Regulation of Alternative Splicing: More Than Just the Abcs*
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Differential Analysis of Gene Expression and Alternative Splicing
i bioRxiv preprint doi: https://doi.org/10.1101/2020.08.23.234237; this version posted August 24, 2020. The copyright holder for this preprint i (which was not certified by peer review)“main” is the author/funder, — 2020/8/23 who has — granted 9:38 — bioRxiv page a1 license — #1 to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. i i EmpiReS: Differential Analysis of Gene Expression and Alternative Splicing Gergely Csaba∗, Evi Berchtold*,y, Armin Hadziahmetovic, Markus Gruber, Constantin Ammar and Ralf Zimmer Department of Informatics, Ludwig-Maximilians-Universitat¨ Munchen,¨ 80333, Munich, Germany ABSTRACT to translation. Different transcripts of the same gene are often expressed at the same time, possibly at different abundance, While absolute quantification is challenging in high- yielding a defined mixture of isoforms. Changes to this throughput measurements, changes of features composition are further referred to as differential alternative between conditions can often be determined with splicing (DAS). Various diseases can be linked to DAS high precision. Therefore, analysis of fold changes events (3). Most hallmarks of cancer like tumor progression is the standard method, but often, a doubly and immune escape (4, 5) can be attributed to changes in differential analysis of changes of changes is the transcript composition (6). DAS plays a prominent role required. Differential alternative splicing is an in various types of muscular dystrophy (MD) (7), splicing example of a doubly differential analysis, i.e. fold intervention by targeted exon removal is a therapeutic option changes between conditions for different isoforms in Duchenne MD (8). -
Serine Arginine-Rich Protein-Dependent Suppression Of
Serine͞arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers El Che´ rif Ibrahim*, Thomas D. Schaal†, Klemens J. Hertel‡, Robin Reed*, and Tom Maniatis†§ *Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115; †Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138; and ‡Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697-4025 Contributed by Tom Maniatis, January 28, 2005 The 5 and 3 splice sites within an intron can, in principle, be joined mechanisms by which exon skipping is prevented. Our data to those within any other intron during pre-mRNA splicing. How- reveal that splicing to the distal 3Ј splice site is suppressed by ever, exons are joined in a strict 5 to 3 linear order in constitu- proximal exonic sequences and that SR proteins are required for tively spliced pre-mRNAs. Thus, specific mechanisms must exist to this suppression. Thus, SR protein͞exonic enhancer complexes prevent the random joining of exons. Here we report that insertion not only function in exon and splice-site recognition but also play of exon sequences into an intron can inhibit splicing to the a role in ensuring that 5Ј and 3Ј splice sites within the same intron .downstream 3 splice site and that this inhibition is independent of are used, thus suppressing exon skipping intron size. The exon sequences required for splicing inhibition were found to be exonic enhancer elements, and their inhibitory Materials and Methods activity requires the binding of serine͞arginine-rich splicing fac- Construction of Plasmids. -
RNA Components of the Spliceosome Regulate Tissue- and Cancer-Specific Alternative Splicing
Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Research RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing Heidi Dvinge,1,2,4 Jamie Guenthoer,3 Peggy L. Porter,3 and Robert K. Bradley1,2 1Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; 2Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; 3Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA Alternative splicing of pre-mRNAs plays a pivotal role during the establishment and maintenance of human cell types. Characterizing the trans-acting regulatory proteins that control alternative splicing has therefore been the focus of much research. Recent work has established that even core protein components of the spliceosome, which are required for splicing to proceed, can nonetheless contribute to splicing regulation by modulating splice site choice. We here show that the RNA components of the spliceosome likewise influence alternative splicing decisions. Although these small nuclear RNAs (snRNAs), termed U1, U2, U4, U5, and U6 snRNA, are present in equal stoichiometry within the spliceosome, we found that their relative levels vary by an order of magnitude during development, across tissues, and across cancer samples. Physiologically relevant perturbation of individual snRNAs drove widespread gene-specific differences in alternative splic- ing but not transcriptome-wide splicing failure. Genes that were particularly sensitive to variations in snRNA abundance in a breast cancer cell line model were likewise preferentially misspliced within a clinically diverse cohort of invasive breast ductal carcinomas. -
