Mouse Eml1 Knockout Project (CRISPR/Cas9)
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Mouse Germ Line Mutations Due to Retrotransposon Insertions Liane Gagnier1, Victoria P
Gagnier et al. Mobile DNA (2019) 10:15 https://doi.org/10.1186/s13100-019-0157-4 REVIEW Open Access Mouse germ line mutations due to retrotransposon insertions Liane Gagnier1, Victoria P. Belancio2 and Dixie L. Mager1* Abstract Transposable element (TE) insertions are responsible for a significant fraction of spontaneous germ line mutations reported in inbred mouse strains. This major contribution of TEs to the mutational landscape in mouse contrasts with the situation in human, where their relative contribution as germ line insertional mutagens is much lower. In this focussed review, we provide comprehensive lists of TE-induced mouse mutations, discuss the different TE types involved in these insertional mutations and elaborate on particularly interesting cases. We also discuss differences and similarities between the mutational role of TEs in mice and humans. Keywords: Endogenous retroviruses, Long terminal repeats, Long interspersed elements, Short interspersed elements, Germ line mutation, Inbred mice, Insertional mutagenesis, Transcriptional interference Background promoter and polyadenylation motifs and often a splice The mouse and human genomes harbor similar types of donor site [10, 11]. Sequences of full-length ERVs can TEs that have been discussed in many reviews, to which encode gag, pol and sometimes env, although groups of we refer the reader for more in depth and general infor- LTR retrotransposons with little or no retroviral hom- mation [1–9]. In general, both human and mouse con- ology also exist [6–9]. While not the subject of this re- tain ancient families of DNA transposons, none view, ERV LTRs can often act as cellular enhancers or currently active, which comprise 1–3% of these genomes promoters, creating chimeric transcripts with genes, and as well as many families or groups of retrotransposons, have been implicated in other regulatory functions [11– which have caused all the TE insertional mutations in 13]. -
EML4-ALK Variants: Biological and Molecular Properties, and the Implications for Patients
cancers Review EML4-ALK Variants: Biological and Molecular Properties, and the Implications for Patients Sarah R. Sabir ID , Sharon Yeoh, George Jackson and Richard Bayliss * ID Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; [email protected] (S.R.S.); [email protected] (S.Y.); [email protected] (G.J.) * Correspondence: [email protected]; Tel.: +44-113-343-9919 Academic Editor: Raymond Lai Received: 9 August 2017; Accepted: 31 August 2017; Published: 5 September 2017 Abstract: Since the discovery of the fusion between EML4 (echinoderm microtubule associated protein-like 4) and ALK (anaplastic lymphoma kinase), EML4-ALK, in lung adenocarcinomas in 2007, and the subsequent identification of at least 15 different variants in lung cancers, there has been a revolution in molecular-targeted therapy that has transformed the outlook for these patients. Our recent focus has been on understanding how and why the expression of particular variants can affect biological and molecular properties of cancer cells, as well as identifying the key signalling pathways triggered, as a result. In the clinical setting, this understanding led to the discovery that the type of variant influences the response of patients to ALK therapy. Here, we discuss what we know so far about the EML4-ALK variants in molecular signalling pathways and what questions remain to be answered. In the longer term, this analysis may uncover ways to specifically treat patients for a better outcome. Keywords: anaplastic lymphoma kinase; echinoderm microtubule-associated protein; non-small cell lung cancer; tyrosine kinase inhibitor 1. -
Revostmm Vol 10-4-2018 Ingles Maquetaciûn 1
