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Towards understanding mechanism and physiological role of nonsense-mediated mRNA decay (NMD)

English title Towards understanding mechanism and physiological role of nonsense-mediated mRNA decay (NMD)
Applicant Mühlemann Oliver
Number 182831
Funding scheme Project funding (Div. I-III)
Research institution Departement für Chemie, Biochemie und Pharmazie Universität Bern
Institution of higher education University of Berne - BE
Main discipline Molecular Biology
Start/End 01.10.2018 - 30.09.2021
Approved amount 834'150.00
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All Disciplines (3)

Discipline
Molecular Biology
Biochemistry
Cellular Biology, Cytology

Keywords (6)

biochemical mRNP purification; posttranscriptional gene regulation; translation termination; Nonsense-mediated mRNA decay; mRNA turnover; genome editing

Lay Summary (German)

Lead
Die korrekte Expression der genetischen Information ist für die Existenz komplexer Organismen unabdingbar. Um dies zu gewährleisten, haben Zellen eine Vielzahl von Qualitätskontrollmechanismen entwickelt. Die zur Zeit bestuntersuchte dieser Qualitätskontrollen erkennt Boten-RNAs (mRNA) die Probleme bei der Translationstermination haben und wird “nonsense-mediated mRNA decay” (NMD) genannt. Das Projekt hat zum Ziel den molekularen Mechanismus von NMD und dessen physiologische Bedeutung zu verstehen.
Lay summary

Die Umsetzung der genetischen Information, d.h. die Genexpression, basiert eine Kaskade komplexer biochemischer Reaktionen von denen jeder Schritt mit einer gewissen Fehlerrate behaftet ist. Um gesamthaft die Akkumulierung zu vieler Fehler in mRNAs zu vermeiden haben eukaryontische Zellen verschiedene Checkpoints entwickelt, die fehlerhaft prozessierte mRNAs erkennen und rasch degradieren. Einer dieser Checkpoints erkennt mRNAs, deren Proteinbauplan vorzeitig abbricht und für den Prozess des schnellen Abbaus dieser sogenannten nonsense mRNAs wurde der Fachbegriff „nonsense-mediated mRNA decay“ (NMD) geprägt. Über seine Qualitätskontrollfunktion hinaus spielt NMD auch eine Rolle bei der Justierung der intrazellulären Konzentration von ungefähr 10% aller bekannten mRNAs. Welche biologischen Prozessen durch NMD beeinflusst oder gar gesteuert werden, ist noch nicht bekannt und ein Ziel dieses Projekts ist deshalb, mehr über die physiologischen Funktionen von NMD in humanen Zellen zu erfahren. Dazu mutieren und deletieren wir mittels CRISPR-Cas Technologie verschiedene NMD Faktoren in induzierbaren pluripotenten Stammzellen (iPSCs) und untersuchen dann,ob diese Veränderungen einen Einfluss auf die Differenzierung der Stammzellen haben. Ein anderer Fokus liegt auf der Aufklärung des molekularen Mechanismus von NMD. Insbesondere versuchen wir die Kriterien zu verstehen, welche die Zellen zur Unterscheidung zwischen „richtig“ (kein NMD Substrat) und „falsch“ (mRNA wird durch NMD abgebaut) anwendet.

Die erwarteten Resultate sollen nicht nur unser Verständnis für die der Genexpression in menschlichen Zellen unterliegenden molekularen Vorgänge erweitern, sondern sind auch von medizinischem Interesse, da ca. ein Drittel aller mit Krankheiten assoziierten Mutationen zur Produktion von nonsense mRNAs führt, die dann durch NMD abgebaut werden. Aus diesem Grund ist NMD ein wichtiger Modulator der klinischen Manifestationen dieser Erbkrankheiten.
Direct link to Lay Summary Last update: 01.10.2018

