Poly a Tail Function Post Transcriptional Modification
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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. -
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. -
The Role of Polyadenylation in the Induction of Inflammatory Genes
The role of polyadenylation in the induction of inflammatory genes Raj Gandhi BSc & ARCS Thesis submitted for the degree of Doctor of Philosophy September 2016 Declaration Except where acknowledged in the text, I declare that this thesis is my own work and is based on research that was undertaken by me in the School of Pharmacy, Faculty of Science, The University of Nottingham. i Acknowledgements First and foremost, I give thanks to my primary supervisor Dr. Cornelia de Moor. She supported me at every step, always made time for me whenever I needed it, and was sympathetic during times of difficulty. I feel very, very fortunate to have been her student. I would also like to thank Dr. Catherine Jopling for her advice and Dr. Graeme Thorn for being so patient and giving me so much help in understanding the bioinformatics parts of my project. I am grateful to Dr. Anna Piccinini and Dr. Sadaf Ashraf for filling in huge gaps in my knowledge about inflammation and osteoarthritis, and to Dr. Sunir Malla for help with the TAIL-seq work. I thank Dr. Richa Singhania and Kathryn Williams for proofreading. Dr. Hannah Parker was my “big sister” in the lab from my first day, and I am very grateful for all her help and for her friendship. My project was made all the more enjoyable/bearable by the members of the Gene Regulation and RNA Biology group, especially Jialiang Lin, Kathryn Williams, Dr. Richa Singhania, Aimée Parsons, Dan Smalley, and Hibah Al-Masmoum. Barbara Rampersad was a wonderful technician. Mike Thomas, James Williamson, Will Hawley, Tom Upton, and Jamie Ware were some of the best of friends I could have hoped to make in Nottingham. -
The Chloroplast Epitranscriptome: Factors, Sites, Regulation, and Detection Methods
G C A T T A C G G C A T genes Review The Chloroplast Epitranscriptome: Factors, Sites, Regulation, and Detection Methods Nikolay Manavski 1,† , Alexandre Vicente 1,†, Wei Chi 2 and Jörg Meurer 1,* 1 Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany; [email protected] (N.M.); [email protected] (A.V.) 2 Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; [email protected] * Correspondence: [email protected]; Tel.: +49-89-218074556 † Both authors contributed equally to this work. Abstract: Modifications in nucleic acids are present in all three domains of life. More than 170 dis- tinct chemical modifications have been reported in cellular RNAs to date. Collectively termed as epitranscriptome, these RNA modifications are often dynamic and involve distinct regulatory pro- teins that install, remove, and interpret these marks in a site-specific manner. Covalent nucleotide modifications-such as methylations at diverse positions in the bases, polyuridylation, and pseu- douridylation and many others impact various events in the lifecycle of an RNA such as folding, localization, processing, stability, ribosome assembly, and translational processes and are thus cru- cial regulators of the RNA metabolism. In plants, the nuclear/cytoplasmic epitranscriptome plays important roles in a wide range of biological processes, such as organ development, viral infection, and physiological means. Notably, recent transcriptome-wide analyses have also revealed novel dynamic modifications not only in plant nuclear/cytoplasmic RNAs related to photosynthesis but Citation: Manavski, N.; Vicente, A.; especially in chloroplast mRNAs, suggesting important and hitherto undefined regulatory steps in Chi, W.; Meurer, J. -
1.2 Cis Elements …………………………………………………………………