108 ORIGINALS / Rev Osteoporos Metab Miner. 2018;10(4):108-18 Roca-Ayats N1, Falcó-Mascaró M1, García-Giralt N2, Cozar M1, Abril JF3, Quesada-Gómez JM4, Prieto-Alhambra D5,6, Nogués X2, Mellibovsky L2, Díez-Pérez A2, Grinberg D1, Balcells S1 1 Departamento de Genética, Microbiología y Estadística - Facultad de Biología - Universidad de Barcelona - Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) - Instituto de Salud Carlos III (ISCIII) - Instituto de Biomedicina de la Universidad de Barcelona (IBUB) - Instituto de Investigación Sant Joan de Déu (IRSJD) - Barcelona (España) 2 Unidad de Investigación en Fisiopatología Ósea y Articular (URFOA); Instituto Hospital del Mar de Investigaciones Médicas (IMIM) - Parque de Salud Mar - Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES); Instituto de Salud Carlos III (ISCIII) - Barcelona (España) 3 Departamento de Genética, Microbiología y Estadística; Facultad de Biología; Universidad de Barcelona - Instituto de Biomedicina de la Universidad de Barcelona (IBUB) - Barcelona (España) 4 Unidad de Metabolismo Mineral; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC); Hospital Universitario Reina Sofía - Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES); Instituto de Salud Carlos III (ISCIII) - Córdoba (España) 5 Grupo de Investigación en Enfermedades Prevalentes del Aparato Locomotor (GREMPAL) - Instituto de Investigación en Atención Primaria (IDIAP) Jordi Gol - Centro de Investigación -
Crystal Structure of EML1 Reveals the Basis for Hsp90 Dependence of Oncogenic EML4-ALK by Disruption of an Atypical Β-Propeller Domain
Crystal structure of EML1 reveals the basis for Hsp90 dependence of oncogenic EML4-ALK by disruption of an atypical β-propeller domain Mark W. Richardsa, Edward W. P. Lawb,La’Verne P. Rennallsc, Sara Busaccab, Laura O’Regana, Andrew M. Frya, Dean A. Fennellb, and Richard Baylissa,1 aDepartment of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom; bDepartment of Cancer Studies and Molecular Medicine, University of Leicester, Leicester LE1 9HN, United Kingdom; and cSection of Structural Biology, Institute of Cancer Research, London SW3 6JB, United Kingdom Edited by Charles David Stout, The Scripps Research Institute, La Jolla, CA, and accepted by the Editorial Board February 24, 2014 (received for review December 9, 2013) Proteins of the echinoderm microtubule-associated protein (EMAP)- variant 1 and regression in some EML4-ALK–positive tumor like (EML) family contribute to formation of the mitotic spindle and models (7, 9, 10). Furthermore, clinical efficacy of an Hsp90 in- interphase microtubule network. They contain a unique hydropho- hibitor in EML4-ALK NSCLC has been confirmed (11), and bic EML protein (HELP) motif and a variable number of WD40 clinical trials are ongoing. However, because neither ALK nor repeats. Recurrent gene rearrangements in nonsmall cell lung cancer EML4 are native Hsp90 clients, it was proposed that Hsp90 sen- fuse EML4 to anaplastic lymphoma kinase (ALK), causing expression sitivity of EML4-ALK fusions was due to their protein-folding of several fusion oncoprotein variants. We have determined a 2.6-Å properties, which might expose hydrophobic residues that lead to crystal structure of the representative ∼70-kDa core of EML1, re- Hsp90 recruitment (12). -
The Transcriptional Roles of ALK Fusion Proteins in Tumorigenesis
cancers Review The Transcriptional Roles of ALK Fusion Proteins in Tumorigenesis 1, 2, , 1, Stephen P. Ducray y , Karthikraj Natarajan y z, Gavin D. Garland z, 1, , 2,3, , Suzanne D. Turner * y and Gerda Egger * y 1 Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge CB20QQ, UK 2 Department of Pathology, Medical University Vienna, 1090 Vienna, Austria 3 Ludwig Boltzmann Institute Applied Diagnostics, 1090 Vienna, Austria * Correspondence: [email protected] (S.D.T.); [email protected] (G.E.) European Research Initiative for ALK-related malignancies; www.erialcl.net. y These authors contributed equally to this work. z Received: 7 June 2019; Accepted: 23 July 2019; Published: 30 July 2019 Abstract: Anaplastic lymphoma kinase (ALK) is a tyrosine kinase involved in neuronal and gut development. Initially discovered in T cell lymphoma, ALK is frequently affected in diverse cancers by oncogenic translocations. These translocations involve different fusion partners that facilitate multimerisation and autophosphorylation of ALK, resulting in a constitutively active tyrosine kinase with oncogenic potential. ALK fusion proteins are involved in diverse cellular signalling pathways, such as Ras/extracellular signal-regulated kinase (ERK), phosphatidylinositol 3-kinase (PI3K)/Akt and Janus protein tyrosine kinase (JAK)/STAT. Furthermore, ALK is implicated in epigenetic regulation, including DNA methylation and miRNA expression, and an interaction with nuclear proteins has been described. Through these mechanisms, ALK fusion proteins enable a transcriptional programme that drives the pathogenesis of a range of ALK-related malignancies. Keywords: ALK; ALCL; NPM-ALK; EML4-ALK; NSCLC; ALK-translocation proteins; epigenetics 1. Introduction Anaplastic lymphoma kinase (ALK) was first successfully cloned in 1994 when it was reported in the context of a fusion protein in cases of anaplastic large cell lymphoma (ALCL) [1]. -
