Publications since 2001

pre-prints

Andrea B. Eberle, Karin Schranz, Sofia Nasif, Lena Grollmus and Oliver Mühlemann (2021)
Dissecting the import and export pathways of the human RNA helicase UPF1.
BioRxiv 454737v1

Peer-reviewed publications

Eberle, A.B., Mühlemann, O. (2022).
Tethered Function Assays to Elucidate the Role of RNA-Binding Proteins.
In: Scheiffele, P., Mauger, O. (eds) Alternative Splicing. Methods in Molecular Biology, vol 2537. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2521-7_17

Evangelos D. Karousis and Oliver Mühlemann (2022)
The broader sense of nonsense
CellPress https://doi.org/10.1016/j.tibs.2022.06.003

Michal Domanski, Emil Dedic, Maria Escura Pérez, Antoine Céry , Sébastien Campagne, Anne-Christine Uldry, Sophie Braga, Manfred Heller, Julius Rabl , Pavel Afanasyev, Daniel Boehringer, Jíří Nováček, Frédéric T. Allain and Oliver Mühlemann (2022)
40S hnRNP particles are a novel class of nuclear biomolecular condensates
Nucleic Acids Research, https://doi.org/10.1093/nar/gkac457

Soumasree De & Oliver Mühlemann (2022)
A comprehensive coverage insurance for cells: revealing links between ribosome collisions, stress responses and mRNA surveillance
RNA Biology https://doi.org/10.1080/15476286.2022.2065116

Michela Taiana, Alessandra Govoni, Sabrina Salani, Nicole Kleinschmidt, Noemi Galli, Matteo Saladini, Stefano Bruno Ghezzi, Valentina Melzi, Margherita Bersani, Roberto Del Bo, Oliver Muehlemann, Enrico Bertini, Valeria Sansone, Emilio Albamonte, Sonia Messina, Francesco Mari, Elisabetta Cesaroni, Liliana Porfiri, Francesco Danilo Tiziano, Gian Luca Vita, Maria Sframeli, Carmen Bonanno, Nereo Bresolin, Giacomo Comi, Stefania Corti, Monica Nizzardo (2022)
Molecular analysis of SMARD1 patient-derived cells demonstrates that nonsense- mediated mRNA decay
is impaired
J Neurol Neurosurg Psychiatry: 10.1136/jnnp-2021-326425

Lukas-Adrian Gurzeler, Jana Ziegelmüller, Oliver Mühlemann, Evangelos D. Karousis (2021)
Production of human translation-competent lysates using dual centrifugation
RNA Biology, DOI: 10.1080/15476286.2021.2014695

Evangelos D. Karousis, Foivos Gypas, Mihaela Zavolan, Oliver Mühlemann (2021)
Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells
Genome Biology, volume 22, Article number: 223 (2021) doi.org/10.1186/s13059-021-02439-3

Stefan Reber, Daniel Jutzi, Helen Lindsay, Anny Devoy, Jonas Mechtersheimer, Brunno Rocha Levone, Michal Domanski, Eva Bentmann, Dorothee Dormann, Oliver Mühlemann, Silvia M.L. Barabino and Marc-David Ruepp (2021)
The phase separation-dependent FUS interactome reveals nuclear and cytoplasmic function of liquid–liquid phase separation
Nucleic Acids Research, 2021, doi.org/10.1093/nar/gkab582

Yeonkyoung Park, Joori Park, Hyun Jung Hwang, Leehyeon Kim, Kwon Jeong, Hyun Kyu Song, Simone C. Rufener, Oliver Mühlemann and Yoon Ki Kim
Translation mediated by the nuclear cap-binding complex is confined to the perinuclear region via a CTIF–DDX19B interaction
Nucleic Acids Research, 2021, doi.org/10.1093/nar/gkab579

Lara Contu, Giuseppe Balistreri, Michal Domanski, Anne-Christine Uldry, Oliver Mühlemann (2021)
Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay.
PLoS Pathog 17(5): e1009603. doi.org/10.1371/journal. ppat.1009603

Brunno Levone, Silvia Lenzken, Marco Antonaci, Andreas Maiser, Alexander Rapp, Francesca Conte, Stefan Reber, Jonas Mechtersheimer, Antonella E Ronchi, Oliver Mühlemann, Heinrich Leonhardt, M. Cristina Cardosa, Marc-David Ruepp, Silvia Barabino (2021)
FUS-dependent liquid-liquid phase separation is important for DNA repair initiation.
J. Cell Biol. 220(5): e202008030 (doi: 10.1083/jcb.202008030).