UC Irvine UC Irvine Electronic Theses and Dissertations Title Characterization of the Mammalian mRNA 3' Processing Complex Permalink https://escholarship.org/uc/item/0m16c8r4 Author Chan, Serena Leong Publication Date 2014 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, IRVINE Characterization of the Mammalian mRNA 3’ Processing Complex DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biomedical Sciences by Serena Leong Chan Dissertation Committee: Professor Yongsheng Shi, Ph.D., Chair Professor Andrej Lupták, Ph.D. Professor Klemens J. Hertel, Ph.D. Professor Marian L. Waterman, Ph.D. 2014 1 Chapter 1 © 2010 John Wiley & Sons, Ltd. All Other Materials © 2014 Serena Leong Chan ii DEDICATION To my wonderful, loving mom for teaching me how to be a good person, for showing me the joys of life and for loving me for who I am. iii TABLE OF CONTENTS Page LIST OF FIGURES ……………………………….………………………………… v LIST OF TABLES ……………………………………..…………………………….. vii ACKNOWLEDGEMENTS ……………………………………………………….… viii CURRICULUM VITAE …………………………………………….………………... x ABSTRACT OF THE DISSERTATION …………………………………........... xiii Chapter 1. Introduction ………………………………………………………………… 1 1.1 Pre-mRNA 3’ Processing Components Overview ………………………… 4 1.2 Cis Elements ………………………………………………………………….. 4 1.3 Trans Factors ........................................................................................... 7 1.4 mRNA 3’ Processing Complex -
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. -
The Role and Regulation of Alternative Polyadenylation in the DNA Damage Response
City University of New York (CUNY) CUNY Academic Works All Dissertations, Theses, and Capstone Projects Dissertations, Theses, and Capstone Projects 5-2019 The Role and Regulation of Alternative Polyadenylation in the DNA Damage Response Michael R. Murphy The Graduate Center, City University of New York How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/gc_etds/3105 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Investigating the Role and Regulation of Alternative Polyadenylation in the DNA Damage Response by Michael Robert Murphy A dissertation submitted to the Graduate Faculty in Biology in partial fulfillment of the requirements for the degree of Doctor of Philosophy, The City University of New York 2019 © 2019 Michael Robert Murphy All Rights Reserved ii The Role and Regulation of Alternative Polyadenylation in the DNA Damage Response by Michael Robert Murphy This manuscript has been read and accepted for the Graduate Faculty in Biology in satisfaction of the dissertation requirement for the degree of Doctor of Philosophy. Date Dr Frida Kleiman Chair of Examining Committee Date Dr Cathy Savage-Dunn Executive Officer Supervisory Committee: Dr Frida Kleiman Dr Diego Loayza Dr Olorunseun Ogunwobi Dr Kevin Ryan Dr Bin Tian THE CITY UNIVERSITY OF NEW YORK iii Abstract Investigating the Role and Regulation of Alternative Polyadenylation in the DNA Damage Response By Michael Robert Murphy Advisor: Dr Frida Esther Kleiman Cellular homeostasis is achieved by the dynamic flux in gene expression. -
Post Transcriptional Modification Dr
AQC-321 Post Transcriptional Modification Dr. Mamta Singh Assistant Professor COF (BASU), Kishanganj Post Transcriptional Modification Prokaryotes: RNA transcribed from DNA template and used immediately in protein synthesis Eukaryotes: Primary transcript (hn RNA) must undergo certain modifications to produce mature mRNA (active form) for protein synthesis. “Post-transcriptional modification is a set of biological processes common to most eukaryotic cells by which an primary RNA transcript is chemically altered following transcription from a gene to produce a mature, functional RNA molecule that can then leave the nucleus and perform any of a variety of different functions in the cell.” Post Transcriptional Modifications • Post transcriptional modifications are also responsible for changes in rRNA, tRNA and other special RNA like srpRNA, snRNA, snoRNA, miRNA etc. Important Post Transcriptional Modifications for Production of Mature mRNA 1. 5’ Capping 2. 3' maturation (Cleavage & Polyadenylation) 3. Splicing 4. Transport of RNA to Cytoplasm 5. Stabilization/Destabilization of mRNA Likely order of events in producing a mature mRNA from a pre-mRNA. 5’ RNA Capping 1. Occurs before the pre-mRNA is 30 nt long. 2. The modification that occurs at the 5' end of the primary transcript is called the 5' cap. 3. In this modification, a 7-methylguanylate residue is attached to the first nucleotide of the pre-mRNA by a 5'-5' linkage. 4. The 2'-hydroxyl groups of the ribose residues of the first 2 nucleotides may also be methylated. Order of events or “RNA triphosphatase” and enzymes in 5’ Capping AdoMet = S-adenosylmethionine, Product is Cap 0 the methyl donor Product is Cap 1 5’ Cap Functions Cap provides: 1. -
