Vesicle-Associated Membrane Protein 7 Is Expressed in Intestinal ER
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Exceptional Conservation of Horse–Human Gene Order on X Chromosome Revealed by High-Resolution Radiation Hybrid Mapping
Exceptional conservation of horse–human gene order on X chromosome revealed by high-resolution radiation hybrid mapping Terje Raudsepp*†, Eun-Joon Lee*†, Srinivas R. Kata‡, Candice Brinkmeyer*, James R. Mickelson§, Loren C. Skow*, James E. Womack‡, and Bhanu P. Chowdhary*¶ʈ *Department of Veterinary Anatomy and Public Health, ‡Department of Veterinary Pathobiology, College of Veterinary Medicine, and ¶Department of Animal Science, College of Agriculture and Life Science, Texas A&M University, College Station, TX 77843; and §Department of Veterinary Pathobiology, University of Minnesota, 295f AS͞VM, St. Paul, MN 55108 Contributed by James E. Womack, December 30, 2003 Development of a dense map of the horse genome is key to efforts ciated with the traits, once they are mapped by genetic linkage aimed at identifying genes controlling health, reproduction, and analyses with highly polymorphic markers. performance. We herein report a high-resolution gene map of the The X chromosome is the most conserved mammalian chro- horse (Equus caballus) X chromosome (ECAX) generated by devel- mosome (18, 19). Extensive comparisons of structure, organi- oping and typing 116 gene-specific and 12 short tandem repeat zation, and gene content of this chromosome in evolutionarily -markers on the 5,000-rad horse ؋ hamster whole-genome radia- diverse mammals have revealed a remarkable degree of conser tion hybrid panel and mapping 29 gene loci by fluorescence in situ vation (20–22). Until now, the chromosome has been best hybridization. The human X chromosome sequence was used as a studied in humans and mice, where the focus of research has template to select genes at 1-Mb intervals to develop equine been the intriguing patterns of X inactivation and the involve- orthologs. -
Mea6 Controls VLDL Transport Through the Coordinated Regulation of COPII Assembly
Cell Research (2016) 26:787-804. npg © 2016 IBCB, SIBS, CAS All rights reserved 1001-0602/16 $ 32.00 ORIGINAL ARTICLE www.nature.com/cr Mea6 controls VLDL transport through the coordinated regulation of COPII assembly Yaqing Wang1, *, Liang Liu1, 2, *, Hongsheng Zhang1, 2, Junwan Fan1, 2, Feng Zhang1, 2, Mei Yu3, Lei Shi1, Lin Yang1, Sin Man Lam1, Huimin Wang4, Xiaowei Chen4, Yingchun Wang1, Fei Gao5, Guanghou Shui1, Zhiheng Xu1, 6 1State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; 2University of Chinese Academy of Sciences, Beijing 100101, China; 3School of Life Science, Shandong University, Jinan 250100, China; 4Institute of Molecular Medicine, Peking University, Beijing 100871, China; 5State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; 6Translation- al Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Lipid accumulation, which may be caused by the disturbance in very low density lipoprotein (VLDL) secretion in the liver, can lead to fatty liver disease. VLDL is synthesized in endoplasmic reticulum (ER) and transported to Golgi apparatus for secretion into plasma. However, the underlying molecular mechanism for VLDL transport is still poor- ly understood. Here we show that hepatocyte-specific deletion of meningioma-expressed antigen 6 (Mea6)/cutaneous T cell lymphoma-associated antigen 5C (cTAGE5C) leads to severe fatty liver and hypolipemia in mice. Quantitative lip- idomic and proteomic analyses indicate that Mea6/cTAGE5 deletion impairs the secretion of different types of lipids and proteins, including VLDL, from the liver. -
BMC Biology Biomed Central
