The Spliceosome: Disorder and Dynamics Defined
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Coupling of Spliceosome Complexity to Intron Diversity
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.19.436190; this version posted March 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Coupling of spliceosome complexity to intron diversity Jade Sales-Lee1, Daniela S. Perry1, Bradley A. Bowser2, Jolene K. Diedrich3, Beiduo Rao1, Irene Beusch1, John R. Yates III3, Scott W. Roy4,6, and Hiten D. Madhani1,6,7 1Dept. of Biochemistry and Biophysics University of California – San Francisco San Francisco, CA 94158 2Dept. of Molecular and Cellular Biology University of California - Merced Merced, CA 95343 3Department of Molecular Medicine The Scripps Research Institute, La Jolla, CA 92037 4Dept. of Biology San Francisco State University San Francisco, CA 94132 5Chan-Zuckerberg Biohub San Francisco, CA 94158 6Corresponding authors: [email protected], [email protected] 7Lead Contact 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.19.436190; this version posted March 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SUMMARY We determined that over 40 spliceosomal proteins are conserved between many fungal species and humans but were lost during the evolution of S. cerevisiae, an intron-poor yeast with unusually rigid splicing signals. We analyzed null mutations in a subset of these factors, most of which had not been investigated previously, in the intron-rich yeast Cryptococcus neoformans. -
Mrna Turnover Philip Mitchell* and David Tollervey†
320 mRNA turnover Philip Mitchell* and David Tollervey† Nuclear RNA-binding proteins can record pre-mRNA are cotransported to the cytoplasm with the mRNP. These processing events in the structure of messenger proteins may preserve a record of the nuclear history of the ribonucleoprotein particles (mRNPs). During initial rounds of pre-mRNA in the cytoplasmic mRNP structure. This infor- translation, the mature mRNP structure is established and is mation can strongly influence the cytoplasmic fate of the monitored by mRNA surveillance systems. Competition for the mRNA and is used by mRNA surveillance systems that act cap structure links translation and subsequent mRNA as a checkpoint of mRNP integrity, particularly in the identi- degradation, which may also involve multiple deadenylases. fication of premature translation termination codons (PTCs). Addresses Cotransport of nuclear mRNA-binding proteins with mRNA Wellcome Trust Centre for Cell Biology, ICMB, University of Edinburgh, from the nucleus to the cytoplasm (nucleocytoplasmic shut- Kings’ Buildings, Edinburgh EH9 3JR, UK tling) was first observed for the heterogeneous nuclear *e-mail: [email protected] ribonucleoprotein (hnRNP) proteins. Some hnRNP proteins †e-mail: [email protected] are stripped from the mRNA at export [1], but hnRNP A1, Current Opinion in Cell Biology 2001, 13:320–325 A2, E, I and K are all exported (see [2]). Although roles for 0955-0674/01/$ — see front matter these hnRNP proteins in transport and translation have been © 2001 Elsevier Science Ltd. All rights reserved. reported [3•,4•], their affects on mRNA stability have been little studied. More is known about hnRNP D/AUF1 and Abbreviations AREs AU-rich sequence elements another nuclear RNA-binding protein, HuR, which act CBC cap-binding complex antagonistically to modulate the stability of a range of DAN deadenylating nuclease mRNAs containing AU-rich sequence elements (AREs) DSEs downstream sequence elements (reviewed in [2]). -
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. -
Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins
Biomolecules 2015, 5, 1441-1466; doi:10.3390/biom5031441 OPEN ACCESS biomolecules ISSN 2218-273X www.mdpi.com/journal/biomolecules/ Article Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins Rebecca Bish 1,†, Nerea Cuevas-Polo 1,†, Zhe Cheng 1, Dolores Hambardzumyan 2, Mathias Munschauer 3, Markus Landthaler 3 and Christine Vogel 1,* 1 Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA; E-Mails: [email protected] (R.B.); [email protected] (N.C.-P.); [email protected] (Z.C.) 2 The Cleveland Clinic, Department of Neurosciences, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA; E-Mail: [email protected] 3 RNA Biology and Post-Transcriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin-Buch, Robert-Rössle-Str. 10, Berlin 13092, Germany; E-Mails: [email protected] (M.M.); [email protected] (M.L.) † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-212-998-3976; Fax: +1-212-995-4015. Academic Editor: André P. Gerber Received: 10 May 2015 / Accepted: 15 June 2015 / Published: 15 July 2015 Abstract: DDX6 (p54/RCK) is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. -
Messenger RNA Reprogramming by Spliceosome-Mediated RNA Trans-Splicing
