Post Transcriptional Modification Definition
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Mutation of the AAUAAA Polyadenylation Signal Depresses in Vitro Splicing of Proximal but Not Distal Introns
Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Mutation of the AAUAAA polyadenylation signal depresses in vitro splicing of proximal but not distal introns Maho Niwa and Susan M. Berget Marrs McClean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030 USA To investigate the relationship between splicing and polyadenylation during the production of vertebrate mRNAs, we examined the effect of mutation of a poly(A) site on splicing of upstream introns. Mutation of the AAUAAA polyadenylation consensus sequence inhibited in vitro splicing of an upstream intron. The magnitude of the depression depended on the magnesium concentration. Dependence of splicing on polyadenylation signals suggests the existence of interaction between polyadenylation and splicing factors. In multi-intron precursor RNAs containing duplicated splice sites, mutation of the poly(A) site inhibited removal of the last intron, but not the removal of introns farther upstream. Inhibition of removal of only the last intron suggests segmental recognition of multi-exon precursor RNAs and is consistent with previous suggestions that signals at both ends of an exon are required for effective splicing of an upstream intron. [Key Words: Polyadenylation signal; splicing; vertebrate RNAs] Received July 31, 1991; revised version accepted September 10, 1991. The majority of vertebrate mRNAs undergo both splic- Using chimeric RNAs competent for both in vitro ing and polyadenylation during maturation. The rela- splicing and polyadenylation, we recently reported that tionship between the two processing steps has been un- in vitro polyadenylation is stimulated when an intron is clear. Polyadenylation has been reported to occur shortly placed upstream of a poly(A) site (Niwa et al. -
A Protein Required for RNA Processing and Splicing in Neurospora
Proc. Nati. Acad. Sci. USA Vol. 89, pp. 1676-1680, March 1992 Genetics A protein required for RNA processing and splicing in Neurospora mitochondria is related to gene products involved in cell cycle protein phosphatase functions BEATRICE TURCQ*, KATHERINE F. DOBINSONt, NOBUFUSA SERIZAWAt, AND ALAN M. LAMBOWITZ§ Departments of Molecular Genetics and Biochemistry, and the Biotechnology Center, The Ohio State University, 484 West Twelfth Avenue, Columbus, OH 43210 Communicated by Thomas R. Cech, November 25, 1991 ABSTRACT The Neurospora crassa cyt4 mutants have specifically affect the splicing of group I introns and have pleiotropic defects in mitochondrial RNA splicing, 5' and 3' end relatively little effect on other mitochondrial RNA processing processing, and RNA turnover. Here, we show that the cyt-4 reactions (1, 4, 7). gene encodes a 120-kDa protein with significant similarity to By contrast, the cyt4 mutants have a complex phenotype the SSD1/SRK1 protein of Saceharomyces cerevisiae and the with defects in a number of different aspects of mitochondrial DIS3 protein of Sclhizosaccharomyces pombe, which have been RNA metabolism in addition to RNA splicing (9, 10). The five implicated in protein phosphatase functions that regulate cell cyt4 mutants are cold sensitive; they grow slowly at 250C and cycle and mitotic chromosome segregation. The CYT-4 protein more rapidly at 370C. Initial studies focusing on the mitochon- is present in mitochondria and is truncated or deficient in two drial large rRNA showed that the cyt4 mutants are defective cyt4 mutants. Assuming that the CYT-4 protein functions in a in both splicing and 3' end synthesis and that the splicing defect manner similar to the SSD1/SRK1 and DIS3 proteins, we infer is more pronounced at lower temperatures (9). -
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). -
Transcription to RNA from Gene to Phenotype
11/8/11 Transcription to RNA From Gene to Phenotype DNA Gene 2 • The central dogma: molecule – DNA->RNA->protein Gene 1 – One Gene, One Enzyme Gene 3 • Beadle & Tatum expts. • Transcription DNA strand 3! 5! – Initiation (template) A C C A A A C C G A G T – Elongation – Termination TRANSCRIPTION U G G U U U G G C U C A • mRNA processing mRNA 5! 3! – Introns and exons Codon TRANSLATION • Other types of RNA 11/9/2011 Protein Trp Phe Gly Ser Amino acid In Prokaryotes transcription and translation occur simultaneously In Eukaryotes Nuclear – Transcription and envelope translation occur in separate compartments TRANSCRIPTION DNA DNA TRANSCRIPTION of the cell Pre-mRNA RNA PROCESSING mRNA Ribosome – RNA transcripts are mRNA TRANSLATION modified before becoming true mRNA Ribosome Polypeptide TRANSLATION Polypeptide Figure 17.3a Figure 17.3b One Gene -> One Enzyme “One Gene -> One Enzyme” EXPERIMENT Class I Class II Class III Wild type Mutants Mutants Mutants Minimal Normal bread-mold cells can medium synthesize arginine from precursors (MM) (control) in the minimal medium MM + Ornithine Mutant 2 could MM + grow if either Citrulline Precursor Ornithine Citrulline Arginine citruline or MM + arginine was Specific enzymes (arrows) Arginine is an essential Arginine amino acid, required for (control) supplied. catalyze each step growth Therefore it must lack the enzyme to make Citruline Precursor Ornithine Citrulline Arginine 1 11/8/11 From Gene to Phenotype RNA Polymerase Non-template strand of DNA DNA Gene 2 RNA nucleotides molecule Gene 1 Gene 3 T C C A A A T 3 C T U ! 3 end DNA strand 3! 5! ! G (template) A C C A A A C C G A G T T A U G G A 5 C A U C C A C TRANSCRIPTION ! A T A A G G T T U G G U U U G G C U C A mRNA 5! 3! Direction of transcription 5! Codon (“downstream) Template TRANSLATION strand of DNA Protein Trp Phe Gly Ser New RNA Amino acid Synthesis of an RNA Transcript DNA is copied to make messenger RNA Promoter Transcription unit 5! 3! 3! 5! RNA polymerase DNA This is the “non-template” Start point binds to a promoter RNA polymerase strand. -
