Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability

Sayeh Gorjifard, Tobias Jores, Jackson Tonnies, Nicholas A. Mueth, Kerry Bubb, Travis Wrightsman, Edward S. Buckler, Stanley Fields, Josh T. Cuperus and Christine Queitsch ()
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Sayeh Gorjifard: University of Washington
Tobias Jores: University of Washington
Jackson Tonnies: University of Washington
Nicholas A. Mueth: University of Washington
Kerry Bubb: University of Washington
Travis Wrightsman: Cornell University
Edward S. Buckler: Cornell University
Stanley Fields: University of Washington
Josh T. Cuperus: University of Washington
Christine Queitsch: University of Washington

Nature Communications, 2024, vol. 15, issue 1, 1-21

Abstract: Abstract The 3’ end of a gene, often called a terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, a massively parallel reporter assay, to measure the activity of over 50,000 terminators from the plants Arabidopsis thaliana and Zea mays. We characterize thousands of plant terminators, including many that outperform bacterial terminators commonly used in plants. Terminator activity is species-specific, differing in tobacco leaf and maize protoplast assays. While recapitulating known biology, our results reveal the relative contributions of polyadenylation motifs to terminator strength. We built a computational model to predict terminator strength and used it to conduct in silico evolution that generated optimized synthetic terminators. Additionally, we discover alternative polyadenylation sites across tens of thousands of terminators; however, the strongest terminators tend to have a dominant cleavage site. Our results establish features of plant terminator function and identify strong naturally occurring and synthetic terminators.

Date: 2024
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DOI: 10.1038/s41467-024-50174-7

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