Giuditta Annibaldis, Michal Domanski, René Dreos, Lara Contu, Sarah Carl, Nina Kläy and Oliver Mühlemann (2020).
Readthrough of stop codons under limiting ABCE1concentration involves frameshifting and inhibitsnonsense-mediated mRNA decay.
Nucleic Acids Res. 2020 Sep 17; gkaa758. doi: 10.1093/nar/gkaa758.

Katharina Schubert*, Evangelos D Karousis*, Ahmad Jomaa, Alain Scaiola, Blanca Echeverria, Lukas-Adrian Gurzeler, Marc Leibundgut, Volker Thiel, Oliver Mühlemann** and Nenad Ban** (2020).
SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.
*both authors contributed equally to this work; **co-corresponding authors

Nat Struct Mol Biol. 2020 Sep 9. doi: 10.1038/s41594-020-0511-8.

Evangelos D. Karousis, Lukas-Adrian Gurzeler, Giuditta Annibaldis, René Dreos & Oliver Mühlemann (2020).
Human NMD ensues independently of stable ribosome stalling.
Nat Commun. 2020 11:4134 | https://doi.org/10.1038/s41467-020-17974-z

Jack Humphrey, Nicol Birsa, Carmelo Milioto, Martha McLaughlin, Agnieszka M. Ule, David Robaldo, Andrea B. Eberle, Rahel Kräuchi, Matthew Bentham, Anna-Leigh Brown, Seth Jarvis, Cristian Bodo, Maria G. Garone, Anny Devoy, Gianni Soraru’, Alessandro Rosa, Irene Bozzoni, Elizabeth M. C. Fisher, Oliver Mühlemann, Giampietro Schiavo, Marc-David Ruepp, Adrian M. Isaacs, Vincent Plagnol and Pietro Fratta (2020).
FUS ALS-causative mutations impair FUS autoregulation and splicing factor networks through intron retention.
Nucleic Acids Research, 48(12):6889–6905 Doi: 10.1093/nar/gkaa410

Alessia Loffreda, Monica Nizzardo, Alessandro Arosio, Marc-David Ruepp, Raffaele A. Calogero, Stefano Volinia, Marco Galasso, Caterina Bendotti, Carlo Ferrarese, Christian Lunetta, Mafalda Rizzuti, Antonella Ronchi, Oliver Mühlemann, Lucio Tremolizzo, Stefania Corti, Silvia M.L. Barabino (2020).
miR-129-5p: A key factor and therapeutic target in amyotrophic lateral sclerosis.
Progress in Neurobiology. Doi: 10.1016/j.pneurobio.2020.101803

Lara Contu, Silvio Steiner, Volker Thiel and Oliver Mühlemann (2019).
The Role of Stress Granules and the Nonsense-mediated mRNA Decay Pathway in Antiviral Defence.
Chimia 29;73(6):374-379. doi: 10.2533/chimia.2019.374.

Fionna E. Loughlin, Peter J. Lukavsky, Tamara Kazeeva, Stefan Reber, Eva-Maria Hock, Martino Colombo, Christine Von Schroetter, Phillip Pauli, Antoine Cléry, Oliver Mühlemann, Magdalini Polymenidou, Marc-David Ruepp and Freédéric H.-T. Allain (2019).
The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity.
Mol Cell 73:1-15. / doi: 10.1016/j.molcel.2018.11.012

Evangelos Karousis and Oliver Mühlemann (2018).
Nonsense-mediated mRNA decay begins where translation ends.
In Cold Spring Harb Perspect Biol: Doi: 10.1101/cshperspect.a032862.

Stefan Reber, Jonas Mechtersheimer, Sofia Nasif, Julio Aguila Benitez, Martino Colombo, Michal Domanski, Daniel Jutzi, Eva Hedlund and Marc-David Ruepp (2018).
CRISPR-Trap: a clean approach for the generation of gene knockouts and gene replacements in human cells.
Mol Biol Cell. 2018 Jan 15;29(2):75-83. doi: 10.1091/mbc.E17-05-0288. Epub 2017 Nov 22.

Sofia Nasif, Lara Contu & Oliver Mühlemann (2018).
Beyond quality control: The role of nonsense-mediated mRNA decay (NMD) in regulating gene expression.
Seminars in Cell & Developmental Biology 75:78-87. Doi: 10.1016/j.semcdb.2017.08.053

Pamela Nicholson, Asimina Gkratsou, Christoph Josi, Martino Colombo and Oliver Mühlemann (2018).
Dissecting the functions of SMG5, SMG7 and PNRC2 in nonsense-mediated mRNA decay of human cells.
RNA 2018 Jan 18. pii: rna.063719.117. doi: 10.1261/rna.063719.117.

