Patrolling the Nucleus: Inner Nuclear Membrane-Associated Degradation
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Association Analyses of Known Genetic Variants with Gene
ASSOCIATION ANALYSES OF KNOWN GENETIC VARIANTS WITH GENE EXPRESSION IN BRAIN by Viktoriya Strumba A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Bioinformatics) in The University of Michigan 2009 Doctoral Committee: Professor Margit Burmeister, Chair Professor Huda Akil Professor Brian D. Athey Assistant Professor Zhaohui S. Qin Research Statistician Thomas Blackwell To Sam and Valentina Dmitriy and Elizabeth ii ACKNOWLEDGEMENTS I would like to thank my advisor Professor Margit Burmeister, who tirelessly guided me though seemingly impassable corridors of graduate work. Throughout my thesis writing period she provided sound advice, encouragement and inspiration. Leading by example, her enthusiasm and dedication have been instrumental in my path to becoming a better scientist. I also would like to thank my co-advisor Tom Blackwell. His careful prodding always kept me on my toes and looking for answers, which taught me the depth of careful statistical analysis. His diligence and dedication have been irreplaceable in most difficult of projects. I also would like to thank my other committee members: Huda Akil, Brian Athey and Steve Qin as well as David States. You did not make it easy for me, but I thank you for believing and not giving up. Huda’s eloquence in every subject matter she explained have been particularly inspiring, while both Huda’s and Brian’s valuable advice made the completion of this dissertation possible. I would also like to thank all the members of the Burmeister lab, both past and present: Sandra Villafuerte, Kristine Ito, Cindy Schoen, Karen Majczenko, Ellen Schmidt, Randi Burns, Gang Su, Nan Xiang and Ana Progovac. -
BMC Cell Biology Biomed Central
BMC Cell Biology BioMed Central Research article Open Access Nuclear envelope transmembrane proteins (NETs) that are up-regulated during myogenesis I-Hsiung Brandon Chen, Michael Huber, Tinglu Guan, Anja Bubeck and Larry Gerace* Address: Department of Cell Biology, The Scripps Research Institute, 10555 N. Torrey Pines Rd., La Jolla CA 92037, USA Email: I-Hsiung Brandon Chen - [email protected]; Michael Huber - [email protected]; Tinglu Guan - [email protected]; Anja Bubeck - [email protected]; Larry Gerace* - [email protected] * Corresponding author Published: 24 October 2006 Received: 01 September 2006 Accepted: 24 October 2006 BMC Cell Biology 2006, 7:38 doi:10.1186/1471-2121-7-38 This article is available from: http://www.biomedcentral.com/1471-2121/7/38 © 2006 Chen et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The nuclear lamina is a protein meshwork lining the inner nuclear membrane, which contains a polymer of nuclear lamins associated with transmembrane proteins of the inner nuclear membrane. The lamina is involved in nuclear structure, gene expression, and association of the cytoplasmic cytoskeleton with the nucleus. We previously identified a group of 67 novel putative nuclear envelope transmembrane proteins (NETs) in a large-scale proteomics analysis. Because mutations in lamina proteins have been linked to several human diseases affecting skeletal muscle, we examined NET expression during differentiation of C2C12 myoblasts. -
TMEM33 (A-17): Sc-244421
SAN TA C RUZ BI OTEC HNOL OG Y, INC . TMEM33 (A-17): sc-244421 BACKGROUND PRODUCT TMEM33 (transmembrane protein 33), also known as protein DB83, is a 247 Each vial contains 200 µg IgG in 1.0 ml of PBS with < 0.1% sodium azide amino acid protein encoded by a gene mapping to human chromosome 4. and 0.1% gelatin. Representing approximately 6% of the human genome, chromosome 4 con - Blocking peptide available for competition studies, sc-244421 P, (100 µg tains nearly 900 genes. Notably, the Huntingtin gene, which is found to en- peptide in 0.5 ml PBS containing < 0.1% sodium azide and 0.2% BSA). code an expanded glutamine tract in cases of Huntington’s disease, is on chromosome 4. FGFR-3 is also encoded on chromosome 4 and has been asso - APPLICATIONS ciated with thanatophoric dwarfism, achondroplasia, Muenke syndrome and bladder cancer. Chromosome 4 is also tied to Ellis-van Creveld syndrome, TMEM33 (A-17) is recommended for detection of TMEM33 of mouse, rat methylmalonic acidemia and polycystic kidney disease. Chromosome 4 report - and human origin by Western Blotting (starting dilution 1:200, dilution range edly contains the largest gene deserts (regions of the genome with no protein 1:100-1:1000), immunofluorescence (starting dilution 1:50, dilution range encoding genes) and has one of the two lowest recombination frequencies 1:50-1:500) and solid phase ELISA (starting dilution 1:30, dilution range of the human chromosomes. 1:30-1:3000); non cross-reactive with other TMEM family members. TMEM33 (A-17) is also recommended for detection of TMEM33 in additional REFERENCES species, including equine, canine, bovine, porcine and avian. -