Polymerse Activity
University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2005 CHARACTERIZATION OF PLANT POLYADENYLATION TRANSACTING FACTORS-FACTORS THAT MODIFY POLY(A) POLYMERSE ACTIVITY Kevin Patrick Forbes University of Kentucky Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Forbes, Kevin Patrick, "CHARACTERIZATION OF PLANT POLYADENYLATION TRANSACTING FACTORS- FACTORS THAT MODIFY POLY(A) POLYMERSE ACTIVITY" (2005). University of Kentucky Doctoral Dissertations. 444. https://uknowledge.uky.edu/gradschool_diss/444 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Kevin Patrick Forbes The Graduate School University of Kentucky 2004 CHARACTERIZATION OF PLANT POLYADENYLATION TRANS- ACTING FACTORS-FACTORS THAT MODIFY POLY(A) POLYMERSE ACTIVITY _________________________________________ ABSTRACT OF DISSERTATION _________________________________________ A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Kevin Patrick Forbes Lexington, Kentucky Director: Dr. Arthur G. Hunt, Professor of Agronomy Lexington, Kentucky 2004 Copyright ” Kevin Patrick Forbes 2004 ABSTRACT OF DISSERTATION CHARACTERIZATION OF PLANT POLYADENYLATION TRANS-ACTING FACTORS-FACTORS THAT MODIFY POLY(A) POLYMERSE ACTIVITY Plant polyadenylation factors have proven difficult to purify and characterize, owing to the presence of excessive nuclease activity in plant nuclear extracts, thereby precluding the identification of polyadenylation signal-dependent processing and polyadenylation in crude extracts. -
Investigation of RNA-Mediated Pathogenic Pathways in a Drosophila Model of Expanded Repeat Disease
Investigation of RNA-mediated pathogenic pathways in a Drosophila model of expanded repeat disease A thesis submitted for the degree of Doctor of Philosophy, June 2010 Clare Louise van Eyk, B.Sc. (Hons.) School of Molecular and Biomedical Science, Discipline of Genetics The University of Adelaide II Table of Contents Index of Figures and Tables……………………………………………………………..VII Declaration………………………………………………………………………………......XI Acknowledgements…………………………………………………………………........XIII Abbreviations……………………………………………………………………………....XV Drosophila nomenclature…………………………………………………………….….XV Abstract………………………………………………………………………………........XIX Chapter 1: Introduction ............................................................................................1 1.0 Expanded repeat diseases....................................................................................1 1.1 Translated repeat diseases...................................................................................2 1.1.1 Polyglutamine diseases .............................................................................2 Huntington’s disease...................................................................................3 Spinal bulbar muscular atrophy (SBMA) .....................................................3 Dentatorubral-pallidoluysian atrophy (DRPLA) ...........................................4 The spinal cerebellar ataxias (SCAs)..........................................................4 1.1.2 Pathogenesis and aggregate formation .....................................................7 -
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. -
RNA Editing at Baseline and Following Endoplasmic Reticulum Stress
RNA Editing at Baseline and Following Endoplasmic Reticulum Stress By Allison Leigh Richards A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Human Genetics) in The University of Michigan 2015 Doctoral Committee: Professor Vivian G. Cheung, Chair Assistant Professor Santhi K. Ganesh Professor David Ginsburg Professor Daniel J. Klionsky Dedication To my father, mother, and Matt without whom I would never have made it ii Acknowledgements Thank you first and foremost to my dissertation mentor, Dr. Vivian Cheung. I have learned so much from you over the past several years including presentation skills such as never sighing and never saying “as you can see…” You have taught me how to think outside the box and how to create and explain my story to others. I would not be where I am today without your help and guidance. Thank you to the members of my dissertation committee (Drs. Santhi Ganesh, David Ginsburg and Daniel Klionsky) for all of your advice and support. I would also like to thank the entire Human Genetics Program, and especially JoAnn Sekiguchi and Karen Grahl, for welcoming me to the University of Michigan and making my transition so much easier. Thank you to Michael Boehnke and the Genome Science Training Program for supporting my work. A very special thank you to all of the members of the Cheung lab, past and present. Thank you to Xiaorong Wang for all of your help from the bench to advice on my career. Thank you to Zhengwei Zhu who has helped me immensely throughout my thesis even through my panic. -
