RESEARCH ARTICLE Systematic Dissection of the Sequence Determinants of Gene 3 ’ End Mediated Expression Control

The 3’end genomic region encodes a wide range of regulatory process including mRNA sta-bility, 3 ’ end processing and translation. Here, we systematically investigate the sequence determinants of 3 ’ end mediated expression control by measuring the effect of 13,000 de-signed 3 ’ end sequence variants on constitutive expression levels in yeast. By including a high resolution scanning mutagenesis of more than 200 native 3 ’ end sequences in this de-signed set, we found that most mutations had only a mild effect on expression, and that the vast majority (~90%) of strongly effecting mutations localized to a single positive TA-rich el-ement, similar to a previously described 3 ’ end processing efficiency element, and resulted in up to ten-fold decrease in expression. Measurements of 3 ’ UTR lengths revealed that these mutations result in mRNAs with aberrantly long 3’UTRs, confirming the role for this el-ement in 3 ’ end processing. Interestingly, we found that other sequence elements that were previously described in the literature to be part of the polyadenylation signal had a minor ef-fect on expression. We further characterize the sequence specificities of the TA-rich ele-ment using additional synthetic 3 ’ end sequences and show that its activity is sensitive t