Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics

Abstract

Nonsense-mediated mRNA decay (NMD) is a translation-dependent mechanism of RNA decay that probably evolved to eliminate abnormal transcripts that are a consequence of routine abnormalities in gene expression. However, NMD also targets naturally occurring transcripts, such as certain alternatively spliced RNAs and some selenoprotein mRNAs. Generally, premature termination codons (PTCs) that are located within mRNA at a position that is more than 50–55 nucleotides (nt) upstream of a splicing-generated exon–exon junction elicit NMD. However, there are exceptions to the rule. For example, edited apolipoprotein B mRNA is immune to NMD. Furthermore, PTCs within the 5′ end of exon 1 of triosephosphate isomerase mRNA fail to elicit NMD because translation reinitiates at an AUG in the middle of exon 1. Also, PTCs within the 3′ end of T-cell receptor-β mRNA elicit NMD, despite the absence of an exon–exon junction located more than 50–55 nt downstream. The role of a splicing-generated exon–exon junction complex in NMD reflects the splicing-dependent deposition of an exon junction complex (EJC) ∼20–24 nt upstream of an exon–exon junction. The EJC recruits up-frameshift (UPF) proteins that are required for NMD. NMD, which is restricted to newly synthesized mRNA, targets mRNA bound by the mostly nuclear cap-binding proteins CBP80 and CBP20 during a pioneer round of translation. After the pioneer round of translation, CBP80–CBP20 is replaced by eukaryotic initiation factor eIF4E, which is mostly cytoplasmic but also nuclear. By the time eIF4E binds to the mRNA cap, the EJC and associated UPF proteins have been removed so that eIF4E-bound mRNA is immune to NMD. Most mRNAs are subject to NMD at a point when they co-purify with nuclei. Nucleus-associated NMD has been proposed to involve translation by nuclear ribosomes or, alternatively, translation by cytoplasmic ribosomes either during the process of mRNA export to the cytoplasm or in a mechanism that feeds back to nuclei. Other mRNAs are subject to NMD in the cytoplasm. NMD is mediated by four UPF proteins (UPF1, UPF2, UPF3 and UPF3X), and four SMG proteins (SMG1, SMG5, SMG6 and SMG7). UPF2, UPF3 and UPF3X are mRNP proteins, whereas UPF1 is not. Evidence indicates that SMG proteins function to phosphorylate or dephosphorylate UPF1. NMD degrades mRNA from both ends and involves decapping, deadenylating and exonucleolytic activities.