BMC Biology BioMed Central Research article Open Access Normal histone modifications on the inactive X chromosome in ICF and Rett syndrome cells: implications for methyl-CpG binding proteins Stanley M Gartler*1,2, Kartik R Varadarajan2, Ping Luo2, Theresa K Canfield2, Jeff Traynor3, Uta Francke3 and R Scott Hansen2 Address: 1Department of Medicine, University of Washington, Seattle, WA, USA, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA and 3Department of Genetics, Stanford University, Stanford, CA, USA Email: Stanley M Gartler* - [email protected]; Kartik R Varadarajan - [email protected]; Ping Luo - [email protected]; Theresa K Canfield - [email protected]; Jeff Traynor - [email protected]; Uta Francke - [email protected]; R Scott Hansen - [email protected] * Corresponding author Published: 20 September 2004 Received: 23 June 2004 Accepted: 20 September 2004 BMC Biology 2004, 2:21 doi:10.1186/1741-7007-2-21 This article is available from: http://www.biomedcentral.com/1741-7007/2/21 © 2004 Gartler 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: In mammals, there is evidence suggesting that methyl-CpG binding proteins may play a significant role in histone modification through their association with modification complexes that can deacetylate and/or methylate nucleosomes in the proximity of methylated DNA. We examined this idea for the X chromosome by studying histone modifications on the X chromosome in normal cells and in cells from patients with ICF syndrome (Immune deficiency, Centromeric region instability, and Facial anomalies syndrome). -
Anti-VAMP7 Monoclonal Antibody, Clone 25G579 (CABT-37960MH) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use
Anti-VAMP7 monoclonal antibody, clone 25G579 (CABT-37960MH) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Product Overview Mouse Monoclonall antibody to Human VAMP7. Antigen Description This gene encodes a transmembrane protein that is a member of the soluble N-ethylmaleimide- sensitive factor attachment protein receptor (SNARE) family. The encoded protein localizes to late endosomes and lysosomes and is involved in the fusion of transport vesicles to their target membranes. Alternate splicing results in multiple transcript variants. Specificity Detected in all tissues tested. Immunogen Recombinant full SYBL1 protein (Human) Isotype IgG1 Source/Host Mouse Species Reactivity Rat, Human Clone 25G579 Purification Affinity purified Conjugate Unconjugated Applications IP, ICC, WB Sequence Similarities Belongs to the synaptobrevin family.Contains 1 longin domain.Contains 1 v-SNARE coiled-coil homology domain. Reconstitution For reconstitution add 100 ul H2O to get a 1mg/ml solution in PBS. Format Lyophilized Size 100 ug Buffer Preservative: None. Constituents: Ascites Preservative None Storage Store at +4°C short term (1-2 weeks). Aliquot and store at -20°C long term. Avoid repeated freeze / thaw cycles. 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved GENE INFORMATION Gene Name VAMP7 vesicle-associated membrane protein 7 [ Homo sapiens ] Official Symbol VAMP7 Synonyms VAMP7; vesicle-associated -
Discovery of Candidate Genes for Stallion Fertility from the Horse Y Chromosome
DISCOVERY OF CANDIDATE GENES FOR STALLION FERTILITY FROM THE HORSE Y CHROMOSOME A Dissertation by NANDINA PARIA Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY August 2009 Major Subject: Biomedical Sciences DISCOVERY OF CANDIDATE GENES FOR STALLION FERTILITY FROM THE HORSE Y CHROMOSOME A Dissertation by NANDINA PARIA Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Terje Raudsepp Committee Members, Bhanu P. Chowdhary William J. Murphy Paul B. Samollow Dickson D. Varner Head of Department, Evelyn Tiffany-Castiglioni August 2009 Major Subject: Biomedical Sciences iii ABSTRACT Discovery of Candidate Genes for Stallion Fertility from the Horse Y Chromosome. (August 2009) Nandina Paria, B.S., University of Calcutta; M.S., University of Calcutta Chair of Advisory Committee: Dr. Terje Raudsepp The genetic component of mammalian male fertility is complex and involves thousands of genes. The majority of these genes are distributed on autosomes and the X chromosome, while a small number are located on the Y chromosome. Human and mouse studies demonstrate that the most critical Y-linked male fertility genes are present in multiple copies, show testis-specific expression and are different between species. In the equine industry, where stallions are selected according to pedigrees and athletic abilities but not for reproductive performance, reduced fertility of many breeding stallions is a recognized problem. Therefore, the aim of the present research was to acquire comprehensive information about the organization of the horse Y chromosome (ECAY), identify Y-linked genes and investigate potential candidate genes regulating stallion fertility. -
