Nuclear Matrix
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PSF and P54nrb/Nono ^ Multi-Functional Nuclear Proteins
FEBS 26628 FEBS Letters 531 (2002) 109^114 View metadata, citation and similar papers at core.ac.uk brought to you by CORE Minireview provided by Elsevier - Publisher Connector PSF and p54nrb/NonO ^ multi-functional nuclear proteins Yaron Shav-Tal, Dov Ziporià Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel Received 30 May 2002; revised 10 September 2002; accepted 11 September 2002 First published online 7 October 2002 Edited by Takashi Gojobori glutamine-rich N-terminus of PSF might be involved in pro- Abstract Proteins are often referred to in accordance with the activity with which they were ¢rst associated or the organelle in tein^protein interactions [2]. nrb which they were initially identi¢ed. However, a variety of nu- p54 (human) and NonO (mouse) are highly homologous clear factors act in multiple molecular reactions occurring si- to the C-terminus of PSF (Fig. 1) [7,8]. Proteomics have iden- multaneously within the nucleus. This review describes the func- ti¢ed PSF and p54nrb/NonO in the nucleolus [9] and in asso- tions of the nuclear factors PSF (polypyrimidine tract-binding ciation with the nuclear membrane [10]. p54nrb/NonO was protein-associated splicing factor) and p54nrb/NonO. PSF was recently shown to be a component of a novel nuclear domain initially termed a splicing factor due to its association with the termed paraspeckles [11].TheDrosophila homolog of these nrb second step of pre-mRNA splicing while p54 /NonO was proteins is the NONA/BJ6 protein encoded by the no-on-tran- thought to participate in transcriptional regulation. -
Localization of Condensin Subunit XCAP-E in Interphase Nucleus, Nucleoid and Nuclear
1 Localization of condensin subunit XCAP-E in interphase nucleus, nucleoid and nuclear matrix of XL2 cells. Elmira Timirbulatova, Igor Kireev, Vladimir Ju. Polyakov, and Rustem Uzbekov* Division of Electron Microscopy, A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119899, Moscow, Russia. *Author for correspondence: telephone. 007-095-939-55-28; FAX 007-095-939-31-81 e-mail: [email protected] Key words: XCAP-E; nucleolus; condensin; nuclear matrix; Xenopus. Abbreviations: DAPI , 4’, 6 diamidino-2-phenylindole; DNP, deoxyribonucleoprotein; DRB, 5,6-dichloro-1b-d-ribofuranosylbenzimidazole; SMC, structural maintenance of chromosomes; XCAP-E, Xenopus chromosome associated protein E. 2 Abstract The Xenopus XCAP-E protein is a component of condensin complex In the present work we investigate its localization in interphase XL2 cells and nucleoids. We shown, that XCAP-E is localizes in granular and in dense fibrillar component of nucleolus and also in small karyoplasmic structures (termed “SMC bodies”). Extraction by 2M NaCl does not influence XCAP-E distribution in nucleolus and “SMC bodies”. DNAse I treatment of interphase cells permeabilized by Triton X-100 or nucleoids resulted in partial decrease of labeling intensity in the nucleus, whereas RNAse A treatment resulted in practically complete loss of labeling of nucleolus and “SMC bodies” labeling. In mitotic cells, however, 2M NaCl extraction results in an intense staining of the chromosome region although the labeling was visible along the whole length of sister chromatids, with a stronger staining in centromore region. The data are discussed in view of a hypothesis about participation of XCAP-E in processing of ribosomal RNA. -
Building the Interphase Nucleus: a Study on the Kinetics of 3D Chromosome Formation, Temporal Relation to Active Transcription, and the Role of Nuclear Rnas
University of Massachusetts Medical School eScholarship@UMMS GSBS Dissertations and Theses Graduate School of Biomedical Sciences 2020-07-28 Building the Interphase Nucleus: A study on the kinetics of 3D chromosome formation, temporal relation to active transcription, and the role of nuclear RNAs Kristin N. Abramo University of Massachusetts Medical School Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/gsbs_diss Part of the Bioinformatics Commons, Cell Biology Commons, Computational Biology Commons, Genomics Commons, Laboratory and Basic Science Research Commons, Molecular Biology Commons, Molecular Genetics Commons, and the Systems Biology Commons