Figure 10.

Schematic of mRNAs that do, or do not, trigger NMD. For each gene, the wild-type allele is diagrammed above a mutant allele. In the diagrams, exons are indicated by boxes, coding regions by thicker boxes, stop codons by red octagons and exon-exon junctions by white gaps. The scale bar shows 100 or 1000 nt for each mRNA. The far-right column indicates whether the allele is an NMD target or not. Examples were chosen to illustrate different classes of NMD targets and are not exhaustive (see text for further examples). Annotations were taken from Ensembl, with 3′ UTR annonations from (Jan et al. 2011). (A) An example of a premature stop codon upstream of exon-exon junctions. lin-29(n546) is a smg-suppressible allele of lin-29 (Hodgkin et al. 1989) that encodes an Arg > Stop mutation in the lin-29 ORF (Rougvie and Ambros 1995). (B) An example of an NMD target from a mono-exonic gene. dpy-5(e61) is a Gly > Stop mutation (Thacker et al. 2006) that confers a smg-suppressible Dpy phenotype (Hodgkin et al. 1989). (C) An example of an allele that converts a normal stop codon to a premature stop codon. unc-54(r293) is a 256 bp deletion spanning the unc-54 3′ UTR and poly(A) site that results in a fusion of the unc-54 transcript with the downstream aex-5 transcript. The unc-54(r293) allele is smg-suppressible (Hodgkin et al. 1989). The exact positions of the exon-exon junctions in the unc-54(r293) transcript are not known; the diagram represents a “best guess” based on the work of Pulak and Anderson (1993), Loepold and Ahmed (2014) and the aex-5 transcript. (D) An example of an allele that creates premature stop codons but does not elicit NMD. unc-73(e936) is a splice site mutation that leads to usage of two cryptic splice sites (−1 and +23 nt relative to the normal splice site) generating out-of-frame premature stop codons. Neither transcript is an NMD target, though the reasons for this are not known (Roller et al. 2000).