNA) in HeLa cells resulted in 80% inhibition of both 18S and 28S rRNA production. The mechanisms underlying this effect remain unclear. Here we show that in mammalian cells, Gu(alpha) physically interacts with ribosomal protein L4 (RPL4), a component of 60S ribosome large subunit. The ATPase activity of Gu(alpha) is important for this interaction and is also necessary for the function of Gu(alpha) in the production of both 18S and 28S rRNAs. Knocking down RPL4 expression using siRNA in mouse LAP3 cells inhibits the production of 47/45S, 32S, 28S, and 18S rRNAs. This inhibition is reversed by exogenous expression of wild-type human RPL4 protein but not the mutant form lacking Gu(alpha)-interacting motif. These observations have suggested that the function of Gu(alpha) in rRNA processing is at least partially dependent on its ability to interact with RPL4.
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Affiliation(s)
- Hushan Yang
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
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37
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Desterro JMP, Keegan LP, Jaffray E, Hay RT, O'Connell MA, Carmo-Fonseca M. SUMO-1 modification alters ADAR1 editing activity. Mol Biol Cell 2005; 16:5115-26. [PMID: 16120648 PMCID: PMC1266412 DOI: 10.1091/mbc.e05-06-0536] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
We identify ADAR1, an RNA-editing enzyme with transient nucleolar localization, as a novel substrate for sumoylation. We show that ADAR1 colocalizes with SUMO-1 in a subnucleolar region that is distinct from the fibrillar center, the dense fibrillar component, and the granular component. Our results further show that human ADAR1 is modified by SUMO-1 on lysine residue 418. An arginine substitution of K418 abolishes SUMO-1 conjugation and although it does not interfere with ADAR1 proper localization, it stimulates the ability of the enzyme to edit RNA both in vivo and in vitro. Moreover, modification of wild-type recombinant ADAR1 by SUMO-1 reduces the editing activity of the enzyme in vitro. Taken together these data suggest a novel role for sumoylation in regulating RNA-editing activity.
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Affiliation(s)
- Joana M P Desterro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
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Louvet E, Junéra HR, Le Panse S, Hernandez-Verdun D. Dynamics and compartmentation of the nucleolar processing machinery. Exp Cell Res 2004; 304:457-70. [PMID: 15748891 DOI: 10.1016/j.yexcr.2004.11.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Revised: 11/08/2004] [Accepted: 11/10/2004] [Indexed: 11/17/2022]
Abstract
In active nucleoli, machineries involved in the biogenesis of ribosomal RNAs (rRNAs) are compartmentalized. The late rRNA processing proteins are localized in the granular component (GC). Here we investigate the behavior of these proteins when production of 28S is impaired and when this blockage is reversed. The 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) provokes dispersion of rDNA clusters and we demonstrate that DRB induces disconnection of the late rRNA processing proteins from the transcription sites. These processing proteins are still associated in independent masses without detectable 28S rRNA, indicating that compartmentation of the late rRNA processing machinery is not necessarily linked to processing activity. Removing DRB reverses this disconnection and promotes rRNA processing. Nucleolar reformation occurs in two successive steps, dynamic recruitment to transcription sites of the processing proteins, followed by rDNA compaction. We demonstrate that both steps are sensitive to temperature, suggesting an energy-dependent process. Traffic of processing proteins analyzed by fluorescence recovery after photobleaching is similar in masses disconnected from transcription sites and in the granular component of the active nucleolus. This suggests that protein dynamics and interactions, and not only their processing activity, determine compartmentation of the nucleolar machineries.