Repository Citation Abramo KN. (2020). Building the Interphase Nucleus: A study on the kinetics of 3D chromosome formation, temporal relation to active transcription, and the role of nuclear RNAs. GSBS Dissertations and Theses. https://doi.org/10.13028/a9gd-gw44. Retrieved from https://escholarship.umassmed.edu/ gsbs_diss/1099 Creative Commons License This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in GSBS Dissertations and Theses by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. BUILDING THE INTERPHASE NUCLEUS: A STUDY ON THE KINETICS OF 3D CHROMOSOME FORMATION, TEMPORAL RELATION TO ACTIVE TRANSCRIPTION, AND THE ROLE OF NUCLEAR RNAS A Dissertation Presented By KRISTIN N. ABRAMO Submitted to the Faculty of the University of Massachusetts Graduate School of Biomedical Sciences, Worcester in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSPOPHY July 28, 2020 Program in Systems Biology, Interdisciplinary Graduate Program BUILDING THE INTERPHASE NUCLEUS: A STUDY ON THE KINETICS OF 3D CHROMOSOME FORMATION, TEMPORAL RELATION TO ACTIVE TRANSCRIPTION, AND THE ROLE OF NUCLEAR RNAS A Dissertation Presented By KRISTIN N. -
Nuclear Domains
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Cold Spring Harbor Laboratory Institutional Repository CELL SCIENCE AT A GLANCE 2891 Nuclear domains dynamic structures and, in addition, nuclear pore complex has been shown to rapid protein exchange occurs between have a remarkable substructure, in which David L. Spector many of the domains and the a basket extends into the nucleoplasm. Cold Spring Harbor Laboratory, One Bungtown nucleoplasm (Misteli, 2001). An The peripheral nuclear lamina lies Road, Cold Spring Harbor, NY 11724, USA extensive effort is currently underway by inside the nuclear envelope and is (e-mail: [email protected]) numerous laboratories to determine the composed of lamins A/C and B and is biological function(s) associated with thought to play a role in regulating Journal of Cell Science 114, 2891-2893 (2001) © The Company of Biologists Ltd each domain. The accompanying poster nuclear envelope structure and presents an overview of commonly anchoring interphase chromatin at the The mammalian cell nucleus is a observed nuclear domains. nuclear periphery. Internal patches of membrane-bound organelle that contains lamin protein are also present in the the machinery essential for gene The nucleus is bounded by a nuclear nucleoplasm (Moir et al., 2000). The expression. Although early studies envelope, a double-membrane structure, cartoon depicts much of the nuclear suggested that little organization exists of which the outer membrane is envelope/peripheral lamina as within this compartment, more contiguous with the rough endoplasmic transparent, so that internal structures contemporary studies have identified an reticulum and is often studded with can be more easily observed. -
Association of DNA with Nuclear Matrix in in Vitro Assembled Nuclei
Cell Research (1997), 7, 107-117 Association of DNA with nuclear matrix in in vitro as- sembled nuclei induced by rDNA from Tetrahymena shang- haiensis in Xenopus egg extracts CHEN YING, BO ZHANG, XIU FEN LI, ZHONG HE ZHAI Department of Cell Biology and Genetics, College of Life Sciences, Peking University, Beijing 100871 ABSTRACT The nuclei assembled from exogenous DNA or chro- matin in egg extracts resemble their in vivo counterparts in many aspects. However, the distribution pattern of DNA in these nuclei remains unknown. We introduced rDNA from the macronuclei of Tetrahymena into Xenopus cell- free extracts to examine the association of specific DNA sequences with nuclear matrix (NM) in the nuclei assem- bled in vitro. Our previous works showed the 5'NTS (non- transcription sequences) of the rDNA specifically bind to the NM system in the macronuclei. We show now the rDNA could induce chromatin assembly and nuclear for- mation in Xenopus cell-free system. When we extracted the NM system and compared the binding affinity of differ- ent regions of rDNA with the NM system, we found that the 5'NTS still hold their binding affinity with insoluble structure of the assembled nuclei in the extracts of Xeno- pus eggs. Key words: Nuclear assembly, nuclear matrix, Xeno- pus egg extracts, Tetrahymena rDNA. On the occasion of Professor Lu Ji SHI's (L. C. Sze), eightieth birthday, we present this paper and extend our sincere greetings to Professor SHI. As we mentioned in our paper, in early 1950's, it is Professor SHI who first studied the behavior of exogenous homologous desoxyribose nucleoprotein (chromatin) in amphibian eggs. -
