DOCSLIB.ORG

The Nuclear Cap-Binding Complex As Choreographer of Gene Transcription and Pre-Mrna Processing

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Nuclear Cap-Binding Complex As Choreographer of Gene Transcription and Pre-Mrna Processing Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW The nuclear cap-binding complex as choreographer of gene transcription and pre-mRNA processing Xavier Rambout1,2 and Lynne E. Maquat1,2 1Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA; 2Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA The largely nuclear cap-binding complex (CBC) binds to tributed to elucidating the role of the CBC in the the 5′ caps of RNA polymerase II (RNAPII)-synthesized cytoplasm during the pioneer round of translation and transcripts and serves as a dynamic interaction platform nonsense-mediated mRNA decay (NMD) (for review, see for a myriad of RNA processing factors that regulate Maquat et al. 2010; Ryu and Kim 2017; Kurosaki et al. gene expression. While influence of the CBC can extend 2019), our current research focuses on the role of the into the cytoplasm, here we review the roles of the CBC CBC during gene transcription by RNAPII (Cho et al. in the nucleus, with a focus on protein-coding genes. We 2018). Here, we review known roles of the CBC in the nu- discuss differences between CBC function in yeast and cleus during the transcription of genes that encode pro- mammals, covering the steps of transcription initiation, teins, stitching together past studies from diverse groups release of RNAPII from pausing, transcription elongation, to describe the continuum of CBC-mediated checks and cotranscriptional pre-mRNA splicing, transcription ter- balances in eukaryotic cells. mination, and consequences of spurious transcription. We describe parameters known to control the binding of generic or gene-specific cofactors that regulate CBC activ- ities depending on the process(es) targeted, illustrating Chromatin-associated steps in the synthesis how the CBC is an ever-changing choreographer of gene and processing of protein-coding transcripts expression. The transcription of eukaryotic protein-coding genes is a stepwise process that can be divided into fundamental stages, all of which are regulated by the CBC: preinitiation complex assembly, transcription initiation, promoter- The nuclear cap-binding complex (CBC), which is a het- proximal pausing, processive transcription elongation, erodimer conserved from Saccharomyces cerevisiae to and transcription termination coupled to pre-mRNA Homo sapiens, is composed of two cap-binding proteins 3′ end processing. The process of pre-mRNA splicing, be- 7 ′ (CBPs). CBP20 directly binds the m G cap at the 5 end ing largely cotranscriptional, is also presented in this of RNA polymerase II (RNAPII)-synthesized transcripts, review. while CBP80 stabilizes the binding of CBP20 to the cap and serves as an interaction platform for numerous factors that control virtually every step of gene expression (Gona- topoulos-Pournatzis and Cowling 2014; Müller-McNicoll Preinitiation complex assembly and Neugebauer 2014). RNAPII-synthesized transcripts The first step of gene transcription is assembly at the core bound by the CBC include precursor and processed promoter of a preinitiation complex (PIC) composed of mRNAs, long noncoding RNAs (lncRNAs), promoter up- RNAPII and general transcription factors (GTFs). PIC as- stream transcripts (PROMPTs), enhancer RNAs (eRNAs), sembly is positively and negatively controlled by a pleth- immature small nuclear RNAs (snRNAs), small nucleolar ora of transcription factors and cofactors as well as RNAs (snoRNAs) of intergenic origin, and primary-micro- chromatin remodelers that regulate promoter accessibili- RNAs (pri-miRNAs). Whereas our lab discovered and con- ty (Eychenne et al. 2017; Nogales et al. 2017). [Keywords: CBP80; CBP20; CBC; transcription preinitiation complex; transcription initiation; promoter-proximal pausing; transcription © 2020 Rambout and Maquat This article is distributed exclusively by elongation; RNA 3′ end formation; transcription termination; pre-mRNA Cold Spring Harbor Laboratory Press for the first six months after the splicing; alternative splicing] full-issue publication date (see http://genesdev.cshlp.org/site/misc/ Corresponding author: [email protected] terms.xhtml). After six months, it is available under a Creative Commons Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.339986. License (Attribution-NonCommercial 4.0 International), as described at 120. http://creativecommons.org/licenses/by-nc/4.0/. GENES & DEVELOPMENT 34:1113–1127 Published by Cold Spring Harbor Laboratory Press; ISSN 0890-9369/20; www.genesdev.org 1113 Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Rambout and Maquat Transcription initiation Transcription elongation can be interrupted by addi- tional pausing events. As one important example, RNAPII Transcription cofactors subsequently convey activating can pause at stable first nucleosomes (i.e., +1 nucleo- cues leading to phosphorylation of the RNAPII carboxy- somes) in mammals (Barski et al. 2007; Chiu et al. 2018; terminal domain (CTD) at serine 5 (S5) and S7 by the cy- Aoi et al. 2020), in fruit fly (Mavrich et al. 2008; Weber clin-dependent kinase 7 (CDK7) subunit of the GTF TFIIH et al. 2014), and in the fission yeast Schizosaccharomyces (Haberle and Stark 2018). CTD phosphorylation enables pombe (Booth et al. 2016). Like promoter-proximal paus- RNAPII to escape the promoter and begin pre-mRNA syn- ing, release from +1 nucleosome pausing relies on thesis; i.e., to initiate transcription. Despite being essen- P-TEFb (Booth et al. 2018; Chiu et al. 2018). However, tial to the process of gene transcription in both lower pausing at +1 nucleosomes is more transient (t <15 and higher eukaryotes (Schier and Taatjes 2020), PIC as- 1/2 sec) than pausing at promoter-proximal regions (t =2– sembly and transcription initiation are preferentially tar- 1/2 30 min) (Core and Adelman 2019). At least in mammals, geted for regulating gene expression in lower eukaryotes, +1 nucleosomes feedback to promoter-proximal pausing such as the budding yeast S. cerevisiae (Hahn and Young (Jimeno-González et al. 2015) as well as pre-mRNA splic- 2011), while promoter-proximal pausing has emerged as ing and early transcription termination (Chiu et al. 2018). the early step that largely regulates gene expression in On one hand, stable +1 nucleosomes enhance promoter- metazoans (Adelman and Lis 2012). proximal pausing by augmenting NELF recruitment (Jimeno-González et al. 2015). On the other hand, RNAPII Promoter-proximal pausing and pre-mRNA capping pausing at +1 nucleosomes located downstream from CpG islands has been proposed to cause premature transcrip- – In higher eukaryotes, RNAPII often pauses 25 50 bp tion termination in cases where the U1 small nuclear ribo- downstream from the transcription start site (TSS), await- nucleoprotein (snRNP) fails to recognize the 5′ splice site ing additional signals to engage in processive transcrip- of the first intron (Chiu et al. 2018). tion (Core and Adelman 2019). As the nascent transcript emerges from the exit channel of RNAPII, RNAPII stall- ing is induced by recruitment of (1) the two-subunit Pre-mRNA splicing β DSIF (dichloro-1- -D-ribofuranosylbenzimidazole [DRB] Consistent with extensive physical interactions between sensitivity-inducing factor) complex composed of SPT4 the transcription machinery and splicing factors, more and SPT5, and (2) the four-subunit NELF (negative elonga- than 75% of splicing events occur cotranscriptionally tion factor) complex composed of NELF-A, NELF-B, either (Neugebauer 2019). Posttranscriptional events are more the NELF-C or NELF-D isoform of the NELFCD gene, and likely to characterize constitutive splicing of 3′-terminal NELF-E. Particularly relevant to this review, promoter- ′ introns and alternative splicing (Neugebauer 2019). proximal pausing and accessibility of the 5 end of pre- Whereas cotranscriptional splicing kinetics may vary mRNA as it emerges from the RNAPII exit channel coin- ′ greatly between species (Neugebauer 2019), the core splic- cide to allow pre-mRNA 5 end capping (Rasmussen and ing machinery is globally well-conserved (Will and Lühr- Lis 1993; Martinez-Rucobo et al. 2015) and CBC recruit- ′ ′ mann 2011). First, 5 splice site recognition by U1 ment to the 5 cap (Visa et al. 1996; Listerman et al. snRNP, SF1 (BBP in yeast) binding to the branchpoint se- 2006; Glover-Cutter et al. 2008). Genome-wide recruit- ′ quence, and U2AF (Mud2p in yeast) binding to the poly- ment of the CBC to 5 caps is facilitated by NELF (Aoi pyrimidine tract and 3′ splice site result in formation of et al. 2020), which directly binds the CBC via the NELF- the early (E) complex (commitment complex in yeast). E subunit (Narita et al. 2007). Second, U2 snRNP replaces SF1/BBP to form the A com- Even though promoter-proximal pausing is less preva- plex. Third, recruitment of the U4/U6•U5 tri-snRNP lent in lower eukaryotes, in S. cerevisiae, promoter-prox- forms the B complex, which is subsequently extensively imal accumulation of RNAPII can be observed following remodeled to form the B∗ complex that catalyzes the first genetic inhibition of the first catalytic step of pre- splicing reaction. The C complex subsequently finalizes mRNA capping (Lahudkar et al. 2014). Nonetheless, splicing, releasing the lariat intron. such pausing does not coincide with CBC recruitment, which occurs more than ∼110 bp downstream from the ′ TSS