Analysis and Functional Evaluation of the Hair-Cell Transcriptome
Analysis and functional evaluation of the hair-cell transcriptome Brian M. McDermott, Jr.*, Jessica M. Baucom, and A. J. Hudspeth† Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 Contributed by A. J. Hudspeth, May 17, 2007 (sent for review March 31, 2007) An understanding of the molecular bases of the morphogenesis, ciated from the lagena, a receptor organ of the zebrafish’s ear. organization, and functioning of hair cells requires that the genes Linear amplification of the RNA from 200 hair cells yielded Ϸ40 expressed in these cells be identified and their functions ascer- g of aRNA, an enhancement of Ϸ1 millionfold. The resultant tained. After purifying zebrafish hair cells and detecting mRNAs labeled aRNA was hybridized to an Affymetrix microarray with oligonucleotide microarrays, we developed a subtractive (Affymetrix, Santa Clara, CA) containing Ϸ15,000 oligonucle- strategy that identified 1,037 hair cell-expressed genes whose otide probe sets. Averaging the outcomes of three experiments cognate proteins subserve functions including membrane trans- (SI Data Set 1) resulted in the identification of 6,472 transcripts port, synaptic transmission, transcriptional control, cellular adhe- scored as ‘‘present’’ (SI Data Set 2). sion and signal transduction, and cytoskeletal organization. To In the second step, we defined the transcriptome from cells of assess the validity of the subtracted hair-cell data set, we verified a nonsensory organ, the liver (SI Data Set 1). Hepatocytes were the presence of 11 transcripts in inner-ear tissue. Functional eval- selected for the subtraction process for three reasons: they are uation of two genes from the subtracted data set revealed their nonneuronal and thus unlikely to express synaptic factors; they importance in hair bundles: zebrafish larvae bearing the seahorse lack cilia (http://members.global2000.net/bowser/cilialist.html) and ift 172 mutations display specific kinociliary defects. -
Genome-Wide Gene Expression Profiling of Randall's Plaques In
CLINICAL RESEARCH www.jasn.org Genome-Wide Gene Expression Profiling of Randall’s Plaques in Calcium Oxalate Stone Formers † † Kazumi Taguchi,* Shuzo Hamamoto,* Atsushi Okada,* Rei Unno,* Hideyuki Kamisawa,* Taku Naiki,* Ryosuke Ando,* Kentaro Mizuno,* Noriyasu Kawai,* Keiichi Tozawa,* Kenjiro Kohri,* and Takahiro Yasui* *Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan; and †Department of Urology, Social Medical Corporation Kojunkai Daido Hospital, Daido Clinic, Nagoya, Japan ABSTRACT Randall plaques (RPs) can contribute to the formation of idiopathic calcium oxalate (CaOx) kidney stones; however, genes related to RP formation have not been identified. We previously reported the potential therapeutic role of osteopontin (OPN) and macrophages in CaOx kidney stone formation, discovered using genome-recombined mice and genome-wide analyses. Here, to characterize the genetic patho- genesis of RPs, we used microarrays and immunohistology to compare gene expression among renal papillary RP and non-RP tissues of 23 CaOx stone formers (SFs) (age- and sex-matched) and normal papillary tissue of seven controls. Transmission electron microscopy showed OPN and collagen expression inside and around RPs, respectively. Cluster analysis revealed that the papillary gene expression of CaOx SFs differed significantly from that of controls. Disease and function analysis of gene expression revealed activation of cellular hyperpolarization, reproductive development, and molecular transport in papillary tissue from RPs and non-RP regions of CaOx SFs. Compared with non-RP tissue, RP tissue showed upregulation (˃2-fold) of LCN2, IL11, PTGS1, GPX3,andMMD and downregulation (0.5-fold) of SLC12A1 and NALCN (P,0.01). In network and toxicity analyses, these genes associated with activated mitogen- activated protein kinase, the Akt/phosphatidylinositol 3-kinase pathway, and proinflammatory cytokines that cause renal injury and oxidative stress. -