Lamin B2 Follows Lamin A/C- Mediated Nuclear Mechanics and Cancer Cell Invasion Efficacy
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.07.028969; this version posted April 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Lamin B2 follows lamin A/C- mediated nuclear mechanics and cancer cell invasion efficacy Short running title: Nuclear lamins in tumor cell migration Marina Vortmeyer-Krause1†, Mariska te Lindert1†, Joost te Riet2†, Veronika te Boekhorst1†, Rene Marke1, Ramanil Perera1, Philipp Isermann3, Tom van Oorschot1, Monika Zwerger3, Fengwei Yang4, Martin Svoreň1, Anotida Madzvamuse 4, Jan Lammerding3, Peter Friedl1,5,6, Katarina Wolf1* †These authors contributed equally to this work. * Correspondence to: [email protected] *Address of corresponding author: Department of Cell Biology (route 283), Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands; [email protected]; Orcid: http://orcid.org/0000-0003-0616-2708 Affiliations 1 Radboud University Medical Center, Department of Cell Biology, 6500 HB Nijmegen, The Netherlands 2 Radboud University Medical Center, Department of Tumor Immunology, 6500 HB Nijmegen, The Netherlands 3 Weill Institute for Cell and Molecular Biology, Meinig School of Biomedical Engineering Cornell University, Ithaca, NY 14853; USA 4 School of Mathematical and Physical Sciences, University of Sussex, Department of Mathematics, BN1 9QH, Falmer, Brighton, United Kingdom 5 David H. Koch Center for Applied Research of Genitourinary Cancers, Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA 6 Cancer Genomics Center, 3584 CG Utrecht, The Netherlands 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.07.028969; this version posted April 8, 2020. -
Deficiencies in Lamin B1 and Lamin B2 Cause Neurodevelopmental Defects and Distinct Nuclear Shape Abnormalities in Neurons
M BoC | ARTICLE Deficiencies in lamin B1 and lamin B2 cause neurodevelopmental defects and distinct nuclear shape abnormalities in neurons Catherine Coffiniera, Hea-Jin Jungb, Chika Nobumoria, Sandy Changa, Yiping Tua, Richard H. Barnes IIa, Yuko Yoshinagac, Pieter J. de Jongc, Laurent Vergnesd, Karen Reued, Loren G. Fonga, and Stephen G. Younga,d aDepartment of Medicine and bMolecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095; cChildren’s Hospital Oakland Research Institute, Oakland, CA 94609; dDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 ABSTRACT Neuronal migration is essential for the development of the mammalian brain. Monitoring Editor Here, we document severe defects in neuronal migration and reduced numbers of neurons in Thomas Michael Magin lamin B1–deficient mice. Lamin B1 deficiency resulted in striking abnormalities in the nuclear University of Leipzig shape of cortical neurons; many neurons contained a solitary nuclear bleb and exhibited an Received: Jun 13, 2011 asymmetric distribution of lamin B2. In contrast, lamin B2 deficiency led to increased numbers Revised: Sep 9, 2011 of neurons with elongated nuclei. We used conditional alleles for Lmnb1 and Lmnb2 to create Accepted: Sep 23, 2011 forebrain-specific knockout mice. The forebrain-specificLmnb1- and Lmnb2-knockout models had a small forebrain with disorganized layering of neurons and nuclear shape abnormalities, similar to abnormalities identified in the conventional knockout mice. A more severe pheno- type, complete atrophy of the cortex, was observed in forebrain-specific Lmnb1/Lmnb2 double-knockout mice. This study demonstrates that both lamin B1 and lamin B2 are essential for brain development, with lamin B1 being required for the integrity of the nuclear lamina, and lamin B2 being important for resistance to nuclear elongation in neurons. -
Irreversible Modifications of Chromatin and the Nuclear Lamina: a Review Inside the Nuclear Origin of Alzheimer's Disease