The Differential Interaction of Snrnps with Pre-Mrna Reveals Splicing Kinetics in Living Cells
Published October 4, 2010 This article has original data in the JCB Data Viewer JCB: Article http://jcb-dataviewer.rupress.org/jcb/browse/3011 The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells Martina Huranová,1 Ivan Ivani,1 Aleš Benda,2 Ina Poser,3 Yehuda Brody,4,5 Martin Hof,2 Yaron Shav-Tal,4,5 Karla M. Neugebauer,3 and David StanČk1 1Institute of Molecular Genetics and 2J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic 3Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany 4The Mina and Everard Goodman Faculty of Life Sciences and 5Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel recursor messenger RNA (pre-mRNA) splicing is Core components of the spliceosome, U2 and U5 snRNPs, catalyzed by the spliceosome, a large ribonucleo- associated with pre-mRNA for 15–30 s, indicating that protein (RNP) complex composed of five small nuclear splicing is accomplished within this time period. Additionally, P Downloaded from RNP particles (snRNPs) and additional proteins. Using live binding of U1 and U4/U6 snRNPs with pre-mRNA oc- cell imaging of GFP-tagged snRNP components expressed curred within seconds, indicating that the interaction of at endogenous levels, we examined how the spliceosome individual snRNPs with pre-mRNA is distinct. These results assembles in vivo. A comprehensive analysis of snRNP are consistent with the predictions of the step-wise model dynamics in the cell nucleus enabled us to determine of spliceosome assembly and provide an estimate on the snRNP diffusion throughout the nucleoplasm as well as rate of splicing in human cells. -
Splicing Graphs and RNA-Seq Data
Splicing graphs and RNA-seq data Herv´ePag`es Daniel Bindreither Marc Carlson Martin Morgan Last modified: January 2019; Compiled: May 19, 2021 Contents 1 Introduction 1 2 Splicing graphs 2 2.1 Definitions and example . .2 2.2 Details about nodes and edges . .2 2.3 Uninformative nodes . .5 3 Computing splicing graphs from annotations 6 3.1 Choosing and loading a gene model . .6 3.2 Generating a SplicingGraphs object . .6 3.3 Basic manipulation of a SplicingGraphs object . .8 3.4 Extracting and plotting graphs from a SplicingGraphs object . 12 4 Splicing graph bubbles 15 4.1 Some definitions . 15 4.2 Computing the bubbles of a splicing graph . 17 4.3 AScodes ............................................... 18 4.4 Tabulating all the AS codes for Human chromosome 14 . 19 5 Counting reads 20 5.1 Assigning reads to the edges of a SplicingGraphs object . 22 5.2 How does read assignment work? . 23 5.3 Counting and summarizing the assigned reads . 25 6 Session Information 26 1 Introduction The SplicingGraphs package allows the user to create and manipulate splicing graphs [1] based on annotations for a given organism. Annotations must describe a gene model, that is, they need to contain the following information: The exact exon/intron structure (i.e., genomic coordinates) for the known transcripts. The grouping of transcripts by gene. Annotations need to be provided as a TxDb or GRangesList object, which is how a gene model is typically represented in Bioconductor. 1 The SplicingGraphs package defines the SplicingGraphs container for storing the splicing graphs together with the gene model that they are based on. -
Sorting out the Complexity of SR Protein Functions
Downloaded from rnajournal.cshlp.org on February 6, 2009 - Published by Cold Spring Harbor Laboratory Press RNA (2000), 6:1197–1211+ Cambridge University Press+ Printed in the USA+ Copyright © 2000 RNA Society+ REVIEW Sorting out the complexity of SR protein functions BRENTON R. GRAVELEY Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut 06030, USA INTRODUCTION been clear whether all of these activities occur during the removal of each intron+ Recent studies now sug- Members of the serine/arginine-rich (SR) protein fam- gest that all of the proposed SR protein functions are ily have multiple functions in the pre-mRNA splicing carried out during each round of splicing, and at least reaction+ In addition to being required for the removal some of these functions are performed by independent of constitutively spliced introns, SR proteins can func- SR protein molecules+ This review discusses recent tion to regulate alternative splicing both in vitro and in advances in understanding the diverse functions of SR vivo (Ge & Manley, 1990; Krainer et al+, 1990a; Fu proteins in metazoan pre-mRNA splicing and presents et al+, 1992; Zahler et al+, 1993a; Caceres et al+, 1994; a model that takes these new findings into account+ Wang & Manley, 1995)+ In the cell, SR proteins migrate Although the reader should keep in mind that the ac- from speckles—subnuclear domains that may function tivity of SR proteins in vivo can be influenced by mod- as storage sites for certain splicing factors—to -
Functional Control of HIV-1 Post-Transcriptional Gene Expression by Host Cell Factors
