Ribosome profiling in mammalian cells to reveal the role of NMD factors in translation termination

Annibaldis, Giuditta (6 July 2016). Ribosome profiling in mammalian cells to reveal the role of NMD factors in translation termination (Unpublished). In: EMBO Conference Ribosome – Structure and Function 2016. Strasbourg, France. 06.-10.07.2016.

Eukaryotes have acquired numerous ways to control the integrity and quality of mRNA. Nonsense-mediated mRNA decay (NMD) is one of these conserved pathways that contribute to mRNA surveillance. It is thought NMD is activated when a ribosome stalls at a termination codon (TC) in a context in which the presence/absence of specific messenger ribonucleoproteins (mRNPs) prevents correct and efficient termination [1-2].
In the past, NMD was believed to degrade exclusively aberrant mRNAs with premature TCs and hence avoid production of potentially deleterious truncated proteins. However, with the advent of transcriptome-wide profiling methods, it became clear that NMD regulates the abundance of 5-10% of all mRNAs, the vast majority of them encoding perfectly functional full-length proteins [3-6]. Unfortunately, the different approaches used in the above-mentioned studies yielded a highly divergent set of apparent endogenous NMD-targeted mRNAs, which so far precluded the identification of a bona fide NMD target set of mRNAs.
Recently, Ingolia and Weissman have developed a technique termed ribosome profiling, which enables to determine a transcriptome-wide snapshot of ribosome occupancy in vivo by the analysis of ribosome-protected mRNA fragments (RPFs) obtained from mild nuclease digestion and identified by deep sequencing [7-8]. Using ribosome profiling, we want to determine the ribosome occupancy at TCs relative to the occupancy within the coding sequence of the same mRNA as a surrogate for translation termination efficiency. With this approach, we aim at testing in mammalian cells whether prolonged stalling of ribosomes at TCs can indeed reliably identify transcriptome-wide the corresponding mRNAs as NMD substrates. Moreover, comparing ribosome profiles from cells depleted of NMD factors or other factors with putative roles in translation termination may give insights into the exact role of these factors in the efficiency and fidelity of translation termination.

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