A08: Impact of nonsense-mediated mRNA decay on gene expression fidelity

Nonsense mediated mRNA decay (NMD) is a eukaryotic quality control mechanism that eliminates mRNAs with premature or aberrant translation termination events. NMD acts as a safeguard, preventing the production of dysfunctional and potentially harmful proteins. The influence of NMD extends far beyond merely targeting mRNAs expressed from mutated genes; it also targets transcript isoforms generated by (regulated) alternative splicing, containing transcription- or processing errors or using alternative translation initiation. Our research in human cultured cells has revealed that the inhibition of NMD results in significant alterations to the expression of approximately 20-30% of the transcriptome in otherwise unperturbed cells. When cells experience genotoxic stress or dysfunctions in their gene expression machinery, their gene expression processes may become more error prone. Consequently, increased involvement of NMD is required to maintain transcriptome integrity and cellular functionality. In support of this hypothesis, studies in C. elegans and Physcomitrella patens demonstrate that NMD mutants are hypersensitive to DNA damage (Gonzalez-Huici et al. 2017; Roberts et al. 2013) Likewise, it has been demonstrated that heterozygous mutations in the NMD protein SMG1 can lead to an increased risk of tumour formation and inflammation in a mouse model (Lloyd et al. 2018). On the one hand, NMD is required to cope with fidelity loss in mRNA production, on the other hand the fidelity loss of NMD itself may contribute to a compromised transcriptome and proteome. To explore the compensatory and regulatory role of NMD under conditions of damaged DNA and perturbed gene expression, we will first identify NMD-targeted mRNAs during different stresses and perturbations with or without an active NMD machinery. By comparing the expression of NMD substrates, we will measure NMD competence and robustness as well as identify key transcripts regulated by NMD under these different conditions. Moreover, we will use NMD inhibition in different cell lines to identify a core set as well as cell-type specific NMD substrates. The latter may be attributed to either differential gene expression patterns or variations in the fidelity of cellular machines, providing insights into the underlying biology of gene expression within these distinct cellular backgrounds. Finally, we aim to evaluate the extent to which NMD activity influences the production of protein isoforms, thereby reshaping the composition of the cellular proteome. In summary, our project will unravel the multifaceted role of NMD as a cellular surveillance mechanism, operating under both normal conditions and during episodes of compromised fidelity arising from external stressors or internal disturbances.