Nonsense-mediated mRNA decay; mRNA turnover; posttranscriptional gene regulation; translation termination; RNA quality control; mRNA surveillance; Nonsense-mediated mRNA decay (NMD); post-transcriptional gene regulation; RNA turnover; mRNA quality control
Nicholson Pamela, Joncourt Raphael, Mühlemann Oliver (2012), Analysis of nonsense-mediated mRNA decay in mammalian cells., in Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.]
, Chapter 27, 27-4.
Mühlemann Oliver, Jensen Torben Heick (2012), mRNP quality control goes regulatory., in Trends in genetics : TIG
, 28(2), 70-7.
Nicholson Pamela, Mühlemann Oliver (2010), Cutting the nonsense: the degradation of PTC containing mRNAs, in Biochem Soc Trans
, 38(6), 1615-1620.
Aeby Eric, Ullu Elisabetta, Yepiskoposyan Hasmik, Schimanski Bernd, Roditi Isabel, Mühlemann Oliver, Schneider André (2010), tRNASec is transcribed by RNA polymerase II in Trypanosoma brucei but not in humans, in Nucleic Acids Res
, 17, 5833-5843.
Mühlemann Oliver, Lykke-Andersen Jens (2010), How and where are nonsense mRNAs degraded in mammalian cells?, in RNA Biology
, 7(1), 28-32.
Nicholson Pamela, Yepiskoposyan Hasmik, Metze Stefanie, Zamudio Orozco Rodolfo, Kleinschmidt Nicole, Mühlemann Oliver (2009), Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors, in Cell Mol Life Sci
, 67(5), 677-700.
Yepiskoposyan Hasmik, Aeschimann Florian, Nilsson Daniel, Okoniewski Michal, Mühlemann Oliver, Autoregulation of the nonsense-mediated mRNA decay pathway in human cells, in RNA
de Turris Valeria, Nicholson Pamela, Zamudio Orozco Rodolfo, Singer Robert H., Mühlemann Oliver, Co-transcriptional Effects of a Premature Termination Codon Revealed by Live-Cell Imaging, in RNA
Background:Many different quality control mechanisms have evolved to recognize mistakes during the molecular processes involved in gene expression and to prevent production of faulty gene products. Among those, nonsense-mediated mRNA decay (NMD) represents a translation-dependent posttranscriptional process that selectively recognizes and degrades mRNAs whose open reading frame (ORF) is truncated by a premature translation-termination codon (PTC, also called „nonsense codon“). In doing so, NMD protects the cell from accumulating C-terminally truncated proteins with potentially deleterious functions. Because 30% of all known disease-causing mutations are predicted to trigger NMD, NMD represents an important modulator of genetic disease phenotypes in humans, and understanding the molecular mechanisms of NMD therefore is key for developing future therapies for many genetic diseases. Transcriptome profiling of NMD-deficient yeast, Drosophila, and human cells revealed that 3-10% of all mRNA levels are regulated (directly or indirectly) by NMD, indicating an important role of NMD in gene regulation that extends beyond quality control. While the phenomenon of NMD and its impact on gene expression is well documented, the understanding of the underlying molecular mechanisms is still fragmented.Current and future research on nonsense-mediated mRNA decay (NMD):A central question of NMD research is how PTCs are recognized and discriminated from natural termination codons. Recent work from my lab and others led to a new model postulating an evolutionarily conserved mechanism for PTC recognition. This so-called “unified NMD model” and its implications for posttranscriptional gene regulation and certain genetic diseases need to be critically scrutinized in the coming years. To further investigate the molecular mechanism of PTC recognition, we concentrate on trying to understand the PABP-mediated promotion of translation termination and the exact role of UPF1 in NMD. For UPF1, we plan to systematically identify interaction partners during the different stages of NMD complex assembly with help of a new mass spectrometry-based technique that enables quantitative identification of interacting factors from affinity purified complexes (SILAC-IP). Another goal is to identify endogenous examples of the postulated posttranscriptional mechanism for gene regulation by spatial rearrangement of the 3’ UTR, a direct implication of the “unified NMD model”. Along these lines, we will also try to identify disease-related human mutations that change the 3’ UTR of the mRNA and experimentally validate those transcripts predicted by our model to have become NMD substrates. Substantial progress in understanding the degradation of nonsense mRNAs in human cells has been made by our recent demonstration that SMG6 is an endonuclease and cleaves the transcript near the PTC. In the future, we want to address if decay of all human NMD substrates is induced by SMG6-mediated endonucleolytic cleavage, or if additional parallel pathways exist. In the case of multiple pathways, we would like to identify the decisive parameters for one or another pathway.Nonsense-mediated transcriptional gene silencing (NMTGS) - quo vadis?Transcriptional silencing of PTC-containing Ig-mu minigenes stably integrated into the genome of HeLa cells was serendipitously discovered in our lab five years ago. Although the biological relevance of this observation still remains elusive, the mechanism itself is intriguing: a translation signal on an mRNA (the PTC) somehow feeds back to its cognate gene and silences its transcription. We are currently trying to establish a more robust experimental system that would enable us to continue our mechanistic dissection of NMTGS. Circumstantial evidence suggests the involvement of small RNAs and components of the RNAi machinery, but more direct evidence is needed. Various experiments are planned to gain more insight into this enigmatic process.