Deciphering human nonsense-mediated mRNA decay (NMD)

在真核细胞中，一些质量控制机制有助于检测有缺陷或不规则的mrna，并避免产生不正确的多肽。一种被广泛研究的降解途径，被称为无义介导的mRNA衰变（NMD），降解含有过早翻译终止密码子（PTC）的转录本。NMD存在于所有真核生物中，并使用一组保守的核心因子来消除不能在适当位置终止翻译的异常转录本。NMD的活性并不局限于携带致病无义突变的mrna。事实上，大多数NMD底物是通过替代mRNA加工产生的，导致ptc包含在成熟的转录物中。因此，NMD作为基因表达的一般调节剂，直接或间接地改变真核细胞中约5%的转录组的表达水平。尽管NMD对转录组的组成很重要，但只有少数通过选择性加工激活NMD的转录本得到了详细的研究。为了缩小这一知识差距，我们将使用最先进的方法来操纵NMD机制，这将使我们能够编制人类细胞中所有NMD激活转录异构体的目录。利用这套新的NMD目标，我们将解决有关NMD早期承诺阶段和退化阶段的重要机制问题。我们还将产生计算方法来系统地测试NMD对基因表达转录后调控的影响。

In eukaryotic cells several quality control mechanisms help to detect defective or irregular mRNAs and to avoid the production of incorrect polypeptides. A well-studied degradation pathway, referred to as nonsense mediated mRNA decay (NMD), degrades transcripts containing premature translation termination codons (PTC). NMD exists in all eukaryotic organisms and employs a conserved set of core factors to eliminate aberrant transcripts that fail to terminate translation at a proper position. The activity of NMD is not restricted to mRNAs carrying disease-causing nonsense mutations. In fact, the majority of NMD substrates is produced by alternative mRNA processing, resulting in the inclusion of PTCs into the mature transcript. Hence, NMD functions as a general modulator of gene expression and directly or indirectly alters the expression levels of about 5% of the transcriptome in eukaryotic cells. Despite the importance of NMD for the composition of the transcriptome, only a small number of transcripts that activate NMD by alternative processing have been studied in detail. In order to close this knowledge gap, we will use state-of-the-art methods to manipulate the NMD machinery, which will allow us to compile a catalogue of all NMD-activating transcript isoforms in human cells. Using this new set of NMD targets we will address important mechanistic questions regarding the early commitment phase as well as the degradation phase of NMD. We will also produce computational methods to systematically test the effect of NMD on post-transcriptional regulation of gene expression.