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MESH Headings
- Active Transport, Cell Nucleus/physiology
- Cell Compartmentation/drug effects
- Cell Compartmentation/physiology
- Cell Nucleolus/drug effects
- Cell Nucleolus/metabolism
- Cell Nucleolus/ultrastructure
- Dichlororibofuranosylbenzimidazole/pharmacology
- HeLa Cells
- Humans
- Microscopy, Electron, Transmission
- Nonlinear Dynamics
- Nuclear Proteins/drug effects
- Nuclear Proteins/metabolism
- Nucleic Acid Synthesis Inhibitors/pharmacology
- Protein Transport/physiology
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal, 28S/drug effects
- RNA, Ribosomal, 28S/metabolism
- Temperature
- Transcription, Genetic/drug effects
- Transcription, Genetic/physiology
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Affiliation(s)
- Emilie Louvet
- Institut Jacques Monod, CNRS, University Paris VI and Paris VII, 2 place Jussieu, 75251 Paris Cedex 05, France
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Niedick I, Froese N, Oumard A, Mueller PP, Nourbakhsh M, Hauser H, Köster M. Nucleolar localization and mobility analysis of the NF-κB repressing factor NRF. J Cell Sci 2004; 117:3447-58. [PMID: 15226370 DOI: 10.1242/jcs.01129] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
NF-κB plays a central role in mediating pathogen and cytokine-stimulated gene transcription. NF-κB repressing factor (NRF) has been shown to interact with specific negative regulatory DNA elements (NRE) to mediate transcriptional repression by inhibition of the NF-κB activity at certain promoters. mRNA ablation experiments demonstrated that the trans-acting NRF protein is involved in constitutive but not post-stimulated silencing of IFN-β, IL-8 and iNOS genes by binding to cis-acting NRE elements in their promoters.
We have examined the subcellular localization and mobility of the NRF protein. Since neither tagging nor overexpression perturbs NRF localization the GFP-tagged protein was used for detailed localization and mobility studies. Owing to an N-terminal nuclear localization sequence, all NRF fragments that contain this signal show a constitutive nuclear accumulation. C-terminal NRF fragments also localize to the nucleus although no canonical NLS motifs were detected. Full-length NRF is highly enriched in nucleoli and only a small fraction of NRF is found in the nucleoplasm and cytoplasm. This relationship was found to be independent of the protein expression rate. FRAP analysis proved to be a sensitive method to determine protein mobility and made it possible to differentiate between the NRF protein fragments. Nucleolar localization correlated inversely with mobility. The data demonstrate that a series of neighboring fragments in a large central domain of the protein contribute to the strong nucleolar affinity. These properties were not altered by viral infection or LPS treatment. Several sequence motifs for RNA binding were predicted by computer-mediated databank searches. We found that NRF binds to double stranded RNA (dsRNA). This property mapped to several NRF fragments which correlate with the nucleolar affinity domain. Since treatment with actinomycin D releases NRF from nucleoli the identified RNA binding motifs might act as nucleolar localization signals.
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Affiliation(s)
- Ina Niedick
- Department of Gene Regulation and Differentiation, German Research Center for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany
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Dimario PJ. Cell and Molecular Biology of Nucleolar Assembly and Disassembly. INTERNATIONAL REVIEW OF CYTOLOGY 2004; 239:99-178. [PMID: 15464853 DOI: 10.1016/s0074-7696(04)39003-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleoli disassemble in prophase of the metazoan mitotic cycle, and they begin their reassembly (nucleologenesis) in late anaphase?early telophase. Nucleolar disassembly and reassembly were obvious to the early cytologists of the eighteenth and nineteenth centuries, and although this has lead to a plethora of literature describing these events, our understanding of the molecular mechanisms regulating nucleolar assembly and disassembly has expanded immensely just within the last 10-15 years. We briefly survey the findings of nineteenth-century cytologists on nucleolar assembly and disassembly, followed by the work of Heitz and McClintock on nucleolar organizers. A primer review of nucleolar structure and functions precedes detailed descriptions of modern molecular and microscopic studies of nucleolar assembly and disassembly. Nucleologenesis is concurrent with the reinitiation of rDNA transcription in telophase. The perichromosomal sheath, prenucleolar bodies, and nucleolar-derived foci serve as repositories for nucleolar processing components used in the previous interphase. Disassembly of the perichromosomal sheath along with the dynamic movements and compositional changes of the prenucleolar bodies and nucleolus-derived foci coincide with reactivation of rDNA synthesis within the chromosomal nucleolar organizers during telophase. Nucleologenesis is considered in various model organisms to provide breadth to our understanding. Nucleolar disassembly occurs at the onset of mitosis primarily as a result of the mitosis-specific phosphorylation of Pol I transcription factors and processing components. Although we have learned much regarding nucleolar assembly and disassembly, many questions still remain, and these questions are as vibrant for us today as early questions were for nineteenth- and early twentieth-century cytologists.