Load more

Recommended publications
  • UTR Directs UPF1-Dependent Mrna Decay in Mammalian Cells
    Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Research A GC-rich sequence feature in the 3′ UTR directs UPF1-dependent mRNA decay in mammalian cells Naoto Imamachi,1 Kazi Abdus Salam,1,3 Yutaka Suzuki,2 and Nobuyoshi Akimitsu1 1Isotope Science Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; 2Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan Up-frameshift protein 1 (UPF1) is an ATP-dependent RNA helicase that has essential roles in RNA surveillance and in post- transcriptional gene regulation by promoting the degradation of mRNAs. Previous studies revealed that UPF1 is associated with the 3′ untranslated region (UTR) of target mRNAs via as-yet-unknown sequence features. Herein, we aimed to identify characteristic sequence features of UPF1 targets. We identified 246 UPF1 targets by measuring RNA stabilization upon UPF1 depletion and by identifying mRNAs that associate with UPF1. By analyzing RNA footprint data of phosphorylated UPF1 and two CLIP-seq data of UPF1, we found that 3′ UTR but not 5′ UTRs or open reading frames of UPF1 targets have GC-rich motifs embedded in high GC-content regions. Reporter gene experiments revealed that GC-rich motifs in UPF1 targets were indispensable for UPF1-mediated mRNA decay. These findings highlight the important features of UPF1 target 3′ UTRs. [Supplemental material is available for this article.] RNA degradation plays a central role in the RNA surveillance ma- degradation (Unterholzner and Izaurralde 2004), respectively. chinery for aberrant mRNAs and the post-transcriptional regula- Thus, UPF1 plays a central role in the NMD pathway.
    [Show full text]
  • Crystal Structure of the UPF2-Interacting Domain of Nonsense-Mediated Mrna Decay Factor UPF1
    JOBNAME: RNA 12#10 2006 PAGE: 1 OUTPUT: Friday September 8 11:24:46 2006 csh/RNA/122854/rna1776 Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Crystal structure of the UPF2-interacting domain of nonsense-mediated mRNA decay factor UPF1 JAN KADLEC, DELPHINE GUILLIGAY, RAIMOND B. RAVELLI, and STEPHEN CUSACK European Molecular Biology Laboratory, Grenoble Outstation, BP 181, 38042 Grenoble Cedex 9, France ABSTRACT UPF1 is an essential eukaryotic RNA helicase that plays a key role in various mRNA degradation pathways, notably nonsense- mediated mRNA decay (NMD). In combination with UPF2 and UPF3, it forms part of the surveillance complex that detects mRNAs containing premature stop codons and triggers their degradation in all organisms studied from yeast to human. We describe the 3 A˚ resolution crystal structure of the highly conserved cysteine–histidine-rich domain of human UPF1 and show that it is a unique combination of three zinc-binding motifs arranged into two tandem modules related to the RING-box and U-box domains of ubiquitin ligases. This UPF1 domain interacts with UPF2, and we identified by mutational analysis residues in two distinct conserved surface regions of UPF1 that mediate this interaction. UPF1 residues we identify as important for the interaction with UPF2 are not conserved in UPF1 homologs from certain unicellular parasites that also appear to lack UPF2 in their genomes. Keywords: nonsense-mediated mRNA decay; NMD; surveillance complex; UPF1; X-ray crystallography INTRODUCTION from the mRNA. If, however, translation terminates at a PTC upstream of an EJC, UPF2 associated with a down- Nonsense-mediated mRNA decay (NMD) is an mRNA stream EJC can be bound by UPF1 that is recruited to the degradation pathway that detects and eliminates aberrant terminating ribosome within the so-called SURF complex, coding transcripts containing premature termination codons which also includes the translation release factors eRF1 and (PTC) originating from nonsense or frameshift mutations.
