Effects of sequence motifs in the yeast 3′ untranslated region determined from massively-parallel assays of random sequences

The 3′ untranslated region (UTR) plays critical roles in determining the level of gene expression, through effects on activities such as mRNA stability and translation. The underlying functional elements within this region have largely been identified through analyses of the limited number of native genes. To explore the effects of sequence elements when not present in biologically evolved sequence backgrounds, we analyzed hundreds of thousands of random 50-mers inserted into the 3′ UTR of a reporter gene in the yeast Saccharomyces cerevisiae. We determined relative protein expression levels from the fitness of a library of transformants in a growth selection. We find that the consensus 3′ UTR efficiency element significantly boosts expression, independent of sequence context; on the other hand, the consensus positioning element has only a small effect on expression. Some sequence motifs that are binding sites for Puf proteins substantially increase expression in this random library, despite these proteins generally being associated with post-transcriptional downregulation when bound to native mRNAs. Thus, the regulatory effects of 3′ UTR sequence features like the positioning element and Puf binding sites appear to be strongly dependent on their context within native genes, where they exist alongside co-evolved sequence features. Our measurements also allowed a systematic examination of the effects of point mutations within efficiency element motifs across diverse sequence backgrounds. These mutational scans reveal the relative in vivo importance of individual bases in the efficiency element, which likely reflects their roles in binding the Hrp1 protein involved in cleavage and polyadenylation.