Responsible applicant and co-applicants

Employees

Publications

Publication
Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells
Karousis Evangelos D., Gypas Foivos, Zavolan Mihaela, Mühlemann Oliver (2021), Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells, in Genome Biology, 22(1), 223-223.
Translation mediated by the nuclear cap-binding complex is confined to the perinuclear region via a CTIF–DDX19B interaction
Park Yeonkyoung, Park Joori, Hwang Hyun Jung, Kim Leehyeon, Jeong Kwon, Song Hyun Kyu, Rufener Simone C, Mühlemann Oliver, Kim Yoon Ki (2021), Translation mediated by the nuclear cap-binding complex is confined to the perinuclear region via a CTIF–DDX19B interaction, in Nucleic Acids Research, 49(14), 8261-8276.
The phase separation-dependent FUS interactome reveals nuclear and cytoplasmic function of liquid–liquid phase separation
Reber Stefan, Jutzi Daniel, Lindsay Helen, Devoy Anny, Mechtersheimer Jonas, Levone Brunno Rocha, Domanski Michal, Bentmann Eva, Dormann Dorothee, Mühlemann Oliver, Barabino Silvia M L, Ruepp Marc-David (2021), The phase separation-dependent FUS interactome reveals nuclear and cytoplasmic function of liquid–liquid phase separation, in Nucleic Acids Research, 49(13), 7713-7731.
Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay
Contu Lara, Balistreri Giuseppe, Domanski Michal, Uldry Anne-Christine, Mühlemann Oliver (2021), Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay, in PLOS Pathogens, 17(5), e1009603-e1009603.
FUS-dependent liquid–liquid phase separation is important for DNA repair initiation
Maiser Andreas, Rapp Alexander, Conte Francesca, Reber Stefan, Mechtersheimer Jonas, Ronchi Antonella E., Mühlemann Oliver, Leonhardt Heinrich, Cardoso M. Cristina, Ruepp Marc-David, Barabino Silvia M.L., Levone Brunno R., Lenzken Silvia C., Antonaci Marco (2021), FUS-dependent liquid–liquid phase separation is important for DNA repair initiation, in Journal of Cell Biology, 220(5), e202008030.
Human NMD ensues independently of stable ribosome stalling
Karousis Evangelos D., Gurzeler Lukas-Adrian, Annibaldis Giuditta, Dreos René, Mühlemann Oliver (2020), Human NMD ensues independently of stable ribosome stalling, in Nature Communications, 11(1), 4134-4134.
Readthrough of stop codons under limiting ABCE1 concentration involves frameshifting and inhibits nonsense-mediated mRNA decay
Annibaldis Giuditta, Domanski Michal, Dreos René, Contu Lara, Carl Sarah, Kläy Nina, Mühlemann Oliver (2020), Readthrough of stop codons under limiting ABCE1 concentration involves frameshifting and inhibits nonsense-mediated mRNA decay, in Nucleic Acids Research, 48(18), 10259-10279.
SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation
Schubert Katharina, Karousis Evangelos D., Jomaa Ahmad, Scaiola Alain, Echeverria Blanca, Gurzeler Lukas-Adrian, Leibundgut Marc, Thiel Volker, Mühlemann Oliver, Ban Nenad (2020), SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation, in Nature Structural & Molecular Biology, 27(10), 959-966.
FUS ALS-causative mutations impair FUS autoregulation and splicing factor networks through intron retention
Humphrey Jack, Birsa Nicol, Milioto Carmelo, McLaughlin Martha, Ule Agnieszka M, Robaldo David, Eberle Andrea B, Kräuchi Rahel, Bentham Matthew, Brown Anna-Leigh, Jarvis Seth, Bodo Cristian, Garone Maria G, Devoy Anny, Soraru Gianni, Rosa Alessandro, Bozzoni Irene, Fisher Elizabeth M C, Mühlemann Oliver, Schiavo Giampietro, Ruepp Marc-David, Isaacs Adrian M, Plagnol Vincent, Fratta Pietro (2020), FUS ALS-causative mutations impair FUS autoregulation and splicing factor networks through intron retention, in Nucleic Acids Research, 48(12), 6889-6905.
miR-129-5p: A key factor and therapeutic target in amyotrophic lateral sclerosis
Loffreda Alessia, Nizzardo Monica, Arosio Alessandro, Ruepp Marc-David, Calogero Raffaele A., Volinia Stefano, Galasso Marco, Bendotti Caterina, Ferrarese Carlo, Lunetta Christian, Rizzuti Mafalda, Ronchi Antonella E., Mühlemann Oliver, Tremolizzo Lucio, Corti Stefania, Barabino Silvia M.L. (2020), miR-129-5p: A key factor and therapeutic target in amyotrophic lateral sclerosis, in Progress in Neurobiology, 190, 101803-101803.
The Role of Stress Granules and the Nonsense-mediated mRNA Decay Pathway in Antiviral Defence
Contu Lara, Steiner Silvio, Thiel Volker, Mühlemann Oliver (2019), The Role of Stress Granules and the Nonsense-mediated mRNA Decay Pathway in Antiviral Defence, in CHIMIA International Journal for Chemistry, 73(5), 374-379.
Nonsense-Mediated mRNA Decay Begins Where Translation Ends
Karousis Evangelos D., Mühlemann Oliver (2019), Nonsense-Mediated mRNA Decay Begins Where Translation Ends, CSHL Press, Cold Spring Hatbor, New York, U.S.A., 11(2), a032862-a032862.
The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity
Loughlin Fionna E., Lukavsky Peter J., Kazeeva Tamara, Reber Stefan, Hock Eva-Maria, Colombo Martino, Von Schroetter Christine, Pauli Phillip, Cléry Antoine, Mühlemann Oliver, Polymenidou Magdalini, Ruepp Marc-David, Allain Frédéric H.-T. (2019), The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity, in Molecular Cell, 73(3), 490-504.e6.

