The Nucleus Introduced
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P80-Coilin: a Component of Coiled Bodies and Interchromatin Granule- Associated Zones
Journal of Cell Science 108, 1143-1153 (1995) 1143 Printed in Great Britain © The Company of Biologists Limited 1995 p80-coilin: a component of coiled bodies and interchromatin granule- associated zones Francine Puvion-Dutilleul1,*, Sylvie Besse1, Edward K. L. Chan2, Eng M. Tan2 and Edmond Puvion1 1Laboratoire de Biologie et Ultrastructure du Noyau de l’UPR 9044 CNRS, BP 8, F-94801 Villejuif Cedex, France 2The Scripps Research Institute, W. M. Keck Autoimmune Disease Center, 10666 N. Torrey Pines Road, La Jolla, California 92037, USA *Author for correspondence SUMMARY We investigated at the electron microscope level the fate of the clusters of interchromatin granules and their associated the three intranuclear structures known to accumulate zones, which were all easily recognizable within the snRNPs, and which correspond to the punctuate immuno- residual nuclear ribonucleoprotein network, was unmodi- fluorescent staining pattern (the coiled bodies, the clusters fied. The data indicate, therefore, that the loosening of interchromatin granules and the interchromatin procedure as well as the high salt extraction procedure granule-associated zones) after exposure to either a low salt preserve the snRNA content of all three spliceosome medium which induces a loosening and partial spreading component-accumulation sites and reveal that interchro- of nucleoprotein fibers or a high ionic strength salt medium matin granule-associated zones are elements of the nuclear and subsequent DNase I digestion, in order to obtain DNA- matrix. The p80-coilin content of coiled bodies was also depleted nuclear matrices. The loosened clusters of inter- preserved whatever the salt treatment used. An intriguing chromatin granules and the coiled bodies could no longer new finding is the detection of abundant p80-coilin within be distinguished from surrounding nucleoprotein fibers the interchromatin granule-associated zones, both before solely by their structure, but constituents of the clusters of and after either low or high salt treatment of cells. -
NPM/B23: the Effector of CDK2 in the Control of Centrosome Duplication and Mrna Processing
UNIVERSITY OF CINCINNATI Date: October 7th, 2004 I, ________________Yukari Tokuyama___________________________, hereby submit this work as part of the requirements for the degree of: Doctor of Philosophy in: Cell and Molecular Biology It is entitled: NPM/B23: The Effector of CDK2 in the Control of Centrosome Duplication and mRNA Processing This work and its defense approved by: Chair: Kenji Fukasawa, Ph.D. Robert W. Brackenbury, Ph.D. Wallace S. Ip, Ph.D. Erik S. Knudsen, Ph.D. Yolanda Sanchez, Ph.D. NPM/B23: THE EFFECTOR OF CDK2 IN THE CONTROL OF CENTROSOME DUPLICATION AND mRNA PROCESSING A dissertation submitted to the Division of Research and Advanced Studies of the University of Cincinnati in partial fulfillment of the requirements for the degree of DOCTORATE OF PHILOSOPHY (Ph.D.) In the Department of Cell Biology, Neurobiology, and Anatomy of the College of Medicine 2004 by Yukari Tokuyama B.S. Texas A&M University, 1998 Committee Chair: Kenji Fukasawa, Ph.D. Robert W. Brackenbury, Ph.D. Wallace S. Ip, Ph.D. Erik S. Knudsen, Ph.D. Yolanda Sanchez, Ph.D. Abstract Nucleophosmin (NPM/B23) is a phosphoprotein predominantly localized in the nucleolus, and is believed to function in ribosome assembly, cytonuclear shuttling, and molecular chaperoning. Here we report novel functions of NPM/B23 in initiation of centrosome duplication and mRNA processing. The centrosome, a major microtubule organizing center of cells, directs the formation of bipolar mitotic spindles, which is essential for proper chromosome segregation to daughter cells. Cancer cells frequently contain abnormal numbers of centrosomes suggesting that centrosome amplification is the major contributing factor for chromosome instability. -
Visualization of Cell Structure by Atomic Force Microscopy