Chromatin Structure of the Inactive X Chromosome
CHROMATIN STRUCTURE OF THE INACTIVE X CHROMOSOME by Sandra L. Gilbert B.A. Biology and B.A. Economics University of Pennsylvania, 1990 Submitted to the Department of Biology in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biology at the Massachusetts Institute of Technology September, 1999 © 1999 Massachusetts Institute of Technology All rights reserved Signature of Author ................................................................................ ..... .... .. .... .. .. ... HUS Department of Biology August 19,1999 MASSACHUSETTS INSTITU 1OFTECHNOLOGY '7 Ce rtifie d by ................. .................... ............ ......................................................... Phillip A. Sharp Salvador E. Luria Professor of Biology Thesis Supervisor A cce pte d by ........................................................................................ ...-- .* ... Terry Orr-Weaver Professor of Biology Chairman, Committee for Graduate Students 2 ABSTRACT X-inactivation is the unusual mode of gene regulation by which most genes on one of the two X chromosomes in female mammalian cells are transcriptionally silenced. The underlying mechanism for this widespread transcriptional repression is unknown. This thesis investigates two key aspects of the X-inactivation process. The first aspect is the correlation between chromatin structure and gene expression from the inactive X (Xi). Two features of the Xi chromatin - DNA methylation and late replication timing - have been shown to correlate with silencing -
Mechanisms of Synaptic Plasticity Mediated by Clathrin Adaptor-Protein Complexes 1 and 2 in Mice
Mechanisms of synaptic plasticity mediated by Clathrin Adaptor-protein complexes 1 and 2 in mice Dissertation for the award of the degree “Doctor rerum naturalium” at the Georg-August-University Göttingen within the doctoral program “Molecular Biology of Cells” of the Georg-August University School of Science (GAUSS) Submitted by Ratnakar Mishra Born in Birpur, Bihar, India Göttingen, Germany 2019 1 Members of the Thesis Committee Prof. Dr. Peter Schu Institute for Cellular Biochemistry, (Supervisor and first referee) University Medical Center Göttingen, Germany Dr. Hans Dieter Schmitt Neurobiology, Max Planck Institute (Second referee) for Biophysical Chemistry, Göttingen, Germany Prof. Dr. med. Thomas A. Bayer Division of Molecular Psychiatry, University Medical Center, Göttingen, Germany Additional Members of the Examination Board Prof. Dr. Silvio O. Rizzoli Department of Neuro-and Sensory Physiology, University Medical Center Göttingen, Germany Dr. Roland Dosch Institute of Developmental Biochemistry, University Medical Center Göttingen, Germany Prof. Dr. med. Martin Oppermann Institute of Cellular and Molecular Immunology, University Medical Center, Göttingen, Germany Date of oral examination: 14th may 2019 2 Table of Contents List of abbreviations ................................................................................. 5 Abstract ................................................................................................... 7 Chapter 1: Introduction ............................................................................ -
ER-To-Golgi Trafficking and Its Implication in Neurological Diseases
cells Review ER-to-Golgi Trafficking and Its Implication in Neurological Diseases 1,2, 1,2 1,2, Bo Wang y, Katherine R. Stanford and Mondira Kundu * 1 Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; [email protected] (B.W.); [email protected] (K.R.S.) 2 Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA * Correspondence: [email protected]; Tel.: +1-901-595-6048 Present address: School of Life Sciences, Xiamen University, Xiamen 361102, China. y Received: 21 November 2019; Accepted: 7 February 2020; Published: 11 February 2020 Abstract: Membrane and secretory proteins are essential for almost every aspect of cellular function. These proteins are incorporated into ER-derived carriers and transported to the Golgi before being sorted for delivery to their final destination. Although ER-to-Golgi trafficking is highly conserved among eukaryotes, several layers of complexity have been