    [Show full text]
  • The Origins and Consequences of UPF1 Variants in Pancreatic Adenosquamous Carcinoma
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.14.248864; this version posted August 14, 2020. 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. The origins and consequences of UPF1 variants in pancreatic adenosquamous carcinoma Jacob T. Polaski1,2, Dylan B. Udy1,2,3, Luisa F. Escobar-Hoyos4,5,6, Gokce Askan4, Steven D. Leach4,5,7,8, Andrea Ventura9, Ram Kannan9,†, 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 3Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, 98195, USA 4David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA 5Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA 6Department of Pathology, Stony Brook University, New York, New York 11794, USA 7Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA 8Dartmouth Norris Cotton Cancer Center, Lebanon, New Hampshire 03766, USA 9Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065 †Correspondence: [email protected], [email protected] Keywords: UPF1, pancreatic adenosquamous carcinoma, cancer genomics bioRxiv preprint doi: https://doi.org/10.1101/2020.08.14.248864; this version posted August 14, 2020.
    [Show full text]
  • Symplekin and Multiple Other Polyadenylation Factors Participate in 3 -End Maturation of Histone Mrnas
    Downloaded from genesdev.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press Symplekin and multiple other polyadenylation factors participate in 3؅-end maturation of histone mRNAs Nikolay G. Kolev and Joan A. Steitz1 Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06536, USA .Most metazoan messenger RNAs encoding histones are cleaved, but not polyadenylated at their 3؅ ends Processing in mammalian cell extracts requires the U7 small nuclear ribonucleoprotein (U7 snRNP) and an unidentified heat-labile factor (HLF). We describe the identification of a heat-sensitive protein complex whose integrity is required for histone pre-mRNA cleavage. It includes all five subunits of the cleavage and polyadenylation specificity factor (CPSF), two subunits of the cleavage stimulation factor (CstF), and symplekin. Reconstitution experiments reveal that symplekin, previously shown to be necessary for cytoplasmic poly(A) tail elongation and translational activation of mRNAs during Xenopus oocyte maturation, is the essential heat-labile component. Thus, a common molecular machinery contributes to the nuclear maturation of mRNAs both lacking and possessing poly(A), as well as to cytoplasmic poly(A) tail elongation. [Keywords: Symplekin; polyadenylation; 3Ј-end processing; U7 snRNP; histone mRNA; Cajal body] Received September 1, 2005; revised version accepted September 12, 2005. During the S phase of the cell cycle, histone mRNA lev- unique component of the U7-specific Sm core, in which els are up-regulated to meet the need for histones to the spliceosomal SmD1 and SmD2 proteins are replaced package newly synthesized DNA. Increased transcrip- by Lsm10 and Lsm11 (Pillai et al.
    [Show full text]
  • A SARS-Cov-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
    A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing Supplementary Information Supplementary Discussion All SARS-CoV-2 protein and gene functions described in the subnetwork appendices, including the text below and the text found in the individual bait subnetworks, are based on the functions of homologous genes from other coronavirus species. These are mainly from SARS-CoV and MERS-CoV, but when available and applicable other related viruses were used to provide insight into function. The SARS-CoV-2 proteins and genes listed here were designed and researched based on the gene alignments provided by Chan et. al. 1 2020 .​ Though we are reasonably sure the genes here are well annotated, we want to note that not every ​ protein has been verified to be expressed or functional during SARS-CoV-2 infections, either in vitro or in vivo. ​ ​ In an effort to be as comprehensive and transparent as possible, we are reporting the sub-networks of these functionally unverified proteins along with the other SARS-CoV-2 proteins. In such cases, we have made notes within the text below, and on the corresponding subnetwork figures, and would advise that more caution be taken when examining these proteins and their molecular interactions. Due to practical limits in our sample preparation and data collection process, we were unable to generate data for proteins corresponding to Nsp3, Orf7b, and Nsp16. Therefore these three genes have been left out of the following literature review of the SARS-CoV-2 proteins and the protein-protein interactions (PPIs) identified in this study.