Macrophage Activation JUNB Is a Key Transcriptional Modulator Of
JUNB Is a Key Transcriptional Modulator of Macrophage Activation Mary F. Fontana, Alyssa Baccarella, Nidhi Pancholi, Miles A. Pufall, De'Broski R. Herbert and Charles C. Kim This information is current as of October 2, 2021. J Immunol 2015; 194:177-186; Prepublished online 3 December 2014; doi: 10.4049/jimmunol.1401595 http://www.jimmunol.org/content/194/1/177 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2014/12/03/jimmunol.140159 Material 5.DCSupplemental References This article cites 40 articles, 7 of which you can access for free at: http://www.jimmunol.org/content/194/1/177.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on October 2, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2014 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology JUNB Is a Key Transcriptional Modulator of Macrophage Activation Mary F. Fontana,* Alyssa Baccarella,* Nidhi Pancholi,* Miles A. -
The Influence of Genetic Variation in Gene Expression
The Influence of Genetic Variation in Gene Expression Eva King-Fan Chan A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy 2007 School of Biotechnology and Biomolecular Sciences University of New South Wales Certificate of originality I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged. ______________________ Eva Chan 18th July 2007 i Abstract Abstract Variations in gene expression have long been hypothesised to be the major cause of individual differences. An initial focus of this research thesis is to elucidate the genetic regulatory architecture of gene expression. Expression quantitative trait locus (eQTL) mapping analyses have been performed on expression levels of over 22,000 mRNAs from three tissues of a panel of recombinant inbred mice. These analyses are “single-locus” where “linkage” (i.e. significant correlation) between an expression trait and a putative eQTL is considered independently of other loci. -
Snapshot: the Nuclear Envelope II Andrea Rothballer and Ulrike Kutay Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
SnapShot: The Nuclear Envelope II Andrea Rothballer and Ulrike Kutay Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland H. sapiens D. melanogaster C. elegans S. pombe S. cerevisiae Cytoplasmic filaments RanBP2 (Nup358) Nup358 CG11856 NPP-9 – – – Nup214 (CAN) DNup214 CG3820 NPP-14 Nup146 SPAC23D3.06c Nup159 Cytoplasmic ring and Nup88 Nup88 (Mbo) CG6819 – Nup82 SPBC13A2.02 Nup82 associated factors GLE1 GLE1 CG14749 – Gle1 SPBC31E1.05 Gle1 hCG1 (NUP2L1, NLP-1) tbd CG18789 – Amo1 SPBC15D4.10c Nup42 (Rip1) Nup98 Nup98 CG10198 Npp-10N Nup189N SPAC1486.05 Nup145N, Nup100, Nup116 Nup 98 complex RAE1 (GLE2) Rae1 CG9862 NPP-17 Rae1 SPBC16A3.05 Gle2 (Nup40) Nup160 Nup160 CG4738 NPP-6 Nup120 SPBC3B9.16c Nup120 Nup133 Nup133 CG6958 NPP-15 Nup132, Nup131 SPAC1805.04, Nup133 SPBP35G2.06c Nup107 Nup107 CG6743 NPP-5 Nup107 SPBC428.01c Nup84 Nup96 Nup96 CG10198 NPP-10C Nup189C SPAC1486.05 Nup145C Outer NPC scaffold Nup85 (PCNT1) Nup75 CG5733 NPP-2 Nup-85 SPBC17G9.04c Nup85 (Nup107-160 complex) Seh1 Nup44A CG8722 NPP-18 Seh1 SPAC15F9.02 Seh1 Sec13 Sec13 CG6773 Npp-20 Sec13 SPBC215.15 Sec13 Nup37 tbd CG11875 – tbd SPAC4F10.18 – Nup43 Nup43 CG7671 C09G9.2 – – – Centrin-21 tbd CG174931, CG318021 R08D7.51 Cdc311 SPCC1682.04 Cdc311 Nup205 tbd CG11943 NPP-3 Nup186 SPCC290.03c Nup192 Nup188 tbd CG8771 – Nup184 SPAP27G11.10c Nup188 Central NPC scaffold Nup155 Nup154 CG4579 NPP-8 tbd SPAC890.06 Nup170, Nup157 (Nup53-93 complex) Nup93 tbd CG7262 NPP-13 Nup97, Npp106 SPCC1620.11, Nic96 SPCC1739.14 Nup53(Nup35, MP44) tbd CG6540 NPP-19 Nup40 SPAC19E9.01c -
Snp Associations with Tuberculosis Susceptibility in a Ugandan
SNP ASSOCIATIONS WITH TUBERCULOSIS SUSCEPTIBILITY IN A UGANDAN HOUSEHOLD CONTACT STUDY by ALLISON REES BAKER Submitted in partial fulfillment of the requirements For the degree of Master of Science Thesis Advisor: Dr. Catherine M. Stein Department of Epidemiology and Biostatistics CASE WESTERN RESERVE UNIVERSITY August, 2010 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of ______________________________________________________ candidate for the ________________________________degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. Table of Contents Table of Contents...............................................................................................................iii List of Tables ..................................................................................................................... iv Acknowledgements............................................................................................................. v List of Commonly Used Abbreviations ............................................................................. vi Chapter 1: Literature -
