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

Author

Listed:
  • Sayeh Gorjifard

    (University of Washington)

  • Tobias Jores

    (University of Washington)

  • Jackson Tonnies

    (University of Washington
    University of Washington)

  • Nicholas A. Mueth

    (University of Washington)

  • Kerry Bubb

    (University of Washington)

  • Travis Wrightsman

    (Cornell University)

  • Edward S. Buckler

    (Cornell University
    United States Department of Agriculture
    Cornell University)

  • Stanley Fields

    (University of Washington
    University of Washington)

  • Josh T. Cuperus

    (University of Washington)

  • Christine Queitsch

    (University of Washington)

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.

Suggested Citation

  • Sayeh Gorjifard & Tobias Jores & Jackson Tonnies & Nicholas A. Mueth & Kerry Bubb & Travis Wrightsman & Edward S. Buckler & Stanley Fields & Josh T. Cuperus & Christine Queitsch, 2024. "Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50174-7
    DOI: 10.1038/s41467-024-50174-7
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    References listed on IDEAS

    as
    1. Xuhong Yu & Pascal G. P. Martin & Scott D. Michaels, 2019. "BORDER proteins protect expression of neighboring genes by promoting 3′ Pol II pausing in plants," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
    2. Jan Zrimec & Christoph S. Börlin & Filip Buric & Azam Sheikh Muhammad & Rhongzen Chen & Verena Siewers & Vilhelm Verendel & Jens Nielsen & Mats Töpel & Aleksej Zelezniak, 2020. "Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
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