Functional control of HIV-1 post-transcriptional gene expression by host cell factors DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Amit Sharma, B.Tech. Graduate Program in Molecular Genetics The Ohio State University 2012 Dissertation Committee Dr. Kathleen Boris-Lawrie, Advisor Dr. Anita Hopper Dr. Karin Musier-Forsyth Dr. Stephen Osmani Copyright by Amit Sharma 2012 Abstract Retroviruses are etiological agents of several human and animal immunosuppressive disorders. They are associated with certain types of cancer and are useful tools for gene transfer applications. All retroviruses encode a single primary transcript that encodes a complex proteome. The RNA genome is reverse transcribed into DNA, integrated into the host genome, and uses host cell factors to transcribe, process and traffic transcripts that encode viral proteins and act as virion precursor RNA, which is packaged into the progeny virions. The functionality of retroviral RNA is governed by ribonucleoprotein (RNP) complexes formed by host RNA helicases and other RNA- binding proteins. The 5’ leader of retroviral RNA undergoes alternative inter- and intra- molecular RNA-RNA and RNA-protein interactions to complete multiple steps of the viral life cycle. Retroviruses do not encode any RNA helicases and are dependent on host enzymes and RNA chaperones. Several members of the host RNA helicase superfamily are necessary for progressive steps during the retroviral replication. RNA helicase A (RHA) interacts with the redundant structural elements in the 5’ untranslated region (UTR) of retroviral and selected cellular mRNAs and this interaction is necessary to facilitate polyribosome formation and productive protein synthesis. -
POLYADENYLATION REGULATION of U1A Mrna: CHARACTERIZING
STUDIES OF POLYADENYLATION REGULATION OF U1A mRNA BY AN RNP COMPLEX CONTAINING U1A AND U1 snRNP By ROSE MARIE CARATOZZOLO A dissertation submitted to the Graduate School – New Brunswick Rutgers, The State University of New Jersey and The Graduate School of Biomedical Sciences University of Medicine and Dentistry of New Jersey In partial fulfillment of the requirements for the degree of Doctor of Philosophy Graduate Program in Biochemistry Written under the direction of Samuel I. Gunderson, Ph.D., And approved by _____________________________ _____________________________ _____________________________ _____________________________ New Brunswick, New Jersey January, 2011 ABSTRACT OF THE DISSERTATION STUDIES OF POLYADENYLATION REGULATION OF U1A mRNA BY AN RNP COMPLEX CONTAINING U1A AND U1 snRNP By Rose Marie Caratozzolo Dissertation Director: Samuel I. Gunderson, Ph.D. The 3’-end processing of nearly all eukaryotic pre-mRNAs comprises multiple steps which culminate in the addition of a poly(A) tail, which is essential for mRNA stability, translation, and export. Consequently, polyadenylation regulation is an important component of gene expression. One way to regulate polyadenylation is to inhibit the activity of a single poly(A) site, as exemplified by the U1A protein that negatively autoregulates itself by binding to a Polyadenylation Inhibitory Element (PIE) site within the 3’ UTR of its own pre-mRNA. U1 snRNP, which is primarily involved in splice site recognition, inhibits poly(A) site activity in papillomaviruses by binding to 5’ splice site-like sequences, which have recently been named “U1-sites”. Here, a recently identified U1-site in the human U1A 3'UTR is examined and shown to synergize with the adjacent PIE site to inhibit polyadenylation. -
Srsf10 and the Minor Spliceosome Control Tissue-Specific and Dynamic
SHORT REPORT Srsf10 and the minor spliceosome control tissue-specific and dynamic SR protein expression Stefan Meinke1, Gesine Goldammer1, A Ioana Weber1,2, Victor Tarabykin2, Alexander Neumann1†, Marco Preussner1*, Florian Heyd1* 1Freie Universita¨ t Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Berlin, Germany; 2Institute of Cell Biology and Neurobiology, Charite´-Universita¨ tsmedizin Berlin, corporate member of Freie Universita¨ t Berlin, Humboldt-Universita¨ t zu Berlin, and Berlin Institute of Health, Berlin, Germany Abstract Minor and major spliceosomes control splicing of distinct intron types and are thought to act largely independent of one another. SR proteins are essential splicing regulators mostly connected to the major spliceosome. Here, we show that Srsf10 expression is controlled through an autoregulated minor intron, tightly correlating Srsf10 with minor spliceosome abundance across different tissues and differentiation stages in mammals. Surprisingly, all other SR proteins also correlate with the minor spliceosome and Srsf10, and abolishing Srsf10 autoregulation by Crispr/ Cas9-mediated deletion of the autoregulatory exon induces expression of all SR proteins in a human cell line. Our data thus reveal extensive crosstalk and a global impact of the minor spliceosome on major intron splicing. *For correspondence: [email protected] (MP); [email protected] (FH) Introduction Present address: †Omiqa Alternative splicing (AS) is a major mechanism that controls gene expression (GE) and expands the Corporation, c/o Freie proteome diversity generated from a limited number of primary transcripts (Nilsen and Graveley, Universita¨ t Berlin, Altensteinstraße, Germany 2010). Splicing is carried out by a multi-megadalton molecular machinery called the spliceosome of which two distinct complexes exist. -
