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Liu P, Panda K, Edwards SA, Swanson R, Yi H, Pandesha P, Hung YH, Klaas G, Ye X, Collins MV, Renken KN, Gilbertson LA, Veena V, Hancock CN, Slotkin RK. Transposase-assisted target-site integration for efficient plant genome engineering. Nature 2024; 631:593-600. [PMID: 38926583 PMCID: PMC11254759 DOI: 10.1038/s41586-024-07613-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
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.
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Affiliation(s)
- Peng Liu
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Seth A Edwards
- Donald Danforth Plant Science Center, St Louis, MO, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Ryan Swanson
- Donald Danforth Plant Science Center, St Louis, MO, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Hochul Yi
- Plant Transformation Facility, Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Pratheek Pandesha
- Donald Danforth Plant Science Center, St Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University, St Louis, MO, USA
| | - Yu-Hung Hung
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Gerald Klaas
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Xudong Ye
- Bayer Crop Science, St Louis, MO, USA
| | | | | | | | - Veena Veena
- Plant Transformation Facility, Donald Danforth Plant Science Center, St Louis, MO, USA
| | | | - R Keith Slotkin
- Donald Danforth Plant Science Center, St Louis, MO, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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