Collaboration

Group / person Country
Types of collaboration
Mihaela Zavolan, Biozentrum Basel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Yoon Ki Kim, KAIST Korean Republic (South Korea) (Asia)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Stefania Corti, U. degli studi di Milano Italy (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Giuseppe Balistreri, Univ. Helsinki Finland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Marc-David Ruepp, Kings College London Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
Volker Thiel, Uni Bern Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Nenad Ban, ETHZ Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Silvia Barabino, U. Milano-Biccoca Italy (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Fred Allain, ETHZ Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
26th Annual Meeting of the RNA Society Talk given at a conference The NMD factor SMG7 plays a role in the tumorigenicity of HT1080 fibrosarcoma cells 25.05.2020 Singapur (virtual), Singapore Mühlemann Oliver; Nasif Sofia;
CSHL Meeting on Translational Control Talk given at a conference Depletion of the ribosome recycling factor ABCE1 inhibits nonsense-mediated mRNA decay 04.09.2019 Cold spring Harbor, United States of America Annibaldis Giuditta; Mühlemann Oliver;
24th Annual Meeting of the RNA Society Talk given at a conference HnRNP proteins organise human pre-mRNAs into 40S ribonucleosome units 11.06.2019 Krakau, Poland Domanski Michal; Mühlemann Oliver;


Associated projects

Number Title Start Funding scheme
162986 Quality control of gene expression: towards understanding mechanism and physiological role of nonsense-mediated mRNA decay (NMD) 01.10.2015 Project funding (Div. I-III)
204161 Towards understanding mechanism and physiological role of nonsense-mediated mRNA decay (NMD) 01.10.2021 Project funding (Div. I-III)

Abstract

Transcriptome profilings have revealed many physiological mRNAs lacking recognizable premature termination codons (PTCs) as targets of “Nonsense-Mediated mRNA Decay” (NMD), indicating that NMD may play a more general role in posttranscriptional regulation of gene expression that extends beyond its classical role in mRNA quality control. There is evidence that NMD influences biological processes as diverse as telomere maintenance, transcription, cell proliferation, cell cycle, cellular transport and organization, and metabolism. One goal of our research is therefore to investigate in which biological contexts NMD plays an important regulatory function. We approach this by editing or inactivating endogenous alleles encoding NMD factors in human induced pluripotent stem cells (iPSCs) and cancer cells (HT1080). Another goal is to further our understanding of the molecular mechanism of NMD and the factors involved. To this end, we will conduct a screen to identify new human NMD factors and characterize their role in NMD. Finally, we will continue our attempts to biochemically purify and analyze specific mRNP species with the aim of comparing composition and architecture of mRNPs assembling on a PTC-containing NMD-targeted mRNA and on its PTC-free, NMD-resistant counterpart.
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