Andrea Eberle (2017).
Spike-In Normalization of ChIP Data Using DNA-DIG-Antibody Complex.
Methods Mol Biol. 2018;1689:227-238. doi: 10.1007/978-1-4939-7380-4_18.

Oliver Mühlemann & Evangelos Karousis (2017).
New functions in translation termination uncovered for NMD factor UPF3B.
The EMBO Journal, 2017 September 21; doi:10.15252/embj.201798063

Giuseppe Balistreri, Claudia Bognanni & Oliver Mühlemann (2017).
Virus Escape and Manipulation of Cellular Nonsense-Mediated mRNA Decay.
Viruses. 2017 Jan 23;9(1). pii: E24. doi: 10.3390/v9010024.

Martino Colombo, Evangelos D. Karousis, Joël Bourquin, Rémy Bruggmann & Oliver Mühlemann (2016).
Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways.
RNA 2016 Nov 18. pii: rna.059055.116; DOI:10.1261/rna.059055.116

Stefan Reber, Jolanda Stettler, Giuseppe Filosa, Martino Colombo, Daniel Jutzi, Silvia C Lenzken, Christoph Schweingruber, Rémy Bruggmann, Angela Bachi, Silvia ML Barabino, Oliver Mühlemann &
Marc-David Ruepp (2016).
Minor intron splicing is regulated by FUS and affected by ALS-associated FUS mutants.
The EMBO Journal, 2016 June 1; doi:10.15252/embj.201593791
See also «News & Views by Emanuele Buratti».

Evangelos D. Karousis, Sofia Nasif and Oliver Mühlemann (2016).
Nonsense-mediated mRNA decay: novel mechanistic insights and biological impact.
Wiley Interdiscip Rev RNA. 2016 May 13. doi:10.1002/wrna.1357

Oliver Mühlemann (2016).
Spermatogenesis Studies Reveal a Distinct Nonsense-Mediated mRNA Decay (NMD) Mechanism for mRNAs with Long 3'UTRs.
PLoS Genet. 2016 May 5;12(5):e1005979

Christoph Schweingruber, Paolo Soffientini, Marc-David Ruepp, Angela Bachi and Oliver Mühlemann (2016).
Identification of Interactions in the NMD Complex Using Proximity-Dependent Biotinylation (BioID).
PLOS ONE | DOI:10.1371/journal.pone.0150239 March 2, 2016

Thomas Jack, Jonathan Simonin, Marc-David Ruepp, Andrew J. Thompson, Jürg Gertsch and Martin Lochner (2015).
Characterizing new fluorescent tools for studying 5-HT3 receptor pharmacology.
Neuropharmacology. Volume 90, March 2015, Pages 63–73

Giuseppe Balistreri, Peter Horvath, Christoph Schweingruber, David
Zünd, Gerald McInerney, Andres Merits, Oliver Mühlemann, Claus Azzalin and Ari Helenius (2014).
The Host Nonsense-Mediated mRNA Decay Pathway Restricts Mammalian RNA Virus Replication.
Cell Host Microbe, 10;16(3):403-11. doi: 10.1016/j.chom.2014.08.007.

Raphael Joncourt, Andrea B. Eberle, Simone C. Rufener and Oliver Mühlemann (2014).
Eukaryotic Initiation Factor 4G Suppresses Nonsense-Mediated mRNA Decay by Two Genetically Separable Mechanisms.
PLoS One, 22;9(8):e104391, doi: 10.1371

Pamela Nicholson, Christoph Josi, Hitomi Kurosawa, Akio Yamashita and Oliver Mühlemann (2014).
A novel phosphorylation-independent interaction between SMG6 and UPF1 is essential for human NMD.
Nucleic Acids Research, doi: 10.1093/nar/gku645

Monica Nizzardo, Chiara Simone, Sabrina Salani, Marc-David Ruepp, Federica Rizz, Margherita Ruggieri, Chiara Zanetta,Simona Brajkovic, Hong M.Moulton, Oliver Mühlemann, Nereo Bresolin, Giacomo P. Comi and Stefania Corti (2014).
Effect of Combined System and Local Morpholino Treatment on the Spinal Muscular Atrophy Δ7 Mouse Model Phenotype.
Clinical Therapeutics / Volume 36, Number 3, 2014.

Thomas Jack, Marc-David Ruepp, Andrew J. Thompson, Oliver Mühlemann and Martin Lochner (2014).
Synthesis and Characterization of Photoaffinity Probes that Target the 5-HT3 Receptor.
Chimia 68:239-242.

