Figure 1. General messenger ribonucleic acid (mRNA) decay pathways in eukaryotes. Deadenylation in yeast is carried out by the Ccr4p/Caf1p complex. A homologous complex is present in mammalian cells, as well as the PARN deadenylase. In the 5¢ decay pathway, deadenylation is followed by Dcp1p-mediated decapping and 5¢3¢ exonucleolytic degradation by Xrn1p. In the 3¢ decay pathway, the exosome complex of 3¢5¢ exonucleases, Ski7p and the Ski complex mediate the 3¢5¢ degradation of the deadenylated mRNA. After the exosome has completely degraded the mRNA, the released cap structure is cleaved by DcpS. The 5¢ decay pathway is the major mechanism in yeast, whereas mammalian cells predominantly use the 3¢ decay pathway.

Figure 2. Model for messenger ribonucleic acid (mRNA) surveillance. mRNA processing events in the nucleus dictate the mRNP structure, exon junction complexes (EJC) indicating the location of spliced sites. Since introns are normally found within the coding regions of genes, the EJCs are normally displaced by the elongating ribosome in the initial round of translation. Translation elongation ceases at a normal stop codon or a premature termination codon (PTC). A surveillance complex (SC) consisting of the Upf factors is assembled by sequential interactions with the release factors (RF) and scans downstream of the stop codon. If the surveillance complex encounters an EJC, the termination event is judged to be premature. The mRNA is degraded by decapping and 5¢3¢ exonucleolytic activity. In yeast, where only a few mRNAs contain introns, the nonsense-mediated decay (NMD) function of the EJC is replaced by the hnRNP protein Hrp1p, which binds to degenerate sites within yeast open reading frames.