Nonsense mutations can increase mRNA levels.

Nonsense mutations can reduce mRNA levels, as premature translation termination may lead to the activation of nonsense-mediated mRNA decay (NMD). To examine how positional context influences these outcomes, we introduced premature translation termination codons (PTCs) at 15 locations within the coding region of a GFP reporter gene in Schizosaccharomyces pombe. PTCs in the first third of the coding region consistently led to reduced mRNA levels. In contrast, most downstream PTCs showed modest or minimal reductions, and several were associated with increased mRNA levels relative to the PTC-less control transcript. Measurement of transcript stability for one such variant indicated that the increased abundance was not attributable to decreased turnover. UPF1 deletion in wild-type cells elevated the levels of transcripts that were reduced and, unexpectedly, further increased transcripts' abundance to exceed the control level. In spliced versions of these constructs, downstream PTCs generally reduced mRNA levels regardless of exon junction position. Overall, these observations indicate that an unexpected consequence of nonsense mutations can be increased mRNA levels. These findings may aid in the interpretation of the effects of nonsense mutations on mRNA abundance beyond the predictions of current NMD models and may also help in the design of eukaryotic gene expression constructs.