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. -
The Nuclear Poly(A) Binding Protein of Mammals, but Not of Fission Yeast, Participates in Mrna Polyadenylation
Downloaded from rnajournal.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press REPORT The nuclear poly(A) binding protein of mammals, but not of fission yeast, participates in mRNA polyadenylation UWE KÜHN, JULIANE BUSCHMANN, and ELMAR WAHLE Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany ABSTRACT The nuclear poly(A) binding protein (PABPN1) has been suggested, on the basis of biochemical evidence, to play a role in mRNA polyadenylation by strongly increasing the processivity of poly(A) polymerase. While experiments in metazoans have tended to support such a role, the results were not unequivocal, and genetic data show that the S. pombe ortholog of PABPN1, Pab2, is not involved in mRNA polyadenylation. The specific model in which PABPN1 increases the rate of poly(A) tail elongation has never been examined in vivo. Here, we have used 4-thiouridine pulse-labeling to examine the lengths of newly synthesized poly(A) tails in human cells. Knockdown of PABPN1 strongly reduced the synthesis of full-length tails of ∼250 nucleotides, as predicted from biochemical data. We have also purified S. pombe Pab2 and the S. pombe poly(A) polymerase, Pla1, and examined their in vitro activities. Whereas PABPN1 strongly increases the activity of its cognate poly(A) polymerase in vitro, Pab2 was unable to stimulate Pla1 to any significant extent. Thus, in vitro and in vivo data are consistent in supporting a role of PABPN1 but not S. pombe Pab2 in the polyadenylation of mRNA precursors. Keywords: poly(A) binding protein; poly(A) polymerase; mRNA polyadenylation; pre-mRNA 3′; processing INTRODUCTION by poly(A) polymerase with the help of the cleavage and poly- adenylation specificity factor (CPSF), which binds the polya- The poly(A) tails of eukaryotic mRNAs are covered by specif- denylation signal AAUAAA. -
Mechanisms of Mrna Polyadenylation
Turkish Journal of Biology Turk J Biol (2016) 40: 529-538 http://journals.tubitak.gov.tr/biology/ © TÜBİTAK Review Article doi:10.3906/biy-1505-94 Mechanisms of mRNA polyadenylation Hızlan Hıncal AĞUŞ, Ayşe Elif ERSON BENSAN* Department of Biology, Arts and Sciences, Middle East Technical University, Ankara, Turkey Received: 26.05.2015 Accepted/Published Online: 21.08.2015 Final Version: 18.05.2016 Abstract: mRNA 3’-end processing involves the addition of a poly(A) tail based on the recognition of the poly(A) signal and subsequent cleavage of the mRNA at the poly(A) site. Alternative polyadenylation (APA) is emerging as a novel mechanism of gene expression regulation in normal and in disease states. APA results from the recognition of less canonical proximal or distal poly(A) signals leading to changes in the 3’ untranslated region (UTR) lengths and even in some cases changes in the coding sequence of the distal part of the transcript. Consequently, RNA-binding proteins and/or microRNAs may differentially bind to shorter or longer isoforms. These changes may eventually alter the stability, localization, and/or translational efficiency of the mRNAs. Overall, the 3’ UTRs are gaining more attention as they possess a significant posttranscriptional regulation potential guided by APA, microRNAs, and RNA-binding proteins. Here we provide an overview of the recent developments in the APA field in connection with cancer as a potential oncogene activator and/or tumor suppressor silencing mechanism. A better understanding of the extent and significance of APA deregulation will pave the way to possible new developments to utilize the APA machinery and its downstream effects in cancer cells for diagnostic and therapeutic applications. -
Targeted Cleavage and Polyadenylation of RNA by CRISPR-Cas13
bioRxiv preprint doi: https://doi.org/10.1101/531111; this version posted January 26, 2019. 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-ND 4.0 International license. Targeted Cleavage and Polyadenylation of RNA by CRISPR-Cas13 Kelly M. Anderson1,2, Pornthida Poosala1,2, Sean R. Lindley 1,2 and Douglas M. Anderson1,2,* 1Center for RNA Biology, 2Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, U.S.A., 14642 *Corresponding Author: Douglas M. Anderson: [email protected] Keywords: NUDT21, PspCas13b, PAS, CPSF, CFIm, Poly(A), SREBP1 1 bioRxiv preprint doi: https://doi.org/10.1101/531111; this version posted January 26, 2019. 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-ND 4.0 International license. Post-transcriptional cleavage and polyadenylation of messenger and long noncoding RNAs is coordinated by a supercomplex of ~20 individual proteins within the eukaryotic nucleus1,2. Polyadenylation plays an essential role in controlling RNA transcript stability, nuclear export, and translation efficiency3-6. More than half of all human RNA transcripts contain multiple polyadenylation signal sequences that can undergo alternative cleavage and polyadenylation during development and cellular differentiation7,8. Alternative cleavage and polyadenylation is an important mechanism for the control of gene expression and defects in 3’ end processing can give rise to myriad human diseases9,10.