Revista Mexicana de Neurociencia REVIEW ARTICLE Irreversible modifications of chromatin and the nuclear lamina: A review inside the nuclear origin of Alzheimer’s disease Laura Gil1¶, Gabriela Capdeville2*¶, Ildefonso Rodríguez-Leyva3, Sandra A. Niño4, and María E. Jiménez-Capdeville4 1Departamento de Genética, Escuela de Medicina, Universidad “Alfonso X el Sabio”, Madrid, España; 2Escuela de Medicina, Universidad Panamericana, Mexico City; 3Servicio de Neurología, Hospital Central “Ignacio Morones Prieto”, San Luis Potosí; 4Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico ¶These authors contributed equally in this study. Abstract Dementia is a public health problem with an extraordinary increase in recent years. Alzheimer’s disease (AD) is the most common cause of dementia. This disease has been considered a consequence of cytoplasmic and extracellular accumula- tions of Tau protein and β- amyloid, respectively. Nevertheless, a nuclear origin of AD has recently emerged. Both Tau protein and the nuclear lamin protect the nuclear and chromatin organization for proper gene expression throughout neuronal life. Accumulation of DNA damage, mainly as a result of aging, drives post-mitotic neurons to initiate DNA repair by entering the cell cycle. The complexity of the nucleus-cytoskeleton prevents neurons from dividing and condemns them to a state of hyperdiploidy ending in neuronal death, after transiently prolonging their life. In AD, hippocampal neurons survive their fatal fate by triggering an aberrant structural and functional transformation of the nucleus. Lamin A expression and Tau protein transfer to the cytoplasm results in loss of the protector role of nuclear Tau and the subsequent global chromatin disorgani- zation. -
Nuclear Matrix Protein Matrin 3 Is a Regulator of ZAP-Mediated Retroviral
Erazo and Goff. Retrovirology (2015) 12:57 DOI 10.1186/s12977-015-0182-4 RESEARCH Open Access Nuclear matrix protein Matrin 3 is a regulator of ZAP‑mediated retroviral restriction Angela Erazo1 and Stephen P Goff1,2* Abstract Background: Matrin 3 is a nuclear matrix protein involved in multiple nuclear processes. In HIV-1 infection, Matrin 3 serves as a Rev cofactor important for the cytoplasmic accumulation of HIV-1 transcripts. ZAP is a potent host restric- tion factor of multiple viruses including retroviruses HIV-1 and MoMuLV. In this study we sought to further character- ize Matrin 3 functions in the regulation of HIV gene expression. Results: Here we describe a function for Matrin 3 as a negative regulator of the ZAP-mediated restriction of retro- viruses. Mass spectrometry analysis of Matrin 3-associated proteins uncovered interactions with proteins of the ZAP degradation complex, DDX17 and EXOSC3. Coimmunoprecipitation studies confirmed Matrin 3 associations with DDX17, EXOSC3 and ZAP, in a largely RNA-dependent manner, indicating that RNA is mediating the Matrin 3 interac- tions with these components of the ZAP degradation complex. Silencing Matrin 3 expression caused a remarkably enhanced ZAP-driven inhibition of HIV-1 and MoMuLV luciferase reporter viruses. This effect was shared with addi- tional nuclear matrix proteins. ZAP targets multiply-spliced HIV-1 transcripts, but in the context of Matrin 3 suppres- sion, this ZAP restriction was broadened to unspliced and multiply-spliced RNAs. Conclusions: Here we reveal an unprecedented role for a nuclear matrix protein, Matrin 3, in the regulation of ZAP’s antiretroviral activity. -
Direct Interaction Between Hnrnp-M and CDC5L/PLRG1 Proteins Affects Alternative Splice Site Choice
Direct interaction between hnRNP-M and CDC5L/PLRG1 proteins affects alternative splice site choice David Llères, Marco Denegri, Marco Biggiogera, Paul Ajuh, Angus Lamond To cite this version: David Llères, Marco Denegri, Marco Biggiogera, Paul Ajuh, Angus Lamond. Direct interaction be- tween hnRNP-M and CDC5L/PLRG1 proteins affects alternative splice site choice. EMBO Reports, EMBO Press, 2010, 11 (6), pp.445 - 451. 10.1038/embor.2010.64. hal-03027049 HAL Id: hal-03027049 https://hal.archives-ouvertes.fr/hal-03027049 Submitted on 26 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. scientificscientificreport report Direct interaction between hnRNP-M and CDC5L/ PLRG1 proteins affects alternative splice site choice David Lle`res1*, Marco Denegri1*w,MarcoBiggiogera2,PaulAjuh1z & Angus I. Lamond1+ 1Wellcome Trust Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, UK, and 2LaboratoriodiBiologiaCellulareandCentrodiStudioperl’IstochimicadelCNR,DipartimentodiBiologiaAnimale, Universita’ di Pavia, Pavia, Italy Heterogeneous nuclear ribonucleoprotein-M (hnRNP-M) is an and affect the fate of heterogeneous nuclear RNAs by influencing their abundant nuclear protein that binds to pre-mRNA and is a structure and/or by facilitating or hindering the interaction of their component of the spliceosome complex. -