Valentin Flury, Umberto Restuccia, Angela Bachi and Oliver Mühlemann (2014).
Characterization of Phosphorylation- and RNA-Dependent UPF1
Interactors by Quantitative Proteomics.

J Proteome Res, doi: 10.1021/pr5002143

David Zünd & Oliver Mühlemann (2014).
Individual-nucleotide-resolution UV Cross-linking and Immunoprecipitation (iCLIP) of UPF1.
Bio-protocol vol. 4, issue 7 / (www.bio-protocol.org)

David Zünd & Oliver Mühlemann (2014).
UPF1 RNA Immunoprecipitation from Mini-μ Construct–expressing Cells.
Bio-protocol vol. 4, issue 7 / (www.bio-protocol.org)

David Zünd & Oliver Mühlemann (2013).
Perspective: Recent transcriptome-wide mapping of UPF1 binding sites reveals
evidence for its recruitment to mRNA before translation.

Translation 1:e26977.

Stefanie Metze, Veronika A. Herzog, Marc-David Ruepp and Oliver Mühlemann (2013).
Comparison of EJC-enhanced and EJC-independent NMD in human cells reveals two partially redundant degradation pathways.
RNA 19:1–17

David Zünd, Andreas R Gruber, Mihaela Zavolan and Oliver Mühlemann (2013).
Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3'UTRs.
Nat Struct Mol Biol., doi:10.1038/nsmb.2635

Simone C Rufener & Oliver Mühlemann (2013).
eIF4E-bound mRNPs are substrates for nonsense-mediated mRNA decay in mammalian cells.
Nat Struct Mol Biol., doi:10.1038/nsmb.2576

Georg Stoecklin & Oliver Mühlemann (2013).
RNA decay mechanisms: Specifcity through diversity (Editorial for special issue on RNA decay mechanisms).
Biochim. Biophys. Acta, in press, doi:10.1016/j.bbagrm.2013.04.002.

Silvia Vivarelli, Silvia C. Lenzken, Marc-David Ruepp, Francesco Ranzini, Andrea Maffioletti, Reinaldo Alvarez, Oliver Mühlemann, Silvia M. L. Barabino (2013).
Paraquat Modulates Alternative Pre-mRNA Splicing by Modifying the Intracellular Distribution of SRPK2.
PLOS ONE, April 2013 | Volume 8 | Issue 4 | e61980

Christoph Schweingruber, Simone Rufener, David Zünd, Akio Yamashita and Oliver Mühlemann (2013).
Nonsense-mediated mRNA decay – mechanisms of substrate mRNA recognition and degradation in mammalian cells.
BBA – Gene Regulatory Mechanisms, doi: 10.1016/j.bbagrm.2013.02.005.

Oliver Mühlemann (2012).
Intimate liaison with SR proteins brings exon junction complexes to unexpected places.
Nat Struct Mol Biol., 19(12):1209-11

Pamela Nicholson, Raphael Joncourt and Oliver Mühlemann (2012).
Analysis of Nonsense-Mediated mRNA Decay in Mammalian Cells.
Current Protocols in Cell Biology 27.4.1-27.4.61.

Oliver Mühlemann and Torben Jensen (2012).
mRNP quality control goes regulatory.
Trends in Genetics, 28:70-77.

Hasmik Yepiskoposyan, Florian Aeschimann, Daniel Nilsson, Michal Okoniewski and Oliver Mühlemann (2011).
Autoregulation of the nonsense-mediated mRNA decay pathway in human cells.
RNA 17:2108-2118

Valeria de Turris, Pamela Nicholson, Rodolfo Zamudio Orozco, Robert H. Singer and Oliver Mühlemann (2011).
Cotranscriptional effect of a premature termination codon revealed by live-cell imaging.
RNA 17:2094-2107

Eric Aeby, Elisabetta Ullu, Hasmik Yepiskoposyan, Bernd Schimanski, Isabel Roditi, Oliver Mühlemann and André Schneider (2010).
tRNASec is transcribed by RNA polymerase II in Trypanosoma brucei but not in humans.
Nucleic Acids Research, 38:5833–5843

Pamela Nicholson and Oliver Mühlemann (2010).
Cutting the nonsense: the degradation of PTC containing mRNAs.
Biochem. Soc. Trans. 38, part 6

Oliver Mühlemann & Jens Lykke-Andersen (2010).
How and where are nonsense mRNAs degraded in mammalian cells?
RNA Biol. 7(1):28-32.

Pamela Nicholson, Hasmik Yepiskoposyan, Stefanie Metze, Rodolfo Zamudio Orozco, Nicole Kleinschmidt and Oliver Mühlemann (2009).
Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors.
Cell. Mol. Life Sci. 67:677-700.