added to meet the increased demands of complex cell types in metazoans. The specialized morphology of neurons and the necessity for precise spatiotemporal control over membrane and secretory protein localization and function make them particularly vulnerable to defects in trafficking. This review summarizes the general mechanisms involved in ER-to-Golgi trafficking and highlights mutations in genes affecting this process, which are associated with neurological diseases in humans. Keywords: COPII trafficking; endoplasmic reticulum; Golgi apparatus; neurological disease 1. Overview Approximately one-third of all proteins encoded by the mammalian genome are exported from the endoplasmic reticulum (ER) and transported to the Golgi apparatus, where they are sorted for delivery to their final destination in membrane compartments or secretory vesicles [1]. -
Cryo-Tomography of Coat Complexes ISSN 2059-7983
research papers Visualizing membrane trafficking through the electron microscope: cryo-tomography of coat complexes ISSN 2059-7983 Evgenia A. Markova and Giulia Zanetti* Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England. Received 8 March 2019 *Correspondence e-mail: [email protected] Accepted 12 April 2019 Coat proteins mediate vesicular transport between intracellular compartments, Keywords: cryo-electron tomography; which is essential for the distribution of molecules within the eukaryotic cell. three-dimensional reconstruction; coat proteins; The global arrangement of coat proteins on the membrane is key to their vesicular transport; COPII; subtomogram function, and cryo-electron tomography and subtomogram averaging have been averaging. used to study membrane-bound coat proteins, providing crucial structural insight. This review outlines a workflow for the structural elucidation of coat proteins, incorporating recent developments in the collection and processing of cryo-electron tomography data. Recent work on coat protein I, coat protein II and retromer performed on in vitro reconstitutions or in situ is summarized. These studies have answered long-standing questions regarding the mechanisms of membrane binding, polymerization and assembly regulation of coat proteins. 1. Introduction Recent advances in cryo-electron microscopy (cryo-EM) have enabled numerous high-resolution studies which have addressed long-standing structural biology questions. The large body of cryo-EM work carried out for protein structure characterization has utilized single-particle electron micro- scopy (Cheng, 2018). Recently, developments in hardware, data collection and data processing have placed cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) at the forefront of structural studies of repetitive assemblies, reaching resolutions comparable to those of single-particle EM (Schur et al., 2016; Wan et al., 2017; Hutchings et al., 2018; Dodonova et al., 2017; Himes & Zhang, 2018). -
Craniofacial Diseases Caused by Defects in Intracellular Trafficking
G C A T T A C G G C A T genes Review Craniofacial Diseases Caused by Defects in Intracellular Trafficking Chung-Ling Lu and Jinoh Kim * Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-515-294-3401 Abstract: Cells use membrane-bound carriers to transport cargo molecules like membrane proteins and soluble proteins, to their destinations. Many signaling receptors and ligands are synthesized in the endoplasmic reticulum and are transported to their destinations through intracellular trafficking pathways. Some of the signaling molecules play a critical role in craniofacial morphogenesis. Not surprisingly, variants in the genes encoding intracellular trafficking machinery can cause craniofacial diseases. Despite the fundamental importance of the trafficking pathways in craniofacial morphogen- esis, relatively less emphasis is placed on this topic, thus far. Here, we describe craniofacial diseases caused by lesions in the intracellular trafficking machinery and possible treatment strategies for such diseases. Keywords: craniofacial diseases; intracellular trafficking; secretory pathway; endosome/lysosome targeting; endocytosis 1. Introduction Citation: Lu, C.-L.; Kim, J. Craniofacial malformations are common birth defects that often manifest as part of Craniofacial Diseases Caused by a syndrome. These developmental defects are involved in three-fourths of all congenital Defects in Intracellular Trafficking. defects in humans, affecting the development of the head, face, and neck [1]. Overt cranio- Genes 2021, 12, 726. https://doi.org/ facial malformations include cleft lip with or without cleft palate (CL/P), cleft palate alone 10.3390/genes12050726 (CP), craniosynostosis, microtia, and hemifacial macrosomia, although craniofacial dys- morphism is also common [2]. -