SR Proteins: a Conserved Family of Pre-Mrna Splicing Factors
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press SR proteins: a conserved family of pre-mRNA splicing factors Alan M. Zahler, William S. Lane/ John A. Stolk, and Mark B. Roth^ Fred Hutchinson Cancer Research Center, Division of Basic Sciences, Seattle, Washington 98104 USA; ^Harvard Microchemistry Facility, Cambridge, Massachusetts 02138 USA We demonstrate that four different proteins from calf thymus are able to restore splicing in the same splicing-deficient extract using several different pre-mRNA substrates. These proteins are members of a conserved family of proteins recognized by a monoclonal antibody that binds to active sites of RNA polymerase II transcription. We purified this family of nuclear phosphoproteins to apparent homogeneity by two salt precipitations. The family, called SR proteins for their serine- and arginine-rich carboxy-terminal domains, consists of at least five different proteins with molecular masses of 20, 30, 40, 55, and 75 kD. Microsequencing revealed that they are related but not identical. In four of the family members a repeated protein sequence that encompasses an RNA recognition motif was observed. We discuss the potential role of this highly conserved, functionally related set of proteins in pre-mRNA splicing. [Key Words: SR proteins; alternative splicing; RNA splicing; splicing factors] Received lanuary 21, 1992; revised version accepted March 2, 1992. Studies of mRNAs from many different tissues and de high levels of spliceosomal components, including sites velopmental stages show that regulation of RNA pro of RNA polymerase II transcription on lampbrush chro cessing can lead to the expression of multiple proteins mosomes and B "snurposomes" in oocyte nuclei, and from single genes (Smith et al. -
Protection Against Retrovirus Pathogenesis by SR Protein Inhibitors
Protection against retrovirus pathogenesis by SR protein inhibitors. Anne Keriel, Florence Mahuteau-Betzer, Chantal Jacquet, Marc Plays, David Grierson, Marc Sitbon, Jamal Tazi To cite this version: Anne Keriel, Florence Mahuteau-Betzer, Chantal Jacquet, Marc Plays, David Grierson, et al.. Protec- tion against retrovirus pathogenesis by SR protein inhibitors.. PLoS ONE, Public Library of Science, 2009, 4 (2), pp.e4533. 10.1371/journal.pone.0004533. hal-00368669 HAL Id: hal-00368669 https://hal.archives-ouvertes.fr/hal-00368669 Submitted on 25 May 2021 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. Distributed under a Creative Commons Attribution| 4.0 International License Protection against Retrovirus Pathogenesis by SR Protein Inhibitors Anne Keriel1, Florence Mahuteau-Betzer2, Chantal Jacquet1, Marc Plays1, David Grierson3,Marc Sitbon1*, Jamal Tazi1* 1 Universite´ Montpellier 2 Universite´ Montpellier 1 CNRS, Institut de Ge´ne´tique Mole´culaire de Montpellier (IGMM), UMR5535, IFR122, Montpellier, France, 2 Laboratoire de Pharmaco-chimie, CNRS-Institut Curie, UMR 176 Bat 110 Centre Universitaire, Orsay, France, 3 Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada Abstract Indole derivatives compounds (IDC) are a new class of splicing inhibitors that have a selective action on exonic splicing enhancers (ESE)-dependent activity of individual serine-arginine-rich (SR) proteins. -
HIV-1: to Splice Or Not to Splice, That Is the Question
viruses Review HIV-1: To Splice or Not to Splice, That Is the Question Ann Emery 1 and Ronald Swanstrom 1,2,3,* 1 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; [email protected] 2 Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA 3 Center for AIDS Research, University of North Carolina, Chapel Hill, NC 27599, USA * Correspondence: [email protected] Abstract: The transcription of the HIV-1 provirus results in only one type of transcript—full length genomic RNA. To make the mRNA transcripts for the accessory proteins Tat and Rev, the genomic RNA must completely splice. The mRNA transcripts for Vif, Vpr, and Env must undergo splicing but not completely. Genomic RNA (which also functions as mRNA for the Gag and Gag/Pro/Pol precursor polyproteins) must not splice at all. HIV-1 can tolerate a surprising range in the relative abundance of individual transcript types, and a surprising amount of aberrant and even odd splicing; however, it must not over-splice, which results in the loss of full-length genomic RNA and has a dramatic fitness cost. Cells typically do not tolerate unspliced/incompletely spliced transcripts, so HIV-1 must circumvent this cell policing mechanism to allow some splicing while suppressing most. Splicing is controlled by RNA secondary structure, cis-acting regulatory sequences which bind splicing factors, and the viral protein Rev. There is still much work to be done to clarify the combinatorial effects of these splicing regulators. These control mechanisms represent attractive targets to induce over-splicing as an antiviral strategy.