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Affiliation(s)
- Patrick J Dimario
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803-1715, USA
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41
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Motta MCM, de Souza W, Thiry M. Immunocytochemical detection of DNA and RNA in endosymbiont-bearing trypanosomatids. FEMS Microbiol Lett 2003; 221:17-23. [PMID: 12694905 DOI: 10.1016/s0378-1097(03)00087-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Research about the kinetoplast of trypanosomatids has yielded valuable information about the organization of extranuclear structure. However, the ultrastructural localization of nucleic acids within these protozoa remains uncertain. We have applied cytochemical and immunocytochemical approaches to precisely identify DNA and RNA in lower endosymbiont-bearing trypanosomatids. Using the Terminal deoxynucleotidyl Transferase (TdT) immunogold technique, we showed that nuclear DNA is seen associated with the nuclear envelope during the trypanosomatid cell cycle. By combining the TdT technique with the acetylation method, which improves the contrast between structures containing fibrils and granules, we have demonstrated that the nucleolus of endosymbiont-bearing trypanosomatids is composed of two constituents: a granular component and a DNA-positive fibrillar zone. Moreover, we revealed that DNA of endosymbiotic bacteria consisted of electron-dense filaments which are usually in close contact with the prokaryote envelope. Using a Lowicryl post-embedding immunogold labeling procedure with anti-RNA antibodies, we showed the presence of RNA not only over the cytoplasm, the interchromatin spaces and the nucleolus, but also over the kinetoplast and virus-like particles present in Crithidia desouzai.
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Affiliation(s)
- Maria Cristina M Motta
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, CCS, Bloco G, Ilha do Fundão, 21940-900 Rio de Janeiro, RJ, Brazil.
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42
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Abstract
The nucleolus is a large nuclear domain and the site of ribosome biogenesis. It is also at the parting of the ways of several cellular processes, including cell cycle progression, gene silencing, and ribonucleoprotein complex formation. Consequently, a functional nucleolus is crucial for cell survival. Recent investigations of nucleolar assembly during the cell cycle and during embryogenesis have provided an integrated view of the dynamics of this process. Moreover, they have generated new ideas about cell cycle control of nucleolar assembly, the dynamics of the delivery of the RNA processing machinery, the formation of prenucleolar bodies, the role of precursor ribosomal RNAs in stabilizing the nucleolar machinery and the fact that nucleolar assembly is completed by cooperative interactions between chromosome territories. This has opened a new area of research into the dynamics of nuclear organization and the integration of nuclear functions.
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Affiliation(s)
- Danièle Hernandez-Verdun
- CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France.
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43
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Olson MOJ, Hingorani K, Szebeni A. Conventional and nonconventional roles of the nucleolus. INTERNATIONAL REVIEW OF CYTOLOGY 2002; 219:199-266. [PMID: 12211630 PMCID: PMC7133188 DOI: 10.1016/s0074-7696(02)19014-0] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As the most prominent of subnuclear structures, the nucleolus has a well-established role in ribosomal subunit assembly. Additional nucleolar functions, not related to ribosome biogenesis, have been discovered within the last decade. Built around multiple copies of the genes for preribosomal RNA (rDNA), nucleolar structure is largely dependent on the process of ribosome assembly. The nucleolus is disassembled during mitosis at which time preribosomal RNA transcription and processing are suppressed; it is reassembled at the end of mitosis in part from components preserved from the previous cell cycle. Expression of preribosomal RNA (pre-rRNA) is regulated by the silencing of individual rDNA genes via alterations in chromatin structure or by controlling RNA polymerase I initiation complex formation. Preribosomal RNA processing and posttranscriptional modifications are guided by a multitude of small nucleolar RNAs. Nearly completed ribosomal subunits are exported to the cytoplasm by an established nuclear export system with the aid of specialized adapter molecules. Some preribosomal and nucleolar components are transiently localized in Cajal bodies, presumably for modification or assembly. The nonconventional functions of nucleolus include roles in viral infections, nuclear export, sequestration of regulatory molecules, modification of small RNAs, RNP assembly, and control of aging, although some of these functions are not well established. Additional progress in defining the mechanisms of each step in ribosome biogenesis as well as clarification of the precise role of the nucleolus in nonconventional activities is expected in the next decade.