Perspectives
FOCUS ON MECHANOTRANSDUCTION PERSPECTIVES network that can promote coordinated OPINION changes in cell, cytoskeletal and nuclear struc- ture in response to mechanical distortion14 Mechanotransduction at a (FIG. 1a). (Herein, the term hard-wired refers to cytoskeletal structures that are stable enough distance: mechanically coupling the as interconnected units to resist mechanical stresses and thereby maintain shape stabil- ity, even though they undergo continuous extracellular matrix with the nucleus dynamic remodelling at the molecular level.) This model takes into account the observa- Ning Wang, Jessica D. Tytell and Donald E. Ingber tion that individual cytoskeletal filaments can bear significant tensile and compressive loads Abstract | Research in cellular mechanotransduction often focuses on how in living cells because their structural integrity extracellular physical forces are converted into chemical signals at the cell surface. is maintained for longer than the turnover However, mechanical forces that are exerted on surface-adhesion receptors, such time of individual protein monomers15–17. as integrins and cadherins, are also channelled along cytoskeletal filaments and Key to the cellular tensegrity model is concentrated at distant sites in the cytoplasm and nucleus. Here, we explore the the idea that overall cell-shape stability and long-distance force transfer are governed by molecular mechanisms by which forces might act at a distance to induce the level of isometric tension, or ‘prestress’, mechanochemical conversion in the nucleus and alter gene activities. in the cytoskeleton that is generated through the establishment of a force balance between Mechanical forces influence the growth and For example, endothelial cells sense fluid opposing structural elements (that is, micro- shape of virtually every tissue and organ in shear through a cell–cell junctional com- tubules, contractile microfilaments and our bodies. -
Identification and Characterization of TMEM33 As a Reticulon-Binding Protein
Kobe J. Med. Sci., Vol. 60, No. 3, pp. E57-E65, 2014 Identification and Characterization of TMEM33 as a Reticulon-binding Protein TAKESHI URADE1,2, YASUNORI YAMAMOTO1, XIA ZHANG1, YONSON KU2, and TOSHIAKI SAKISAKA*1 1Division of Membrane Dynamics, Department of Physiology and Cell Biology, 2Division of Hepato-biliary-pancreatic surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe 650-0017 Japan Received 16 July, 2014/ Accepted 31 July, 2014 Key words: TMEM33, Reticulon, ER tubules ABSTRACT Endoplasmic reticulum (ER) is an organelle that has an elaborate and continuous membrane system composed of sheet-like cisternae and a network of interconnected tubules. The ER tubules are shaped by reticulons, a conserved ER membrane protein family. However, how the membrane-shaping activity is regulated remains to be elucidated. To understand the mode of action of reticulons, we isolated TMEM33, a conserved protein harboring three transmembrane domains, as a reticulon 4C-binding protein by affinity chromatography. In addition to reticulon 4C, TMEM33 binds to reticulon 1A, -2B, -3C and a reticulon homology domain-containing protein Arl6IP1. Exogenously expressed TMEM33 localizes at both the ER membrane and the nuclear envelope. Exogenously expressed TMEM33 co-localizes with exogenously expressed reticulon 4C well at the ER sheets and partially at the ER tubules. Exogenously expressed TMEM33 suppresses the exogenously expressed reticulon 4C-induced tubulation of ER. These results suggest that TMEM33 has a potency to suppress the membrane-shaping activity of reticulons, thereby regulating the tubular structure of ER. INTRODUCTION The ER (endoplasmic reticulum) is a continuous membrane system extended from nuclear envelope and composed of interconnected sheets and tubules [11,20,21,25,28]. -
The RNA-Protein Interactome of Differentiated Kidney Tubular Epithelial Cells