Chromosome Territory Reorganization in a Human Disease with Altered DNA Methylation
Chromosome territory reorganization in a human disease with altered DNA methylation Maria R. Matarazzo*, Shelagh Boyle†, Maurizio D’Esposito*‡, and Wendy A. Bickmore†‡ *Institute of Genetics and Biophysics ‘‘Adriano Buzzati Traverso,’’ Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; and †Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, United Kingdom Edited by Mark T. Groudine, Fred Hutchinson Cancer Research Center, Seattle, WA, and approved September 4, 2007 (received for review April 2, 2007) Chromosome territory (CT) organization and chromatin condensa- nodeficiency centromeric instability facial anomalies (ICF) syn- tion have been linked to gene expression. Although individual drome patients (14) lead to loss of DNA methylation at specific genes can be transcribed from inside CTs, some regions that have genomic sites (15, 16). Prominent sites of hypomethylation in constitutively high expression or are coordinately activated loop ICF are satellite DNAs in the juxtacentromeric heterochromatin out from CTs and decondense. The relationship between epige- at chromosome regions 1qh, 16qh, and 9qh, and aberrant netic marks, such as DNA methylation, and higher-order chromatin association of the satellite II-rich 1qh and 16qh regions has been structures is largely unexplored. DNMT3B mutations in immuno- seen in nuclei of ICF cells (17). Sites on the female inactive X deficiency centromeric instability facial anomalies (ICF) syndrome chromosome (Xi), especially CpG islands, are also hypomethy- result in loss of DNA methylation at particular sites, including CpG lated in ICF syndrome. This does not reflect a chromosome-wide islands on the inactive X chromosome (Xi). -
DNA Methylation in Transcriptional Repression of Two Differentially Expressed X-Linked Genes, GPC3 and SYBL1
Proc. Natl. Acad. Sci. USA Vol. 96, pp. 616–621, January 1999 Genetics DNA methylation in transcriptional repression of two differentially expressed X-linked genes, GPC3 and SYBL1 i REID HUBER*†‡,R.SCOTT HANSEN§,MARIA STRAZZULLO¶,GINA PENGUE ,RICHARD MAZZARELLA**, MICHELE D’URSO¶,DAVID SCHLESSINGER*, GIUSEPPE PILIA††,STANLEY M. GARTLER§,§§, AND MAURIZIO D’ESPOSITO¶ *Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224; Departments of §Medicine and §§Genetics, University of Washington, Seattle, WA 98195; ¶International Institute of Genetics and Biophysics, 80125 Naples, Italy; iDepartment of Internal Medicine and **Institute for Biomedical Computing, Washington University, St. Louis, MO 63110; and ††Instituto di Ricerca, Talassemie e Anemie Mediterranee, 09100 Cagliari, Italy Contributed by Stanley M. Gartler, November 9, 1998 ABSTRACT Methylation of CpG islands is an established 5-azacytidine results in the transcriptional activation of many transcriptional repressive mechanism and is a feature of repressed genes (7). silencing in X chromosome inactivation. Housekeeping genes Although the way in which methylation may influence that are subject to X inactivation exhibit differential methyl- transcription is beginning to be understood (8), the degree to ation of their CpG islands such that the inactive alleles are which it is necessary andyor sufficient for repression in various hypermethylated. In this report, we examine two contrasting cases remains unknown. To analyze the influence of methyl- X-linked genes with CpG islands for regulation by DNA ation on transcription further, we have compared the extent methylation: SYBL1, a housekeeping gene in the Xq pseudo- and effects of methylation on two genes, each of which is autosomal region, and GPC3, a tissue-specific gene in Xq26 repressed strongly by two distinct mechanisms.