MOJ Anatomy & Physiology Mini Review Open Access Visualization of cell structure by atomic force microscopy Abstract Volume 3 Issue 5 - 2017 Cell structure has been extensively studied by light and electron microscopy. However, María de Lourdes Segura-Valdez,1 Alma there are relatively few papers on the study of internal cell structure with the atomic force 2 1 microscope. In this mini review, efforts to visualize and analyze inner cell structure with Zamora-Cura, Luis F Jiménez-García 1Department of Cell Biology, Universidad Nacional Autónoma the atomic force microscope are here presented, using the technique for sample preparation de México (UNAM), México derived from the standard transmission electron microscopy. Semithin sections of epon 2National Institute of Genomic Medicine, México embedded samples mounted on glass slides are scanned with a microscope working on contact or intermittent modes. The surface of sections revealed internal cell structure. Animal Correspondence: Luis F Jiménez García, Laboratorio de and plant cells show structures as nuclei, nucleoli, chromatin, cell wall, mitochondria. These Nanobiología Celular Departamento de Biología Celular, works opens up the perspective to analyze these organelles and structures at a nanoscale Universidad Nacional Autónoma de México (UNAM), Circuito under liquid physiological conditions. Exterior, C.U., 04510, Cd. Mx., México, Tel (55)56224988, Fax (55)56224828, Email [email protected] Keywords: atomic force microscopy, cell structure, nanoscale Received: December 27, 2016 | Published: June 01, 2017 Introduction In plants, cell wall was a marker to recognize plant cell, and structure within. However, animal cell were more difficult to visualize. Using 1 Since its invention in 1986 atomic force microscopy (AFM) has tapping mode on Hep2 cells, images of cell nuclei were obtained and been used to study properties of surface of materials at the nanoscale. -
397 M. Pavelka, J. Roth, Functional Ultrastructure: Atlas of Tissue Biology and Pathology, Third Edition, DOI 10.1007/978-3-7091
Index A Blood , 380–394 Actin fi laments , 38, 176, 184, 186, 196, 258, 340, 350, 352 basophilic granulocytes , 386 brush border , 176 eosinophilic granulocytes , 384 brush cell , 186 erythrocytes , 380 nuclear actin , 26 erythropoiesis , 380 Adhering junctions , 196, 226, 258, 290, 294, 350 lymphocytes , 390 Adipose tissue , 330, 332 monocytes , 388 brown , 332 neutrophilic granulocytes , 382 white , 330 reticulocytes , 380 Aggresomes , 52, 180 thrombocytes , 392, 394 Alport’s syndrome , 214 Blood–brain barrier , 358 Alveoli , 288 Bone , 336, 338 Amphisomes , 148 mineralization , 336 Amyloid fi brils , 326, 328 osteoblasts , 336 Amyloidosis , 326 osteoclasts , 338 Anchoring junctions , 196 osteocyte , 336 Anderson disease , 64 osteoid , 336 Annulate lamellae , 42 resorption , 338 Apomucin , 40 Bone marrow , 380, 392 Apoptosis , 30, 48, 148, 268 cells of the erythroid lineage , 380 Arterial wall , 300 megakaryocytes , 392 Articular cartilague , 334 Bowman’s layer , 324 Astrocytes , 356, 358, 368 Brefeldin A , 94, 96, 98 Atomic force microscopy , 24, 328 effect on retrograde transport of internalized WGA , 98 Autophagic cell death , 30 Golgi apparatus disassembly , 94, 96 Autophagy , 148, 150, 152 tubulation of Golgi apparatus and endosomes , 96 autolysosomes , 148 Brush border , 176, 188, 258, 262 autophagosomes , 148 Brush cell , 186 crinophagy , 226 cytosolic protein aggregates , 152 ER-phagy , 152 C mitophagy , 152 CADASIL. See Cerebral Autosomal Dominant Arteriopathy pexophagy , 150 (CADASIL) selective autophagy of cellular organelles -
Nuclear Speckles
Nuclear Speckles David L. Spector1 and Angus I. Lamond2 1Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724 2Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, MSI/WTB/JBC Complex Dow Street, Dundee DD1 5EH, United Kingdom Correspondence: [email protected], [email protected] Nuclear speckles, also known as interchromatin granule clusters, are nuclear domains enriched in pre-mRNA splicing factors, located in the interchromatin regions of the nucleo- plasm of mammalian cells. When observed by immunofluorescence microscopy, they usually appear as 20–50 irregularly shaped structures that vary in size. Speckles are dynamic structures, and their constituents can exchange continuously with the nucleoplasm and other nuclear locations, including active transcription sites. Studies on the composition, structure, and dynamics of speckles have provided an important paradigm for understanding the functional organization of the nucleus and the dynamics of the gene expression machinery. he mammalian cell nucleus is a highly com- compartments (Phair et al. 2000)” (Figs. 1 and Tpartmentalized yet