Translation of upstream open reading frames generally does not trigger nonsense-mediated decay in Arabidopsis

ABSTRACT Upstream ORFs (uORFs) are common regulatory elements in the 5’ untranslated regions of eukaryotic mRNAs. In addition to repressing main ORF translation, uORF translation in animals also reduces mRNA stability through nonsense-mediated decay (NMD). In contrast, the roles of uORFs in plants are less understood. Here, we identified actively translated uORFs (TuORFs) in Arabidopsis through ribosome profiling and systematically examined their roles in gene expression. Like animal systems, Arabidopsis TuORFs are associated with 38%, 14%, and 43% reductions in translation efficiency, mRNA half-lives, and protein levels, respectively. However, we found TuORF-containing mRNAs have 51% higher transcript levels, and this phenomenon is persistent in diverse tissues and developmental stages across plants. We present multiple lines of evidence that indicate Arabidopsis uORF-containing mRNAs generally exhibit distinct behavior from known NMD targets. First, TuORF-containing mRNAs are not increased in NMD mutants. Second, TuORF-containing mRNAs and known NMD targets have distinct expression patterns, and they are translationally repressed via different mechanisms. Finally, TuORF- containing mRNAs and NMD targets are degraded through separate pathways. Our results suggest that Arabidopsis TuORFs reduce mRNA stability and translation through mechanisms different from NMD and highlight a fundamental difference in gene regulation mediated by TuORFs in plants and animals.