Messenger RNA reprogramming by spliceosome-mediated RNA trans-splicing Mariano A. Garcia-Blanco J Clin Invest. 2003;112(4):474-480. https://doi.org/10.1172/JCI19462. Perspective Series In the human genome, the majority of protein-encoding genes are interrupted by introns, which are removed from primary transcripts by a macromolecular enzyme known as the spliceosome. Spliceosomes can constitutively remove all the introns in a primary transcript to yield a fully spliced mRNA or alternatively splice primary transcripts leading to the production of many different mRNAs from one gene. This review examines how spliceosomes can recombine two primary transcripts in trans to reprogram messenger RNAs. Find the latest version: https://jci.me/19462/pdf PERSPECTIVE SERIES Genetic repair | Bruce A. Sullenger, Series Editor Messenger RNA reprogramming by spliceosome-mediated RNA trans-splicing Mariano A. Garcia-Blanco Department of Molecular Genetics and Microbiology and Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA In the human genome, the majority of protein-encoding genes are interrupted by introns, which are removed from primary transcripts by a macromolecular enzyme known as the spliceosome. Spliceo- somes can constitutively remove all the introns in a primary transcript to yield a fully spliced mRNA or alternatively splice primary transcripts leading to the production of many different mRNAs from one gene. This review examines how spliceosomes can recombine two primary transcripts in trans to reprogram messenger RNAs. J. Clin. Invest. 112:474–480 (2003). doi:10.1172/JCI200319462. Reprogramming of mRNA mediated RNA trans-splicing (SMaRT) has been used The reprogramming of mRNA is a form of gene ther- to reprogram mRNAs in animal cells in culture, in apy that modifies mRNA without directly changing xenografts, and in animals (9–13). -
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. -
Mechanism of Regulation of Spliceosome Activation by Brr2 And
I Mechanism of regulation of spliceosome activation by Brr2 and Prp8 and links to retinal disease Dissertation for the award of the degree “Doctor of Philosophy” (Ph.D.) in the Molecular Biology Program Division of Mathematics and Natural Sciences of the Georg-August-Universität Göttingen submitted by Sina Mozaffari-Jovin born in Sabzevar, Iran Göttingen 2012 II Members of the thesis committee: Prof. Dr. Reinhard Lührmann (Reviewer) Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen Prof. Dr. Reinhard Jahn Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen Prof. Dr. Ralf Ficner Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Date of submission of Thesis: December, 14th, 2012 III Affidavit I declare that my Ph.D. thesis entitled “Mechanism of regulation of spliceosome activation by Brr2 and Prp8 and links to retinal disease” has been written independently and with no other sources and aids than quoted. Sina Mozaffari-Jovin Göttingen, 2012 IV “The knowledge of anything, since all things have causes, is not acquired or complete unless it is known by its causes” Avicenna (Father of Modern Medicine; c. 980- June 1037) V Table of Contents 1 Abstract ......................................................................................................................... 1 2 Introduction .................................................................................................................. 4 2.1 The chemistry -
Distinct Domains of Splicing Factor Prp8 Mediate Different Aspects of Spliceosome Activation
Distinct domains of splicing factor Prp8 mediate different aspects of spliceosome activation Andreas N. Kuhn*, Elizabeth M. Reichl†, and David A. Brow‡ Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, WI 53706-1532 Communicated by James E. Dahlberg, University of Wisconsin Medical School, Madison, WI, May 21, 2002 (received for review March 25, 2002) Prp8 is the largest and most highly conserved protein in the splicing. Although Prp8 is two-thirds identical between yeast and spliceosome yet its mechanism of function is poorly understood. humans (21), it contains no recognizable structural motifs. To Our previous studies implicate Prp8 in control of spliceosome define domains important for the function of Prp8 in catalytic activation for the first catalytic step of splicing, because substitu- activation for the first transesterification reaction, we isolated tions in five distinct regions (a–e) of Prp8 suppress a cold-sensitive over 40 additional single amino acid substitutions in Prp8 that block to activation caused by a mutation in U4 RNA. Catalytic suppress U4-cs1 (11), here collectively called prp8-cat mutations, activation of the spliceosome is thought to require unwinding of because of their positive effect on catalytic activation. These the U1 RNA͞5 splice site and U4͞U6 RNA helices by the Prp28 and mutations cluster in five regions named a–e (see Fig. 4) and are Prp44͞Brr2 DExD͞H-box helicases, respectively. Here we show that distinct from mutations in Prp8 that suppress defects in the mutations in regions a, d, and e of Prp8 exhibit allele-specific second transesterification reaction. genetic interactions with mutations in Prp28, Prp44͞Brr2, and U6 We hypothesized that Prp8 regulates spliceosome activation RNA, respectively. -
The RNA Splicing Response to DNA Damage
Biomolecules 2015, 5, 2935-2977; doi:10.3390/biom5042935 OPEN ACCESS biomolecules ISSN 2218-273X www.mdpi.com/journal/biomolecules/ Review The RNA Splicing Response to DNA Damage Lulzim Shkreta and Benoit Chabot * Département de Microbiologie et d’Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-819-821-8000 (ext. 75321); Fax: +1-819-820-6831. Academic Editors: Wolf-Dietrich Heyer, Thomas Helleday and Fumio Hanaoka Received: 12 August 2015 / Accepted: 16 October 2015 / Published: 29 October 2015 Abstract: The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging. -
Group II Intron Rnps and Reverse Transcriptases: from Retroelements to Research Tools