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Affiliation(s)
- Mark O J Olson
- Department of Biochemistry, University of Mississippi Medical Center, Jackson 39216, USA
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44
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Verheggen C, Le Panse S, Almouzni G, Hernandez-Verdun D. Maintenance of nucleolar machineries and pre-rRNAs in remnant nucleolus of erythrocyte nuclei and remodeling in Xenopus egg extracts. Exp Cell Res 2001; 269:23-34. [PMID: 11525636 DOI: 10.1006/excr.2001.5304] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The nuclear functions in erythrocytes are almost completely extinct. There is no RNA polymerase I transcription, although a remnant nucleolar structure is still present. The remnant nucleolus of Xenopus laevis erythrocytes maintains a morphologically organized structure, nearly exclusively fibrillar. In this inactive nucleolar remnant, we revealed the presence of a modified form of transcription factor UBF. Several proteins of the processing machinery such as fibrillarin, nucleolin and B23/NO38, snoRNAs U3 and U8, and partially processed preribosomal RNAs colocalized in these remnant structures. Attempts to reprogram these erythrocyte nuclei in Xenopus egg extract showed that import of several nucleolar proteins was induced while the nucleolar remnant was disorganized. UBF became abundant and showed a necklace-like distribution on the decondensed ribosomal genes. Fibrillarin, nucleolin, and snoRNAs U3 and U8, also largely imported from the extract, were associated in large prenuclear bodies scattered in the nucleoplasm. B23/NO38 was present in different small bodies formed only in the most decondensed nuclei. In these remodeled erythrocyte nuclei, there was no imported preribosomal RNA and the initial presence of a residual nucleolar structure containing several partners of ribosome biogenesis was not sufficient to promote reassembly of newly imported nucleolar machineries. These nuclei, which reproduce the early events of nucleogenesis are also transcriptionally silent and thus compare to the early embryonic nuclei of Xenopus laevis.
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Affiliation(s)
- C Verheggen
- Institut Jacques Monod, UMR 7592, Paris, France
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45
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Seither P, Iben S, Thiry M, Grummt I. PAF67, a novel protein that is associated with the initiation-competent form of RNA polymerase I. Biol Chem 2001; 382:1163-70. [PMID: 11592397 DOI: 10.1515/bc.2001.146] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Mammalian RNA polymerase I (Pol I) is a multisubunit enzyme that is decorated with accessory proteins, termed PAFs (polymerase-associated factors). The presence or absence of distinct PAFs may account for the functional differences of distinct fractions of cellular Pol I, and suggests that PAFs could be targets of regulatory pathways. Here we describe and functionally characterize PAF67, a novel 67 kDa protein that is tightly associated with a subpopulation of cellular Pol I. Both PAF67-containing and -deficient Pol I transcribe non-specific templates with similar efficiency, however, only the enzyme that contains PAF67 is capable of specifically transcribing rDNA templates. PAF67 co-localizes with Pol I in the nucleolus at sites of active rDNA transcription, indicating that PAF67 serves a role in rDNA transcription initiation. The results suggest that association of PAF67 with the 'core' enzyme endows Pol I with the capability to assemble into a productive transcription initiation complex at the rDNA promoter.
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Affiliation(s)
- P Seither
- German Cancer Research Center, Molecular Biology of the Cell II, Heidelberg
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46
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Baran V, Brochard V, Renard JP, Flechon JE. Nopp 140 involvement in nucleologenesis of mouse preimplantation embryos. Mol Reprod Dev 2001; 59:277-84. [PMID: 11424213 DOI: 10.1002/mrd.1032] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
As it was shown earlier, resumption of rRNA transcription in early mouse embryo is localized in the peripheral region of nucleolus precursor body/NPB/during the two-cell stage. Recently, nucleolar phosphoprotein Nopp140 was presented to shuttle between the nucleolus and cytoplasm as chaperone of snoRNPs. Nopp140 interacts with RNA polymerase I in nucleolus and also accumulates in CBs, suggesting a pathway between the two organelles. The aim of the study was to describe the changing location of Nopp140 during the first cleavage stages of mouse embryos and its re-location after inhibition of rRNA synthesis with actinomycin D. Light microscope immunocytochemical staining showed Nopp140 in the periphery of NPBs before activation of rDNA transcription and in addition confirmed its localization in CBs. Immunolabelling with antibodies against RNA Pol I and UBF gave co-localization of these proteins, implicating that Nopp140 may actively participate to rDNA transcription. We suggest that fundamental differences in molecular organization of rDNA synthesis and postranscriptional processes between cycling somatic and pre-implantation embryonic cells may be in selective transport of transcription and/or processing-complexes of proteins to the nucleolar organizer regions (NOR). Mol. Reprod. Dev. 59:277-284, 2001.