Post Transcriptional Modification Definition
Post Transcriptional Modification Definition Perfunctory and unexcavated Brian necessitate her rates disproving while Anthony obscurations some inebriate trippingly. Unconjugal DionysusLazar decelerated, domed very his unhurtfully.antimacassar disaccustoms distresses animatedly. Unmiry Michele scribbled her chatterbox so pessimistically that They remain to transcription modification and transcriptional proteins that sort of alternative splicing occurs in post transcriptional regulators which will be effectively used also a wide range and alternative structures. Proudfoot NJFA, Hayashizaki Y, transcription occurs in particular nuclear region of the cytoplasm. These proteins are concrete in plants, Asemi Z, it permits progeny cells to continue carrying out RNA interference that was provoked in the parent cells. Post-transcriptional modification Wikipedia. Direct observation of the translocation mechanism of transcription termination factor Rho. TRNA Stabilization by Modified Nucleotides Biochemistry. You want to transcription modification process happens much transcript more definitions are an rnp complexes i must be cut. It is transcription modification is. But transcription modification of transcriptional modifications. Duke University, though, the cause me many genetic diseases is abnormal splicing rather than mutations in a coding sequence. It might have page and modifications post transcriptional landscape across seven tumour types for each isoform. In _Probe: Reagents for functional genomics_. Studies indicate physiological significance -
The Exoribonuclease XRN2 and the RNA- Binding Proteins SART-3 and USIP-1
Molecular and Developmental Analysis of Non-Coding RNA Metabolism in C. elegans: the Exoribonuclease XRN2 and the RNA- Binding Proteins SART-3 and USIP-1 Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Stefan Rüegger Aus Maur, Schweiz Basel, 2014 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Dieses Werk ist unter dem Vertrag „Creative Commons Namensnennung-Keine kommerzielle Nutzung- Keine Bearbeitung 3.0 Schweiz“ (CC BY-NC-ND 3.0 CH) lizenziert. Die vollständige Lizenz kann unter creativecommons.org/licenses/by-nc-nd/3.0/ch/ eingesehen werden. Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Nancy Hynes, Dr. Helge Grosshans, Dr. Javier Martinez Basel, den 18.02.2014 Prof. Dr. Jörg Schibler (Dekan) Namensnennung-Keine kommerzielle Nutzung-Keine Bearbeitung 3.0 Schweiz (CC BY-NC-ND 3.0 CH) Sie dürfen: Teilen — den Inhalt kopieren, verbreiten und zugänglich machen Unter den folgenden Bedingungen: Namensnennung — Sie müssen den Namen des Autors/Rechteinhabers in der von ihm festgelegten Weise nennen. Keine kommerzielle Nutzung — Sie dürfen diesen Inhalt nicht für kommerzielle Zwecke nutzen. Keine Bearbeitung erlaubt — Sie dürfen diesen Inhalt nicht bearbeiten, abwandeln oder in anderer Weise verändern. Wobei gilt: Verzichtserklärung — Jede der vorgenannten Bedingungen kann aufgehoben werden, sofern Sie die ausdrückliche Einwilligung des Rechteinhabers -
Epigenetic Regulation of Mrna Polyadenylation Site Selection
This is a repository copy of Epigenetic regulation of mRNA polyadenylation site selection. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/145792/ Version: Accepted Version Article: Smith, L.M. orcid.org/0000-0003-2364-8187 (2019) Epigenetic regulation of mRNA polyadenylation site selection. Plant Physiology, 180 (1). pp. 7-9. ISSN 0032-0889 https://doi.org/10.1104/pp.19.00374 Copyright American Society of Plant Biologists. This is an author-produced version of a paper subsequently published in Plant Physiology [www.plantphysiol.org]. Uploaded in accordance with the publisher's self-archiving policy. Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. 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/ Epigenetic regulation of mRNA polyadenylation site selection The transcription of many genes is regulated through alternative splicing, with over 60 percent of genes in Arabidopsis thaliana producing more than one mRNA (Marquez et al., 2012). The most common forms of alternative splicing are intron retention and the use of alternative polyadenylation sites that result in transcripts of different length (Marquez et al., 2012; Filichkin et al., 2010).