Lukas Stalder and Oliver Mühlemann (2009).
Processing bodies are not required for mammalian nonsense-mediated mRNA decay.
RNA 7:1265-73.

Andrea B Eberle, Herrmann K, Hans-Martin Jäck, Oliver Mühlemann (2009).
Equal transcription rates of productively and nonproductively rearranged immunoglobulin mu heavy chain alleles in a pro-B cell line.
RNA 6:1021-8.

Andrea B Eberle, Soren Lykke-Andersen, Oliver Mühlemann and Torben Heick Jensen (2008).
SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells.
Nature Structural & Molecular Biology: doi:10.1038/nsmb.1530

Oliver Mühlemann, Andrea Eberle, Lukas Stalder and Rodolfo Zamudio Orozco (2008).
Recognition and elimination of nonsense mRNA.
BBA-GRM 1779:538-49.

Lukas Stalder and Oliver Mühlemann (2008).
Opinion article: The meaning of nonsense.
Trends Cell Biol. 18:315-21.

Oliver Mühlemann (2008).
Recognition of nonsense mRNA: towards a unified model.
Biochem. Soc. Trans. 36:497-501.

Andrea Eberle, Lukas Stalder, Hansruedi Mathys, Rodolfo Zamudio Orozco and Oliver Mühlemann (2008).
Posttranscriptional Gene Regulation by Spatial Rearrangement of the 3′ Untranslated Region.
PLoS Biology, 6(4):e92.

Lukas Stalder and Oliver Mühlemann (2007).
Transcriptional Silencing of Nonsense Codon - Containing Immunoglobulin µ Genes Requires Translation of its mRNA.
J. Biol. Chem., 282:16079-85.

Lukas Stalder, Andrea Eberle and Oliver Mühlemann (2007).
Quality control of gene expression: recognition of nonsense mRNAs prevents synthesis of truncated proteins.
BioForum Europe, 11:21-23.

Marc Bühler, Silvia Steiner, Fabio Mohn, Alexandra Paillusson and Oliver Mühlemann (2006).
EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3' UTR length.
Nature Struct. Mol. Biol. 13:462-464.

Sarah Newbury, Oliver Mühlemann and Georg Stoecklin (2006).
Turnover in the Alps; an mRNA perspective. Review of EMBO Workshop on Mechanisms and Regulation of mRNA Turnover.
EMBO Reports, 7:143-48.

Oliver Mühlemann (2005).
News & Views: Applying the brakes on gene expression.
Nature Struct. Mol. Biol. 12:1024-25.

Marc Bühler, Fabio Mohn, Lukas Stalder and Oliver Mühlemann (2005).
Transcriptional silencing of nonsense codon-containing immunoglobulin minigenes.
Mol. Cell, 18:307-317.

Alexandra Paillusson, Nadine Hirschi, Claudio Vallan, Claus M. Azzalin and Oliver Mühlemann (2005).
A GFP-based reporter system to monitor nonsense-mediated mRNA decay.
Nucleic Acids Research, 33: e54

Fabio Mohn, Marc Bühler and Oliver Mühlemann (2005).
Nonsense-associated alternative splicing of T-cell receptor beta genes: No evidence for frame dependence.
RNA 11:147-156.

Marc Bühler aned Oliver Mühlemann (2005).
Alternative splicing induced by nonsense mutations in the immunoglobulin mu VDJ exon is independent of truncation of the open reading frame.
RNA 11:139-146.

Marc Bühler, Alexandra Paillusson and Oliver Mühlemann (2004).
Efficient downregulation of immunoglobulin mu mRNA with premature translation-termination codons requires the 5'-half of the VDJ exon.
Nucleic Acids Res. 32:3304-3315.

Marc Bühler, Miles F. Wilkinson and Oliver Mühlemann (2002).
Intranuclear degradation of nonsense codon-containing mRNA.
EMBO Reports 3:646-651

Georg Stoecklin, Xiu-Fen Ming, Pascal Stoeckle, Min Lu, Oliver Mühlemann and Christoph Moroni (2001).
A Common mRNA Degradation Pathway Targets Structurally Different Cytokine AU-rich Elements.
RNA 7:1578-1588.

Oliver Mühlemann, Caroline S. Mock-Casagrande, Jun Wang, Noélia Custódio, Shulin Li, Maria Carmo-Fonseca, Miles F. Wilkinson and Melissa J. Moore (2001).
Precursor RNAs harboring nonsense codons accumulate near the site of transcription.
Mol. Cell 8:33-44.

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