Transposase-assisted target-site integration for efficient plant genome engineering

Peng Liu, Kaushik Panda, Seth A. Edwards, Ryan Swanson, Hochul Yi, Pratheek Pandesha, Yu-Hung Hung, Gerald Klaas, Xudong Ye, Megan V. Collins, Kaili N. Renken, Larry A. Gilbertson, Veena Veena, C. Nathan Hancock and R. Keith Slotkin ()
Additional contact information
Peng Liu: Donald Danforth Plant Science Center
Kaushik Panda: Donald Danforth Plant Science Center
Seth A. Edwards: Donald Danforth Plant Science Center
Ryan Swanson: Donald Danforth Plant Science Center
Hochul Yi: Donald Danforth Plant Science Center
Pratheek Pandesha: Donald Danforth Plant Science Center
Yu-Hung Hung: Donald Danforth Plant Science Center
Gerald Klaas: Donald Danforth Plant Science Center
Xudong Ye: Bayer Crop Science
Megan V. Collins: University of South Carolina-Aiken
Kaili N. Renken: University of South Carolina-Aiken
Larry A. Gilbertson: Bayer Crop Science
Veena Veena: Donald Danforth Plant Science Center
C. Nathan Hancock: University of South Carolina-Aiken
R. Keith Slotkin: Donald Danforth Plant Science Center

Nature, 2024, vol. 631, issue 8021, 593-600

Abstract: Abstract The current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone, and this inefficiency hampers genome-editing approaches to develop improved crops1,2. Often considered to be genome ‘parasites’, transposable elements (TEs) evolved to insert their DNA seamlessly into genomes3–5. Eukaryotic TEs select their site of insertion based on preferences for chromatin contexts, which differ for each TE type6–9. Here we developed a genome engineering tool that controls the TE insertion site and cargo delivered, taking advantage of the natural ability of the TE to precisely excise and insert into the genome. Inspired by CRISPR-associated transposases that target transposition in a programmable manner in bacteria10–12, we fused the rice Pong transposase protein to the Cas9 or Cas12a programmable nucleases. We demonstrated sequence-specific targeted insertion (guided by the CRISPR gRNA) of enhancer elements, an open reading frame and a gene expression cassette into the genome of the model plant Arabidopsis. We then translated this system into soybean—a major global crop in need of targeted insertion technology. We have engineered a TE ‘parasite’ into a usable and accessible toolkit that enables the sequence-specific targeting of custom DNA into plant genomes.

Date: 2024
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DOI: 10.1038/s41586-024-07613-8

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