extremely dynamic org- 2). The first detailed description of the nuclear anelle (reviewed in Misteli 2001a; Spector domains that we presently refer to as nuclear 2006; Zhao et al. 2009). Many nuclear factors speckles was reported by Santiago Ramo´ny are localized in distinct structures, such as Cajal in 1910 (Ramo´n y Cajal 1910; reviewed speckles, paraspeckles, nucleoli, Cajal bodies, in Lafarga et al. 2009). Ramo´n y Cajal used polycomb bodies, and promyelocytic leukemia acid aniline stains to identify structures he bodies and show punctate staining patterns referred to as “grumos hialinas” (literally “tran- when analyzed by indirect immunofluorescence slucent clumps”). -
Exploring Mammalian Genome Within Phase-Separated Nuclear Bodies: Experimental Methods and Implications for Gene Expression
G C A T T A C G G C A T genes Review Exploring Mammalian Genome within Phase-Separated Nuclear Bodies: Experimental Methods and Implications for Gene Expression Annick Lesne 1,2,*, Marie-Odile Baudement 1,3 , Cosette Rebouissou 1 and Thierry Forné 1,* 1 IGMM, Univ. Montpellier, CNRS, F-34293 Montpellier, France; [email protected] (M.-O.B.); [email protected] (C.R.) 2 Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, F-75252 Paris, France 3 Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway * Correspondence: [email protected] (A.L.); [email protected] (T.F.); Tel.: +33-434-359-682 (T.F.) Received: 6 November 2019; Accepted: 13 December 2019; Published: 17 December 2019 Abstract: The importance of genome organization at the supranucleosomal scale in the control of gene expression is increasingly recognized today. In mammals, Topologically Associating Domains (TADs) and the active/inactive chromosomal compartments are two of the main nuclear structures that contribute to this organization level. However, recent works reviewed here indicate that, at specific loci, chromatin interactions with nuclear bodies could also be crucial to regulate genome functions, in particular transcription. They moreover suggest that these nuclear bodies are membrane-less organelles dynamically self-assembled and disassembled through mechanisms of phase separation. We have recently developed a novel genome-wide experimental method, High-salt Recovered Sequences sequencing (HRS-seq), which allows the identification of chromatin regions associated with large ribonucleoprotein (RNP) complexes and nuclear bodies. -
RNA-Binding Proteins and the Complex Pathophysiology of ALS
International Journal of Molecular Sciences Review RNA-Binding Proteins and the Complex Pathophysiology of ALS Wanil Kim 1,†, Do-Yeon Kim 2,* and Kyung-Ha Lee 1,* 1 Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea; [email protected] 2 Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu 41940, Korea * Correspondence: [email protected] (D.-Y.K.); [email protected] (K.-H.L.); Tel.: +82-53-660-6880 (D.-Y.K.); +82-53-819-7743 (K.-H.L.) † Current Address: Department of Biochemistry, College of Medicine, Gyeongsang National University, Jinju 52828, Korea. Abstract: Genetic analyses of patients with amyotrophic lateral sclerosis (ALS) have identified disease- causing mutations and accelerated the unveiling of complex molecular pathogenic mechanisms, which may be important for understanding the disease and developing therapeutic strategies. Many disease-related genes encode RNA-binding proteins, and most of the disease-causing RNA or proteins encoded by these genes form aggregates and disrupt cellular function related to RNA metabolism. Disease-related RNA or proteins interact or sequester other RNA-binding proteins. Eventually, many disease-causing mutations lead to the dysregulation of nucleocytoplasmic shuttling, the dysfunction of stress granules, and the altered dynamic function of the nucleolus as well as other membrane- less organelles. As RNA-binding proteins are usually components of several RNA-binding protein complexes that have other roles, the dysregulation of RNA-binding proteins tends to cause diverse forms of cellular dysfunction. Therefore, understanding the role of RNA-binding proteins will help elucidate the complex pathophysiology of ALS. -
Disassembly of Interchromatin Granule Clusters Alters the Coordination of Transcription and Pre-Mrna Splicing
