translation termination; Nonsense-mediated mRNA decay; mRNA surveillance; mRNA turnover; posttranscriptional gene regulation; RNA quality control
Nicholson Pamela, Gkratsou Asimina, Josi Christoph, Colombo Martino, Mühlemann Oliver (2018), Dissecting the functions of SMG5, SMG7, and PNRC2 in nonsense-mediated mRNA decay of human cells, in RNA
, 24(4), 557-573.
Nasif Sofia, Contu Lara, Mühlemann Oliver (2018), Beyond quality control: The role of nonsense-mediated mRNA decay (NMD) in regulating gene expression, in Seminars in Cell & Developmental Biology
, 75, 78-87.
Reber Stefan, Mechtersheimer Jonas, Nasif Sofia, Benitez Julio Aguila, Colombo Martino, Domanski Michal, Jutzi Daniel, Hedlund Eva, Ruepp Marc-David (2018), CRISPR-Trap: a clean approach for the generation of gene knockouts and gene replacements in human cells, in Molecular Biology of the Cell
, 29(2), 75-83.
Mühlemann Oliver, Karousis Evangelos D (2017), New functions in translation termination uncovered for NMD factor UPF3B, in The EMBO Journal
, 36(20), 2928-2930.
Balistreri Giuseppe, Bognanni Claudia, Mühlemann Oliver (2017), Virus Escape and Manipulation of Cellular Nonsense-Mediated mRNA Decay., in Viruses
, 9(1), 24.
Reber Stefan, Stettler Jolanda, Filosa Giuseppe, Colombo Martino, Jutzi Daniel, Lenzken Silvia C, Schweingruber Christoph, Bruggmann Rémy, Bachi Angela, Barabino Silvia ML, Mühlemann Oliver, Ruepp Marc‐David (2016), Minor intron splicing is regulated by FUS and affected by ALS‐associated FUS mutants, in The EMBO Journal
, 35(14), 1504-1521.
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), 0150239-0150239.
Karousis Evangelos D, Nasif Sofia, Mühlemann Oliver (2016), Nonsense-mediated mRNA decay: novel mechanistic insights and biological impact., in Wiley interdisciplinary reviews. RNA
, 7(5), 661-82.
Mühlemann Oliver (2016), Spermatogenesis Studies Reveal a Distinct Nonsense-Mediated mRNA Decay (NMD) Mechanism for mRNAs with Long 3'UTRs., in PLoS genetics
, 12(5), 1005979-1005979.
Colombo Martino, Karousis Evangelos D, Bourquin Joël, Bruggmann Rémy, Mühlemann Oliver (2016), Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways., in RNA (New York, N.Y.)
, 23(2), 189-201.
The term “Nonsense-Mediated mRNA Decay” (NMD) was originally coined to describe 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 serves as a quality control of gene expression and protects the cell from accumulating C-terminally truncated proteins with potentially toxic functions. However, a more general role of NMD in posttranscriptional regulation of gene expression emerged from transcriptome-wide mRNA profilings that identified many physiological (i.e. PTC-free) mRNAs as NMD targets, overall affecting the mRNA levels of 3 - 10% of all genes in yeast, Drosophila, and human cells. 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.Over the past 10 years, our lab has contributed both to the dissection of the molecular mechanism of NMD as well as to a better understanding of the biological function of NMD in mammalian cells. With the projects proposed here, we aim at continuing our research along these two lines by using a combination of biochemical, molecular biology, cell biology and reverse genetics methods. We plan to generate several inducible pluripotent stem cell (iPSC) lines with mutations in various NMD factors and assess their effect on the transcriptome and the capability of the cells to differentiate. The mutations will be introduced using recently developed genome-editing techniques (CRISPR/Cas). Compared to traditional knockdown-rescue experiments, the genome editing approach has the advantage that the effect of the mutant proteins can be assessed in the absence of any remaining low levels of WT protein possibly confounding the phenotype. On the biochemical side, one of our main goals is to establish a protocol to purify specific messenger ribonucleoprotein (mRNP) populations that have been arrested at different stages along the NMD pathway and characterizing their composition by mass spectrometry. This will give us important insight into mRNP remodeling events during NMD. A third line of research concerns a follow-up of our recent finding that NMD appears to play a role in defending cells from RNA virus replication. We want to find out what makes the Semliki Forest Virus genomic RNA an NMD substrate and test other viruses for their sensitivity to NMD.Collectively, our research aims at understanding the molecular mechanism of NMD and its physiological role in human cells. This is the basis for the future development of highly specific approaches to manipulate in a controlled way NMD activity in different disease contexts.