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Affiliation(s)
- V Baran
- Institute of Animal Physiology, SAS, Kosice, Slovakia.
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47
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Savino TM, Gébrane-Younès J, De Mey J, Sibarita JB, Hernandez-Verdun D. Nucleolar assembly of the rRNA processing machinery in living cells. J Cell Biol 2001; 153:1097-110. [PMID: 11381093 PMCID: PMC2174343 DOI: 10.1083/jcb.153.5.1097] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
To understand how nuclear machineries are targeted to accurate locations during nuclear assembly, we investigated the pathway of the ribosomal RNA (rRNA) processing machinery towards ribosomal genes (nucleolar organizer regions [NORs]) at exit of mitosis. To follow in living cells two permanently transfected green fluorescence protein-tagged nucleolar proteins, fibrillarin and Nop52, from metaphase to G1, 4-D time-lapse microscopy was used. In early telophase, fibrillarin is concentrated simultaneously in prenucleolar bodies (PNBs) and NORs, whereas PNB-containing Nop52 forms later. These distinct PNBs assemble at the chromosome surface. Analysis of PNB movement does not reveal the migration of PNBs towards the nucleolus, but rather a directional flow between PNBs and between PNBs and the nucleolus, ensuring progressive delivery of proteins into nucleoli. This delivery appeared organized in morphologically distinct structures visible by electron microscopy, suggesting transfer of large complexes. We propose that the temporal order of PNB assembly and disassembly controls nucleolar delivery of these proteins, and that accumulation of processing complexes in the nucleolus is driven by pre-rRNA concentration. Initial nucleolar formation around competent NORs appears to be followed by regroupment of the NORs into a single nucleolus 1 h later to complete the nucleolar assembly. This demonstrates the formation of one functional domain by cooperative interactions between different chromosome territories.
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Affiliation(s)
| | | | - Jan De Mey
- Institut Curie/Section de Recherche, UMR 146, 91405 Orsay, France
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48
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Fair T, Hyttel P, Lonergan P, Boland MP. Immunolocalization of nucleolar proteins during bovine oocyte growth, meiotic maturation, and fertilization. Biol Reprod 2001; 64:1516-25. [PMID: 11319160 DOI: 10.1095/biolreprod64.5.1516] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
During the growth phase of the bovine oocyte transcripts, polypeptides and ribosomes are accumulated in the oocyte to drive and sustain future meiotic maturation, fertilization, and early embryonic development. The oocyte also furnishes the early embryo with the components required to establish a functional transcriptionally active nucleolus at the time of maternal embryonic transition. The aim of the present study was to describe the behavior of key components of the nucleolus. The temporal localization of nucleolar proteins fibrillarin, nucleophosmin, nucleolin, RNA polymerase I (RNA pol I), topoisomerase I, upstream binding factor (UBF), and coilin 5P10 was investigated in growing and fully grown immature bovine oocytes during in vitro maturation and during the first postfertilization cell cycle using whole-mount immunocytochemistry and confocal microscopy. During the oocyte growth phase, fibrillarin, nucleophosmin, nucleolin, RNA pol I, and UBF were localized to the oocyte nucleolus. On completion of the growth phase, nucleolin and nucleophosmin appeared to migrate to the periphery of the nucleolus and into the nucleoplasm, and the proportion of oocytes displaying RNA pol I localization had decreased. Topoisomerase I was not detected at any stage. Fibrillarin appeared to be localized to large foci within the nucleolus and/or nucleoplasm. Nucleophosmin and nucleolin labeling was characterized by a homogeneous signal over the nucleolus. RNA pol I and UBF were characterized by the localization of the antibodies to individual or clustered foci in the nucleolus and/or nucleoplasm. Following oocyte nucleus breakdown (ONBD), the proteins appeared to disperse into the cytoplasm. All proteins were undetectable during meiotic maturation and were not relocalized until 5-10 h postinsemination (hpi). UBF was localized to the fertilizing sperm head of most zygotes at 5 hpi. By 10 hpi, all proteins were detected in most oocytes displaying two pronuclei. Nucleolar protein localization was exclusive to or more abundant in one pronucleus up to 20 hpi; thereafter, the pattern was more evenly distributed. Fibrillarin, nucleophosmin, nucleolin, UBF, and Pol I are present in the nuclei of growing and fully grown bovine oocytes until ONBD. They reappear at the late telophase stage of meiosis II and continue to be present up to the first mitotic division of embryo development.