JCBArticle Disassembly of interchromatin granule clusters alters the coordination of transcription and pre-mRNA splicing Paula Sacco-Bubulya and David L. Spector Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 o examine the involvement of interchromatin granule speckles. Our data suggest that the protein–protein inter- clusters (IGCs) in transcription and pre-mRNA splicing actions responsible for the clustering of interchromatin gran- T in mammalian cell nuclei, the serine-arginine (SR) ules are disrupted when SR proteins are hyperphosphorylated protein kinase cdc2-like kinase (Clk)/STY was used as a tool to and stabilized when SR proteins are hypophosphorylated. manipulate IGC integrity in vivo. Both immunofluorescence Interestingly, cells without intact IGCs continue to synthesize and transmission electron microscopy analyses of cells nascent transcripts. However, both the accumulation of overexpressing Clk/STY indicate that IGC components are splicing factors at sites of pre-mRNA synthesis as well as completely redistributed to a diffuse nuclear localization, pre-mRNA splicing are dramatically reduced, demonstrating leaving no residual structure. Conversely, overexpression of that IGC disassembly perturbs coordination between a catalytically inactive mutant, Clk/STY(K190R), causes transcription and pre-mRNA splicing in mammalian cell retention of hypophosphorylated SR proteins in nuclear nuclei. Introduction Pre-mRNA splicing factors localize by immunofluorescence tors, and the hyperphosphorylated form of the large subunit microscopy to 20–50 irregularly shaped nuclear speckles set of RNA polymerase II (Bregman et al., 1995). The majority against a diffuse distribution within the nucleoplasm of of the protein constituents of IGCs have now been identi- mammalian cells (for reviews see Spector, 1993; Lamond fied (Mintz et al., 1999, and unpublished results), making it and Earnshaw, 1998). -
Electron Microscopy of Nuclear Nanoribonucleoproteins (Nanornps)
MOJ Anatomy & Physiology Mini Review Open Access Electron microscopy of nuclear nanoribonucleoproteins (nanoRNPs) Abstract Volume 7 Issue 1 - 2020 In the cell nucleus several ribonucleoproteins related to gene expression are present. The nucleolus, coiled bodies and other nuclear particles are among these structures. Particles Segura-Valdez ML, Mendoza-Sánchez AC, of nanometer size include perichromatin fibrils, perichromatin and Balbiani ring granules, García-Mauleón PMR, Agredano-Moreno LT, interchromatin granules and Lacandonia granules. All of them are involved in pre-messenger Jiménez-García LF RNA intranuclear metabolism. Previous and recent research suggests that these particles are Department of Cell Biology, Faculty of Sciences, National involved in transcription and processing of pre-messenger RNA within the cell nucleus. Autonomous University of Mexico (UNAM), México Keywords: Balbiani ring, cell nucleus, Lacandonia, microscopy, nucleolus, RNPs Correspondence: Luis F Jiménez-García, Cell Nanobiology Laboratory and Electron Microscopy Laboratory, Department of Cell Biology, National Autonomous University of Mexico (UNAM), Circuito Exterior, Ciudad Universitaria, Mexico City (CdMx), Coyoacán 04510, Mexico, Tel 555-622-498-8, Fax 555- 622-482-8, Email Received: January 24, 2020 | Published: February 04, 2020 Abbreviations: BRG, Balbiani ring granules; IGCs, Perichromatin fibrils (PFs) were described for the first time by interchromatin granules; LGs, lacandonia granules; nanoRNPs, Monneron & Bernhard7 in a number of mammalian -
In Vivo Analysis of the Stability and Transport of Nuclear Poly(A) + RNA Sui Huang, Thomas J
In Vivo Analysis of the Stability and Transport of Nuclear Poly(A) + RNA Sui Huang, Thomas J. Deerinck,* Mark H. EUisman,* and David L. Spector Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724; and * University of California at San Diego, Department of Neurosciences and San Diego Microscopy and Imaging Resource, La Jolla, California 92093 Abstract. We have studied the distribution of chromatin granule clusters along with pre-mRNA poly(A) + RNA in the mammalian cell nucleus and its splicing factors. This stable population of nuclear transport through nuclear pores by fluorescence and RNA may play an important role in nuclear function. electron microscopic in situ hybridization. Poly(A)+ Furthermore, we have observed that, in actively tran- RNA was detected in the nucleus as a speckled pattern scribing cells, the regions of poly(A) ÷ RNA which which includes interchromatin granule clusters and reached the nuclear