RNA quality control; mRNA turnover; posttranscriptional gene regulation; Nonsense-mediated mRNA decay; mRNA surveillance; translation termination
Schweingruber Christoph, Soffientini Paolo, Ruepp Marc-David, Bachi Angela, Mühlemann Oliver (2016), Identification of Interactions in the NMD Complex Using Proximity-Dependent Biotinylation (BioID), in PLoS one
, 11(3), e0150239.
Nicholson Pamela, Josi Christoph, Kurosawa Hitomi, Yamashita Akio, Mühlemann Oliver (2014), A novel phosphorylation-independent interaction between SMG6 and UPF1 is essential for human NMD., in Nucleic acids research
, 42(14), 9217-35.
Flury Valentin, Restuccia Umberto, Bachi Angela, Mühlemann Oliver (2014), Characterization of phosphorylation- and RNA-dependent UPF1 interactors by quantitative proteomics., in Journal of proteome research
, 13(6), 3038-53.
Joncourt Raphael, Eberle Andrea B, Rufener Simone C, Mühlemann Oliver (2014), Eukaryotic initiation factor 4G suppresses nonsense-mediated mRNA decay by two genetically separable mechanisms., in PloS one
, 9(8), 104391-104391.
David Zünd, Oliver Mühlemann (2014), Individual-nucleotide-resolution UV Cross-linking and Immunoprecipitation (iCLIP) of UPF1
, Bioprotocols, Sunnyvale, CA, USA.
Balistreri Giuseppe, Horvath Peter, Schweingruber Christoph, Zünd David, McInerney Gerald, Merits Andres, Mühlemann Oliver, Azzalin Claus, Helenius Ari (2014), The host nonsense-mediated mRNA decay pathway restricts Mammalian RNA virus replication., in Cell host & microbe
, 16(3), 403-11.
David Zünd, Oliver Mühlemann (2014), UPF1 RNA Immunoprecipitation from Mini-μ Construct–expressing Cells
, Bioprotocols, Sunnyvale, CA, USA.
Metze Stefanie, Herzog Veronika A, Ruepp Marc-David, Mühlemann Oliver (2013), Comparison of EJC-enhanced and EJC-independent NMD in human cells reveals two partially redundant degradation pathways., in RNA (New York, N.Y.)
, 19(10), 1432-48.
Rufener Simone C, Mühlemann Oliver (2013), eIF4E-bound mRNPs are substrates for nonsense-mediated mRNA decay in mammalian cells., in Nature structural & molecular biology
, 20(6), 710-7.
Schweingruber Christoph, Rufener Simone C, Zünd David, Yamashita Akio, Mühlemann Oliver (2013), Nonsense-mediated mRNA decay - mechanisms of substrate mRNA recognition and degradation in mammalian cells., in Biochimica et biophysica acta
, 1829(6-7), 612-23.
Zünd David, Mühlemann Oliver (2013), Recent transcriptome-wide mapping of UPF1 binding sites reveals evidence for its recruitment to mRNA before translation, in Translation
, 1, e26977.
Georg Stoecklin, Oliver Mühlemann (2013), RNA decay mechanisms: Specifcity through diversity (Editorial for special issue on RNA decay mechanisms)., in Biochem Biophys Acta - Gene Regulatory Mechanisms
, 1829(6-7), 487-490.
Zünd David, Gruber Andreas R, Zavolan Mihaela, Mühlemann Oliver (2013), Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3' UTRs., in Nature structural & molecular biology
, 20(8), 936-43.
Oliver Mühlemann (2012), News and Views: Intimate liaison with SR proteins brings exon junction complexes to unexpected places, in Nat Struct Mol Biol
, 19(12), 1209-1211.
Accurate expression of the genetic information is achieved with the help of several quality control (QC) systems that recognize mistakes along the cascade of complex biochemical reactions from RNA synthesis to functional proteins and so prevent production of faulty gene products. One of these QC systems is “nonsense-mediated mRNA decay” (NMD), a translation-dependent process that degrades mRNAs with truncated open reading frames (ORFs). By recognizing and degrading mRNAs with premature termination codons (PTCs), many of which arise by alternative splicing, NMD protects the cell from accumulating C-terminally truncated proteins with potentially toxic functions. Transcriptome profiling of NMD-deficient yeast, Drosophila, and human cells revealed that NMD affects (directly or indirectly) the mRNA levels of 3 - 10% of all genes, indicating a role of NMD in gene regulation that extends beyond QC. NMD is essential in vertebrates and an important modulator of genetic disease phenotypes in humans, since 30% of all known disease-causing mutations are predicted to trigger NMD. While the phenomenon of NMD and its impact on gene expression and genetic diseases is well documented, the understanding of the underlying molecular mechanisms is still fragmented.Altogether, the projects proposed here aim at unraveling the molecular mechanism and physiological role of NMD in human cells. We use a combination of state-of-the-art biochemical, molecular biology, cell biology and reverse genetics methods to elucidate which features render an mRNA a NMD substrate, and which factors interact how, where and in which temporal order with these features and with each other to achieve the rapid degradation of target mRNAs. In this context, we also try to decipher the puzzling nuclear effects observed with NMD-targeted mRNAs. Given its tight coupling to translation, NMD is commonly assumed to occur in the cytoplasm, and the recurring NMD factor-dependent effects of PTCs on nuclear processes like transcription and splicing are enigmatic. Besides trying to get further insight into the mechanism of NMD, we also attempt to reveal the roles that NMD plays in regulating gene expression. To this end, we want to identify and characterize transcriptome-wide mRNAs regulated by NMD and thereby discover specific biological functions that are controlled by NMD. In particular, we also want to test the hypothesis that spatial rearrangements of the 3’ UTR configuration represent a way by which the half-life of mRNAs can be differentially regulated by NMD.In terms of methodological progress, we began to utilize lentiviral constructs to engineer cell lines that allow inducible expression of two or even three transgenes separately. We will need such cell lines to achieve our ambitious goal of purifying from cells and characterizing by mass spectrometry the composition of specific mRNP populations that have been arrested a different stages along the NMD pathway. If successful, this method will have a wide range of interesting applications in different areas of the molecular life sciences.