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Affiliation(s)
- T Fair
- Department of Animal Science & Production and The Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Lyons Research Farm, Newcastle, County Dublin, Ireland.
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49
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Dundr M, Misteli T, Olson MO. The dynamics of postmitotic reassembly of the nucleolus. J Cell Biol 2000; 150:433-46. [PMID: 10931858 PMCID: PMC2175201 DOI: 10.1083/jcb.150.3.433] [Citation(s) in RCA: 209] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2000] [Accepted: 06/09/2000] [Indexed: 12/13/2022] Open
Abstract
Mammalian cell nucleoli disassemble at the onset of M-phase and reassemble during telophase. Recent studies showed that partially processed preribosomal RNA (pre-rRNA) is preserved in association with processing components in the perichromosomal regions (PRs) and in particles called nucleolus-derived foci (NDF) during mitosis. Here, the dynamics of nucleolar reassembly were examined for the first time in living cells expressing fusions of the processing-related proteins fibrillarin, nucleolin, or B23 with green fluorescent protein (GFP). During telophase the NDF disappeared with a concomitant appearance of material in the reforming nuclei. Prenucleolar bodies (PNBs) appeared in nuclei in early telophase and gradually disappeared as nucleoli formed, strongly suggesting the transfer of PNB components to newly forming nucleoli. Fluorescence recovery after photobleaching (FRAP) showed that fibrillarin-GFP reassociates with the NDF and PNBs at rapid and similar rates. The reentry of processing complexes into telophase nuclei is suggested by the presence of pre-rRNA sequences in PNBs. Entry of specific proteins into the nucleolus approximately correlated with the timing of processing events. The mitotically preserved processing complexes may be essential for regulating the distribution of components to reassembling daughter cell nucleoli.
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Affiliation(s)
- Miroslav Dundr
- Department of Biochemistry, University of Mississippi Medical Center, Jackson Mississippi 39216
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Mark O.J. Olson
- Department of Biochemistry, University of Mississippi Medical Center, Jackson Mississippi 39216
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50
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Verheggen C, Almouzni G, Hernandez-Verdun D. The ribosomal RNA processing machinery is recruited to the nucleolar domain before RNA polymerase I during Xenopus laevis development. J Cell Biol 2000; 149:293-306. [PMID: 10769023 PMCID: PMC2175160 DOI: 10.1083/jcb.149.2.293] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/1999] [Accepted: 03/07/2000] [Indexed: 11/22/2022] Open
Abstract
Transcription and splicing of messenger RNAs are temporally and spatially coordinated through the recruitment by RNA polymerase II of processing factors. We questioned whether RNA polymerase I plays a role in the recruitment of the ribosomal RNA (rRNA) processing machinery. During Xenopus laevis embryogenesis, recruitment of the rRNA processing machinery to the nucleolar domain occurs in two steps: two types of precursor structures called prenucleolar bodies (PNBs) form independently throughout the nucleoplasm; and components of PNBs I (fibrillarin, nucleolin, and the U3 and U8 small nucleolar RNAs) fuse to the nucleolar domain before components of PNBs II (B23/NO38). This fusion process is independent of RNA polymerase I activity, as shown by actinomycin D treatment of embryos and by the lack of detectable RNA polymerase I at ribosomal gene loci during fusion. Instead, this process is concomitant with the targeting of maternally derived pre-rRNAs to the nucleolar domain. Absence of fusion was correlated with absence of these pre-rRNAs in nuclei where RNA polymerase II and III are inhibited. Therefore, during X. laevis embryogenesis, the recruitment of the rRNA processing machinery to the nucleolar domain could be dependent on the presence of pre-rRNAs, but is independent of either zygotic RNA polymerase I transcription or the presence of RNA polymerase I itself.
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Affiliation(s)
- Céline Verheggen
- Institut Jacques Monod, UMR 7592, 75251 Paris, France
- Institut Curie, Section de Recherche, UMR 144, 75248 Paris, France
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