BASIC RESEARCH www.jasn.org The RNA-Protein Interactome of Differentiated Kidney Tubular Epithelial Cells Michael Ignarski,1 Constantin Rill,1 Rainer W.J. Kaiser,1 Madlen Kaldirim,1 René Neuhaus,1 Reza Esmaillie,1 Xinping Li,2 Corinna Klein,3 Katrin Bohl,1 Maike Petersen,1 Christian K. Frese,3 Martin Höhne ,1 Ilian Atanassov,2 Markus M. Rinschen,1 Katja Höpker,1 Bernhard Schermer,1,4,5 Thomas Benzing,1,4,5 Christoph Dieterich,6,7 Francesca Fabretti,1 and Roman-Ulrich Müller 1,4,5 1Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany; 2Proteomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany; 3Proteomics Facility, Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases, 4Nephrolab, Cologne Excellence Cluster on Cellular Stress Responses in Aging- associated Diseases, Faculty of Medicine and University Hospital Cologne, and 5Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany; 6Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany; and 7German Center for Cardiovascular Research (DZHK)–Partner site, Heidelberg/Mannheim, Germany ABSTRACT Background RNA-binding proteins (RBPs) are fundamental regulators of cellular biology that affect all steps in the generation and processing of RNA molecules. Recent evidence suggests that regulation of RBPs that modulate both RNA stability and translation may have a profound effect on the proteome. However, regulation of RBPs in clinically relevant experimental conditions has not been studied systematically. Methods We used RNA interactome capture, a method for the global identification of RBPs to characterize the global RNA‐binding proteome (RBPome) associated with polyA-tailed RNA species in murine ciliated epithelial cells of the inner medullary collecting duct. -
Compositionally Distinct Nuclear Pore Complexes of Functionally Distinct Dimorphic Nuclei in the Ciliate Tetrahymena
© 2017. Published by The Company of Biologists Ltd | Journal of Cell Science (2017) 130, 1822-1834 doi:10.1242/jcs.199398 RESEARCH ARTICLE Compositionally distinct nuclear pore complexes of functionally distinct dimorphic nuclei in the ciliate Tetrahymena Masaaki Iwamoto1, Hiroko Osakada1, Chie Mori1, Yasuhiro Fukuda2, Koji Nagao3, Chikashi Obuse3, Yasushi Hiraoka1,4,5 and Tokuko Haraguchi1,4,5,* ABSTRACT targeted transport of components to the MIC versus MAC, for which The nuclear pore complex (NPC), a gateway for nucleocytoplasmic differences in the NPCs may be important determinants. trafficking, is composed of ∼30 different proteins called nucleoporins. Previously, we analyzed 13 Tetrahymena nucleoporins (Nups), It remains unknown whether the NPCs within a species are and discovered that four paralogs of Nup98 were differentially homogeneous or vary depending on the cell type or physiological localized to the MAC and MIC (Iwamoto et al., 2009). The MAC- condition. Here, we present evidence for compositionally distinct and MIC-specific Nup98s are characterized by Gly-Leu-Phe-Gly NPCs that form within a single cell in a binucleated ciliate. In (GLFG) and Asn-Ile-Phe-Asn (NIFN) repeats, respectively, and this Tetrahymena thermophila, each cell contains both a transcriptionally difference is important for the nucleus-specific import of linker active macronucleus (MAC) and a germline micronucleus (MIC). By histones (Iwamoto et al., 2009). The full extent of the compositional combining in silico analysis, mass spectrometry analysis for immuno- differentiation of MAC and MIC NPCs could not, however, isolated proteins and subcellular localization analysis of GFP-fused be assessed, since only a small subset of the expected NPC proteins, we identified numerous novel components of MAC and MIC components were detected. -
The SUN Rises on Meiotic Chromosome Dynamics
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Developmental Cell Review Feature The SUN Rises on Meiotic Chromosome Dynamics Yasushi Hiraoka1,2,* and Abby F. Dernburg3,4,* 1Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan 2Kobe Advanced ICT Research Center, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan 3Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3220, USA 4Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA *Correspondence: [email protected] (Y.H.), [email protected] (A.F.D.) DOI 10.1016/j.devcel.2009.10.014 Recent studies in diverse eukaryotes have implicated a family of nuclear envelope proteins containing SUN domains as key components of meiotic nuclear organization and chromosome dynamics. In many cases, these transmembrane proteins are also known to contribute to centrosome or spindle pole body function in mitotically dividing cells. During meiotic prophase, the apparent role of these SUN-domain proteins, together with their partner KASH-domain proteins, is to connect chromosomes through the intact nuclear envelope to force-generating mechanisms in the cytoplasm. A Family of SUN Proteins In this review, we use these existing names and also refer to these The SUN domain was named for homologous sequences shared genes and their orthologs in mouse and human genomes as Sun4 by Sad1 and UNC-84 proteins (Malone et al., 1999).