EML1 (3E8): Sc-100938
SANTA CRUZ BIOTECHNOLOGY, INC. EML1 (3E8): sc-100938 The Power to Question BACKGROUND SOURCE Echinoderm microtubule-associated proteins function to modify the assembly EML1 (3E8) is a mouse monoclonal antibody raised against recombinant dynamics of microtubules by making microtubules slightly longer yet more EML1 of human origin. dynamic. They are classified as ubiquitous due to their expression in most tis- sues, however, their expression does not occur in the thymus nor the peripher- PRODUCT al blood lymphocytes. In the human form of the protein, there is a WD40 Each vial contains 100 µl ascites containing IgM with < 0.1% sodium azide. domain, also contained in a number of eukaryotic proteins, that carries out functions including signal transduction using adaptor/regulatory modules, APPLICATIONS pre-mRNA processing and cytoskeleton assembly. EML1 (echinoderm micro- tubule-associated protein-like 1 or EMAP-1) may be a candidate gene for EML1 (3E8) is recommended for detection of EML1 of human origin by Usher syndrome type 1A. Usher syndromes (USHs) are a group of genetic dis- Western Blotting (starting dilution to be determined by researcher, dilution orders consisting of congenital deafness, retinitis pigmentosa, and vestibular range 1:100-1:5000), immunoprecipitation [1-2 µl per 100-500 µg of total dysfunction of variable onset and severity depending on the genetic type. protein (1 ml of cell lysate)] and solid phase ELISA (starting dilution to be determined by researcher, dilution range 1:100-1:5000). REFERENCES Suitable for use as control antibody for EML1 siRNA (h): sc-60576, EML1 1. Li, Q. and Suprenant, K.A. 1995. -
EML1 (CNG-Modulin) Controls Light Sensitivity in Darkness and Under Continuous Illumination in Zebrafish Retinal Cone Photoreceptors
The Journal of Neuroscience, November 6, 2013 • 33(45):17763–17776 • 17763 Cellular/Molecular EML1 (CNG-Modulin) Controls Light Sensitivity in Darkness and under Continuous Illumination in Zebrafish Retinal Cone Photoreceptors Juan I. Korenbrot,1 Milap Mehta,2 Nomingerel Tserentsoodol,2 John H. Postlethwait,3 and Tatiana I. Rebrik2 1Departments of Ophthalmology and Physiology, School of Medicine, University of California, San Francisco, San Francisco, California 94143, 2Albert Eye Research Institute, Duke University Medical Center, Durham, North Carolina 27710, and 3Department of Biology, University of Oregon, Eugene, Oregon 97403 The ligand sensitivity of cGMP-gated (CNG) ion channels in cone photoreceptors is modulated by CNG-modulin, a Ca 2ϩ-binding protein. We investigated the functional role of CNG-modulin in phototransduction in vivo in morpholino-mediated gene knockdown zebrafish. Through comparative genomic analysis, we identified the orthologue gene of CNG-modulin in zebrafish, eml1, an ancient gene present in the genome of all vertebrates sequenced to date. We compare the photoresponses of wild-type cones with those of cones that do not express the EML1 protein. In the absence of EML1, dark-adapted cones are ϳ5.3-fold more light sensitive than wild-type cones. Previous qualitative studies in several nonmammalian species have shown that immediately after the onset of continuous illumination, cones are less light sensitive than in darkness, but sensitivity then recovers over the following 15–20 s. We characterize light sensitivity recovery in continuously illuminated wild-type zebrafish cones and demonstrate that sensitivity recovery does not occur in the absence of EML1. Introduction dependent changes in cone outer segment free Ca 2ϩ (Sampath et The transduction signal in retinal cone photoreceptors is gener- al., 1999; Leung et al., 2007). -
Fusion of EML1 to ABL1 in T-Cell Acute Lymphoblastic Leukemia with Cryptic T(9;14)(Q34;Q32)