    [Show full text]
  • NUCLEOPROTEINS of CELL NUCLEI by A
    344 ZOOLOGY: MIRSK YA ND POLLISTER PROC, N. A. S. NUCLEOPROTEINS OF CELL NUCLEI By A. E. MIRSKY AND A. W. POLLISTER HOSPITAL OF THE ROCKEFELLER INSTITUTE FOR MEDICAL RESEARCH, AND DEPARTMENT OF Z6OLOGY, COLUMBIA UNIVERSITY Communicated August 3, 1942 We have prepared nucleoproteins from a wide variety of animal cells- from mammalian liver, kidney, pancreas, spleen, thymus, brain, from the liver, spleen and blood cells of the dogfish, and from the sperm of the trout, shad, frog and sea urchin. These nucleoproteins are located in the nuclei of the cells from which they are derived. In this paper we shall briefly de- scribe the method of preparation, some properties of the nucleoproteins and the evidence that they are in fact derived from cell nuclei. I. Preparation.-To extract these nucleoproteins from the cell and to separate them from other cellular constituents nothing more drastic is used than neutral sodium chloride solutions of varying concentrations. Before extraction, much cytoplasmic material is removed by thoroughly washing the minced tissue with physiological saline. From liver more than 60 per cent of all the protein present can be removed in this manner with- out destroying the main outlines of cell structure. The washed tissue is then extracted with 1 M NaCl (2 M NaCl is needed for extraction of sea- urchin sperm). As soon as the more concentrated salt solution is added the mixture becomes exceedingly viscous. By centrifugation at high speed (10,000 to 12,000 r. p. m.) a viscous, slightly opalescent supernatant fluid is obtained. The supernatant fluid is viscous because of the nucleoprotein dissolved in it.
    [Show full text]
  • Genes with 5' Terminal Oligopyrimidine Tracts Preferentially Escape Global Suppression of Translation by the SARS-Cov-2 NSP1 Protein
    Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein Shilpa Raoa, Ian Hoskinsa, Tori Tonna, P. Daniela Garciaa, Hakan Ozadama, Elif Sarinay Cenika, Can Cenika,1 a Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA 1Corresponding author: [email protected] Key words: SARS-CoV-2, Nsp1, MeTAFlow, translation, ribosome profiling, RNA-Seq, 5′ TOP, Ribo-Seq, gene expression 1 Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-Seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation level. We discover that a functionally-coherent subset of human genes are preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5′ terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes.
    [Show full text]
  • 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]).
    [Show full text]
  • This Thesis Has Been Submitted in Fulfilment of the Requirements for a Postgraduate Degree (E.G
    This thesis has been submitted in fulfilment of the requirements for a postgraduate degree (e.g. PhD, MPhil, DClinPsychol) at the University of Edinburgh. Please note the following terms and conditions of use: • This work is protected by copyright and other intellectual property rights, which are retained by the thesis author, unless otherwise stated. • A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. • This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author. • The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author. • When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Expression and subcellular localisation of poly(A)-binding proteins Hannah Burgess PhD The University of Edinburgh 2010 Abstract Poly(A)-binding proteins (PABPs) are important regulators of mRNA translation and stability. In mammals four cytoplasmic PABPs with a similar domain structure have been described - PABP1, tPABP, PABP4 and ePABP. The vast majority of research on PABP mechanism, function and sub-cellular localisation is however limited to PABP1 and little published work has explored the expression of PABP proteins. Here, I examine the tissue distribution of PABP1 and PABP4 in mouse and show that both proteins differ markedly in their expression at both the tissue and cellular level, contradicting the widespread perception that PABP1 is ubiquitously expressed. PABP4 is shown to be widely expressed though with an expression pattern distinct from PABP1, and thus may have a biological function in many tissues.
    [Show full text]
  • Proteomics Analysis of Cellular Proteins Co-Immunoprecipitated with Nucleoprotein of Influenza a Virus (H7N9)
    Article Proteomics Analysis of Cellular Proteins Co-Immunoprecipitated with Nucleoprotein of Influenza A Virus (H7N9) Ningning Sun 1,:, Wanchun Sun 2,:, Shuiming Li 3, Jingbo Yang 1, Longfei Yang 1, Guihua Quan 1, Xiang Gao 1, Zijian Wang 1, Xin Cheng 1, Zehui Li 1, Qisheng Peng 2,* and Ning Liu 1,* Received: 26 August 2015 ; Accepted: 22 October 2015 ; Published: 30 October 2015 Academic Editor: David Sheehan 1 Central Laboratory, Jilin University Second Hospital, Changchun 130041, China; [email protected] (N.S.); [email protected] (J.Y.); [email protected] (L.Y.); [email protected] (G.Q.); [email protected] (X.G.); [email protected] (Z.W.); [email protected] (X.C.); [email protected] (Z.L.) 2 Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun 130062, China; [email protected] 3 College of Life Sciences, Shenzhen University, Shenzhen 518057, China; [email protected] * Correspondence: [email protected] (Q.P.); [email protected] (N.L.); Tel./Fax: +86-431-8879-6510 (Q.P. & N.L.) : These authors contributed equally to this work. Abstract: Avian influenza A viruses are serious veterinary pathogens that normally circulate among avian populations, causing substantial economic impacts. Some strains of avian influenza A viruses, such as H5N1, H9N2, and recently reported H7N9, have been occasionally found to adapt to humans from other species. In order to replicate efficiently in the new host, influenza viruses have to interact with a variety of host factors. In the present study, H7N9 nucleoprotein was transfected into human HEK293T cells, followed by immunoprecipitated and analyzed by proteomics approaches.