pore complexes appeared as nar- perichromatin fibrils. When cells are fractionated by row concentrations of RNA suggesting a limited or detergent and salt extraction as well as DNase I diges- directed pathway of movement. All of the observed tion, the majority of the nuclear poly(A) + RNA was nuclear pores contained poly(A)÷ RNA staining sug- found to remain associated with the nonchromatin gesting that they are all capable of exporting RNA. In RNP-enriched fraction of the nucleus. After inhibition addition, we have directly visualized, for the first time of RNA polymerase H transcription for 5-10 h, a sta- in mammalian cells, the transport of poly(A) ÷ RNA ble population of poly(A)+ RNA remained in the nu- through the nuclear pore complexes. -
Proteomic Analysis of Interchromatin Granule Clusters Noriko Saitoh,*† Chris S
Molecular Biology of the Cell Vol. 15, 3876–3890, August 2004 Proteomic Analysis of Interchromatin Granule Clusters Noriko Saitoh,*† Chris S. Spahr,‡ Scott D. Patterson,‡ Paula Bubulya,* Andrew F. Neuwald,* and David L. Spector*§ *Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724; and ‡Amgen Center, Thousand Oaks, California 91320-1789 Submitted March 25, 2004; Accepted May 20, 2004 Monitoring Editor: Joseph Gall A variety of proteins involved in gene expression have been localized within mammalian cell nuclei in a speckled distribution that predominantly corresponds to interchromatin granule clusters (IGCs). We have applied a mass spec- trometry strategy to identify the protein composition of this nuclear organelle purified from mouse liver nuclei. Using this approach, we have identified 146 proteins, many of which had already been shown to be localized to IGCs, or their functions are common to other already identified IGC proteins. In addition, we identified 32 proteins for which only sequence information is available and thus these represent novel IGC protein candidates. We find that 54% of the identified IGC proteins have known functions in pre-mRNA splicing. In combination with proteins involved in other steps of pre-mRNA processing, 81% of the identified IGC proteins are associated with RNA metabolism. In addition, proteins involved in transcription, as well as several other cellular functions, have been identified in the IGC fraction. However, the predominance of pre-mRNA processing factors supports the proposed role of IGCs as assembly, modifi- cation, and/or storage sites for proteins involved in pre-mRNA processing. INTRODUCTION composition was characterized by mass spectrometry analysis. -
Functional Ultrastructure of the Excretory Gland Cell in Zoonotic Anisakids (Anisakidae, Nematoda)
cells Article Functional Ultrastructure of the Excretory Gland Cell in Zoonotic Anisakids (Anisakidae, Nematoda) Ivona Mladineo 1,*, Jerko Hrabar 1, Hrvoje Smodlaka 2, Lauren Palmer 3, Kristen Sakamaki 4, Kleoniki Keklikoglou 5 and Pantelis Katharios 5 1 Institute of Oceanography and Fisheries, 21000 Split, Croatia; [email protected] 2 Western University of Health Sciences, College of Veterinary Medicine, Pomona, CA 91766, USA; [email protected] 3 Marine Mammal Care Center Los Angeles, San Pedro, CA 90731, USA; [email protected] 4 Pacific Marine Mammal Center, Laguna Beach, CA 92651, USA; ksakamaki@pacificmmc.org 5 Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece; [email protected] (K.K.); [email protected] (P.K.) * Correspondence: [email protected]; Tel.: +385-21-408-047 Received: 30 October 2019; Accepted: 15 November 2019; Published: 17 November 2019 Abstract: Excretory and secretory products are crucial for parasite infectivity and host immunomodulation, but the functioning and ultrastructure of the excretory gland cell (EC) that produces these products are still scarcely understood and described. In light of growing reports on anisakiasis cases in Europe, we aimed to characterise the EC of larval Anisakis pegreffii and adult Pseudoterranova azarasi. In the latter, EC starts 0.85 mm from the head tip, measuring 1.936 0.564 mm. × Larval EC shows a long nucleus with thorn-like extravaginations toward the cytoplasm, numerous electron-dense and -lucent secretory granules spanning from the perinuclear to subplasmalemmal space, an elevated number of free ribosomes, small, spherical mitochondria with few cristae and a laminated matrix, small and few Golgi apparatuses, and few endoplasmic reticula, with wide cisternae complexes.