Downloaded from http://cshperspectives.cshlp.org/ on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Group II Intron RNPs and Reverse Transcriptases: From Retroelements to Research Tools Marlene Belfort1 and Alan M. Lambowitz2 1Department of Biological Sciences and RNA Institute, University at Albany, State University of New York, Albany, New York 12222 2Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 Correspondence: [email protected]; [email protected] SUMMARY Group II introns, self-splicing retrotransposons, serve as both targets of investigation into their structure, splicing, and retromobility and a source of tools for genome editing and RNA anal- ysis. Here, we describe the first cryo-electron microscopy (cryo-EM) structure determination, at 3.8–4.5 Å, of a group II intron ribozyme complexed with its encoded protein, containing a reverse transcriptase (RT), required for RNA splicing and retromobility. We also describe a method called RIG-seq using a retrotransposon indicator gene for high-throughput integration profiling of group II introns and other retrotransposons. Targetrons, RNA-guided gene targeting agents widely used for bacterial genome engineering, are described next. Finally, we detail thermostable group II intron RTs, which synthesize cDNAs with high accuracy and processiv- ity, for use in various RNA-seq applications and relate their properties to a 3.0-Å crystal structure of the protein poised for reverse transcription. Biological insights from these group II intron revelations are discussed. Outline 1 Introduction 5 Technique 4. RTs with novel enzymatic properties as potent research tools 2 Technique 1. -
Structural Studies of the Spliceosome: Zooming Into the Heart Of
Available online at www.sciencedirect.com ScienceDirect Structural studies of the spliceosome: zooming into the heart of the machine Wojciech P Galej, Thi Hoang Duong Nguyen, Andrew J Newman and Kiyoshi Nagai Spliceosomes are large, dynamic ribonucleoprotein complexes canonical subunits: U1, U2, U4, U5 and U6 small nuclear that catalyse the removal of introns from messenger RNA ribonucleoprotein particles (snRNPs) and various other precursors via a two-step splicing reaction. The recent crystal non-snRNP factors [2]. The assembly process begins with 0 0 structure of Prp8 has revealed Reverse Transcriptase-like, the recognition of the 5 splice site (5 SS) and the branch Linker and Endonuclease-like domains. The intron branch- point sequence (BP) by U1 and U2 snRNPs, respectively, point cross-link with the Linker domain of Prp8 in active and further recruitment of the U4/U6.U5 tri-snRNP leads 0 0 spliceosomes and together with suppressors of 5 and 3 splice to the formation of the pre-catalytic complex B. A major site mutations this unambiguously locates the active site cavity. remodeling event catalyzed by the two DExD/H box Structural and mechanistic similarities with group II self- helicases Prp28 and Brr2 [3] leads to formation of the splicing introns have encouraged the notion that the catalytically competent complex B*, in which the first spliceosome is at heart a ribozyme, and recently the ligands for step of splicing occurs. two catalytic magnesium ions were identified within U6 snRNA. They position catalytic divalent metal ions in the same way as The enormous complexity and highly dynamic nature of Domain V of group II intron RNA, suggesting that the the spliceosome present a formidable challenge for struc- spliceosome and group II intron use the same catalytic tural and mechanistic studies. -
The Chloroplast Trans-Splicing RNA–Protein Supercomplex from the Green Alga Chlamydomonas Reinhardtii
cells Review The Chloroplast Trans-Splicing RNA–Protein Supercomplex from the Green Alga Chlamydomonas reinhardtii Ulrich Kück * and Olga Schmitt Allgemeine und Molekulare Botanik, Faculty for Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-234-32-28951 Abstract: In eukaryotes, RNA trans-splicing is a significant RNA modification process for the end-to- end ligation of exons from separately transcribed primary transcripts to generate mature mRNA. So far, three different categories of RNA trans-splicing have been found in organisms within a diverse range. Here, we review trans-splicing of discontinuous group II introns, which occurs in chloroplasts and mitochondria of lower eukaryotes and plants. We discuss the origin of intronic sequences and the evolutionary relationship between chloroplast ribonucleoprotein complexes and the nuclear spliceosome. Finally, we focus on the ribonucleoprotein supercomplex involved in trans-splicing of chloroplast group II introns from the green alga Chlamydomonas reinhardtii. This complex has been well characterized genetically and biochemically, resulting in a detailed picture of the chloroplast ribonucleoprotein supercomplex. This information contributes substantially to our understanding of the function of RNA-processing machineries and might provide a blueprint for other splicing complexes involved in trans- as well as cis-splicing of organellar intron RNAs. Keywords: group II intron; trans-splicing; ribonucleoprotein complex; chloroplast; Chlamydomonas reinhardtii Citation: Kück, U.; Schmitt, O. The Chloroplast Trans-Splicing RNA–Protein Supercomplex from the Green Alga Chlamydomonas reinhardtii. 1. Introduction Cells 2021, 10, 290. https://doi.org/ One of the unexpected and outstanding discoveries in 20th century biology was the 10.3390/cells10020290 identification of discontinuous eukaryotic genes [1,2].