Nuclear Envelope Protein MAN1 Regulates Clock Through BMAL1
RESEARCH ARTICLE elifesciences.org Nuclear envelope protein MAN1 regulates clock through BMAL1 Shu-Ting Lin1†, Luoying Zhang1†, Xiaoyan Lin1†‡, Linda Chen Zhang1, Valentina Elizabeth Garcia1, Chen-Wei Tsai1, Louis Ptáček1,2, Ying-Hui Fu1* 1Department of Neurology, University of California, San Francisco, San Francisco, United States; 2Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States Abstract Circadian clocks serve as internal pacemakers that influence many basic homeostatic processes; consequently, the expression and function of their components are tightly regulated by intricate networks of feedback loops that fine-tune circadian processes. Our knowledge of these components and pathways is far from exhaustive. In recent decades, the nuclear envelope has emerged as a global gene regulatory machine, although its role in circadian regulation has not been explored. We report that transcription of the core clock component BMAL1 is positively modulated by the inner nuclear membrane protein MAN1, which directly binds the BMAL1 promoter and enhances its transcription. Our results establish a novel connection between the nuclear periphery and circadian rhythmicity, therefore bridging two global regulatory systems that modulate all aspects of bodily functions. DOI: 10.7554/eLife.02981.001 *For correspondence: ying-hui. [email protected] Introduction † These authors contributed Most organisms, ranging from cyanobacteria to humans, are governed by their circadian rhythms: equally to this work endogenous and self-sustained oscillations with a period of roughly 24 hr, which manifest in diverse Present address: ‡Neurogenetics metabolic, physiological, and behavioral processes (Ueda et al., 2005). This internal pacemaker is Branch, National Institute of charged with two important roles: to perpetuate its own rhythms and to regulate the expression of Neurological Disorders and genes that are under circadian control. -
Effects of Hyperthermia on Chromatin Condensation and Nucleoli
(CANCER RESEARCH 49, 1254-1260. March 1. 1989] Effects of Hyperthermia on Chromatin Condensation and Nucleoli Disintegration as Visualized by Induction of Premature Chromosome Condensation in Interphase Mammalian Cells1 George E. Iliakis and Gabriel E. Pantelias2 Thomas Jefferson University Hospital, Department of Radiation Oncology and Nuclear Medicine, Philadelphia, Pennsylvania 19107 [G. E. I., G. E. P.]; and the National Research Center for Physical Sciences "Demokritos", Aghia Paraskevi Attikis, Athens, Greece [G. E. P.] ABSTRACT nuclei (13), in chromatin (14-17), and in nuclear matrices (18, 19), and it was proposed that disruption of important nuclear The effects of hyperthermia on chromatin condensation and nucleoli processes by this nuclear protein binding may be the reason for disintegration, as visualized by induction of premature chromosome con cell killing (17). Beyond cell killing the excess nuclear proteins densation in interphase mammalian cells, was studied in exponentially have been implicated in the inhibition of DNA synthesis (5, 6) growing and plateau phase Chinese hamster ovary cells. Exposure to heat reduced the ability of interphase chromatin to condense and the and the inhibition of DNA repair following both ionizing (20, ability of the nucleolar organizing region to disintegrate under the influ 21) and uv (22) irradiation. It is thought that inhibition of ence of factors provided by mitotic cells when fused to interphase cells. these cellular functions may be due to alterations induced in Based on these effects treated cells were classified in three categories. chromatin conformation and in particular to restriction of DNA Category 1 contained cells able to condense their chromatin and disinte supercoiling changes as a result of protein addition to the grate the nucleolar organizing region.