Figure 1

The mammalian nonsense-mediated mRNA decay (NMD) rule. Stop codons located > 50 to 55 nucleotides upstream of the 3' most splice-generated exon-exon junction usually trigger NMD in mammals [16]. Mammalian genes are transcribed from the genome, which produces the precursor of mRNA (pre-mRNA). Pre-mRNA still contains exons (Ex) and introns (In), and is subject to processes including capping, polyadenylation and splicing. The splicing step removes the introns from pre-mRNA and ligates the exons. The spliced mRNA then undergoes the first round of translation during export [17]. If the distance from the normal stop codon to the exon-exon junction closest to the 3'-end (labelled 'Distance' in the figure) is > 55 nucleotides, in most cases the mRNA will be degraded by the NMD pathway – we refer to these transcripts as putative NMD targets. mRNAs for which the distance from the normal stop codon to the exon-exon junction closest to the 3'-end is < 50 to 55 nucleotides are free of NMD decay. These mRNAs and ones with stop codons in the last exon are classified as putative non-NMD targets.