    [Show full text]
  • Extensive Cross-Regulation of Post- Transcriptional Regulatory Networks in Drosophila
    Downloaded from genome.cshlp.org on October 3, 2021 - Published by Cold Spring Harbor Laboratory Press Extensive cross-regulation of post- transcriptional regulatory networks in Drosophila Marcus H. Stoibera,b, Sara Olsonc, Gemma E. Mayc, Michael O. Duffc, Jan Manentd, Robert Obard, K. G. Guruharshad,e, Spyros Artavanis-Tsakonasd,e,*, James B. Brownb,f,*, Brenton R. Graveleyc,* and Susan E. Celnikerb,* a Department of Biostatistics, University of California Berkeley, Berkeley, CA b Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, CA c Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT d Department of Cell Biology, Harvard Medical School, Boston, MA e Biogen Idec Inc, 14 Cambridge Center, Cambridge, MA 02142 USA f Department of Statistics, University of California Berkeley, Berkeley, CA * Corresponding Authors Susan Celniker, PhD Deputy of Science, Life Sciences Division Adjunct Professor, Comparative Biochemistry, University of California, Berkeley Co-Director Berkeley Drosophila Genome Project Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS 977-180 Berkeley, CA 94720, USA E-mail: celniker @fruitfly.org Telephone: (510) 486-6258 Fax Number: (510) 495-2723 Brenton R. Graveley Department of Genetics and Genome Sciences Institute for Systems Genomics University of Connecticut Health Center Farmington, CT Email: [email protected] Phone: (860) 679-2090 Fax: (860) 679-8345 Downloaded from genome.cshlp.org on October 3, 2021
    [Show full text]
  • The Interactome Analysis of the Respiratory Syncytial Virus Protein M2-1 Suggests a New Role in Viral Mrna Metabolism Post-Trans
    www.nature.com/scientificreports OPEN The Interactome analysis of the Respiratory Syncytial Virus protein M2-1 suggests a new role in viral mRNA metabolism post- transcription Camille Bouillier1, Gina Cosentino1, Thibaut Léger 2, Vincent Rincheval1, Charles-Adrien Richard 3, Aurore Desquesnes1, Delphine Sitterlin1, Sabine Blouquit-Laye1, Jean-Francois Eléouët3, Elyanne Gault1,4 & Marie-Anne Rameix-Welti 1,4* Human respiratory syncytial virus (RSV) is a globally prevalent negative-stranded RNA virus, which can cause life-threatening respiratory infections in young children, elderly people and immunocompromised patients. Its transcription termination factor M2-1 plays an essential role in viral transcription, but the mechanisms underpinning its function are still unclear. We investigated the cellular interactome of M2-1 using green fuorescent protein (GFP)-trap immunoprecipitation on RSV infected cells coupled with mass spectrometry analysis. We identifed 137 potential cellular partners of M2-1, among which many proteins associated with mRNA metabolism, and particularly mRNA maturation, translation and stabilization. Among these, the cytoplasmic polyA-binding protein 1 (PABPC1), a candidate with a major role in both translation and mRNA stabilization, was confrmed to interact with M2-1 using protein complementation assay and specifc immunoprecipitation. PABPC1 was also shown to colocalize with M2-1 from its accumulation in inclusion bodies associated granules (IBAGs) to its liberation in the cytoplasm. Altogether, these results strongly suggest that M2-1 interacts with viral mRNA and mRNA metabolism factors from transcription to translation, and imply that M2-1 may have an additional role in the fate of viral mRNA downstream of transcription. Human respiratory syncytial virus (RSV) is the most common cause of respiratory infection in neonates and infants worldwide.
    [Show full text]