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Dadun, University of Navarra NEOPLASIA Brief report Fusion of EML1 to ABL1 in T-cell acute lymphoblastic leukemia with cryptic t(9;14)(q34;q32) Kim De Keersmaecker, Carlos Graux, Maria D. Odero, Nicole Mentens, Riet Somers, Johan Maertens, Iwona Wlodarska, Peter Vandenberghe, Anne Hagemeijer, Peter Marynen, and Jan Cools The BCR-ABL1 fusion kinase is frequently (HOX11). Echinoderm microtubule-associ- ties of the fusion kinase. EML1-ABL1 and associated with chronic myeloid leukemia ated protein–like 1–Abelson 1 (EML1-ABL1) breakpoint cluster region (BCR)–ABL1 were and B-cell acute lymphoblastic leukemia but is a constitutively phosphorylated tyrosine equally sensitive to the tyrosine kinase inhib- is rare in T-cell acute lymphoblastic leuke- kinase that transforms Ba/F3 cells to growth itor imatinib. These data further demon- mia (T-ALL). We recently identified NUP214- factor–independent growth through activa- strate the involvement of ABL1 fusions in ABL1 as a variant ABL1 fusion gene in 6% of tion of survival and proliferation pathways, the pathogenesis of T-ALL and identify T-ALL patients. Here we describe the identi- including extracellular signal-related kinase EML1-ABL1 as a novel therapeutic target of fication of another ABL1 fusion, EML1- 1/2 (Erk1/2), signal transducers and activa- imatinib. (Blood. 2005;105:4849-4852) ABL1, in a T-ALL patient with a cryptic tors of transcription 5 (Stat5), and Lyn ki- t(9;14)(q34;q32) associated with deletion of nase. Deletion of the coiled-coil domain of CDKN2A (p16) and expression of TLX1 EML1 abrogated the transforming proper- © 2005 by The American Society of Hematology Introduction T-cell acute lymphoblastic leukemia (T-ALL) is frequently character- remission 15 months after diagnosis. -
Disruption in Murine Eml1 Perturbs Retinal Lamination During Early Development
The Jackson Laboratory The Mouseion at the JAXlibrary Faculty Research 2020 Faculty Research 3-27-2020 Disruption in murine Eml1 perturbs retinal lamination during early development. Gayle B. Collin The Jackson Laboratory, [email protected] J Won Mark P. Krebs The Jackson Laboratory, [email protected] W J Hicks Jeremy R. Charette The Jackson Laboratory, [email protected] See next page for additional authors Follow this and additional works at: https://mouseion.jax.org/stfb2020 Part of the Life Sciences Commons, and the Medicine and Health Sciences Commons Recommended Citation Collin, Gayle B.; Won, J; Krebs, Mark P.; Hicks, W J; Charette, Jeremy R.; Naggert, Juergen K.; and Nishina, Patsy M., "Disruption in murine Eml1 perturbs retinal lamination during early development." (2020). Faculty Research 2020. 67. https://mouseion.jax.org/stfb2020/67 This Article is brought to you for free and open access by the Faculty Research at The Mouseion at the JAXlibrary. It has been accepted for inclusion in Faculty Research 2020 by an authorized administrator of The Mouseion at the JAXlibrary. For more information, please contact [email protected]. Authors Gayle B. Collin, J Won, Mark P. Krebs, W J Hicks, Jeremy R. Charette, Juergen K. Naggert, and Patsy M. Nishina This article is available at The Mouseion at the JAXlibrary: https://mouseion.jax.org/stfb2020/67 www.nature.com/scientificreports OPEN Disruption in murine Eml1 perturbs retinal lamination during early development G. B. Collin1,2, J. Won1,2, M. P. Krebs1, W. J. Hicks1, J. R. Charette1, J. K. Naggert1 & P. M. Nishina1* During mammalian development, establishing functional neural networks in stratifed tissues of the mammalian central nervous system depends upon the proper migration and positioning of neurons, a process known as lamination. -
EML Proteins in Microtubule Regulation and Human Disease
This is a repository copy of EML proteins in microtubule regulation and human disease.. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/109979/ Version: Accepted Version Article: Fry, AM, O'Regan, L, Montgomery, J et al. (2 more authors) (2016) EML proteins in microtubule regulation and human disease. Biochemical Society Transactions, 44 (5). pp. 1281-1288. ISSN 0300-5127 https://doi.org/10.1042/BST20160125 © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society. This is an author produced version of a paper published in Biochemical Society Transactions. Uploaded in accordance with the publisher's self-archiving policy. Reuse Unless indicated otherwise, fulltext items are protected by copyright with all rights reserved. The copyright exception in section 29 of the Copyright, Designs and Patents Act 1988 allows the making of a single copy solely for the purpose of non-commercial research or private study within the limits of fair dealing. The publisher or other rights-holder may allow further reproduction and re-use of this version - refer to the White Rose Research Online record for this item. Where records identify the publisher as the copyright holder, users can verify any specific terms of use on the publisher’s website. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Fry et al.