Optimised genome editing for precise DNA insertion and substitution using Prime Editors in zebrafish Article Swipe
Yosuke Ono
,
Martin Peterka
,
Michael I. Love
,
A.R. Bhandari
,
Euan Gordon
,
Jonathan S. Ball
,
Charles R. Tyler
,
Steve Rees
,
Mohammad Bohlooly‐Y
,
Marcello Maresca
,
Steffen Scholpp
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.04.23.650248
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.04.23.650248
CRISPR/Cas9-mediated genome editing has rapidly become a popular tool for studying gene functions and generating genetically modified organisms. However, using this system, stochastic integration of random insertions and deletions restricts precise genome manipulation. Advanced CRISPR/Cas9 technologies using Prime Editors (PEs), Cas9 proteins fused with reverse transcriptase, enable programmed integration of short DNA modifications into the genome. However, its application in precise genome editing in animal models is challenging. Here, we utilise a nickase- and a nuclease-based PE to perform programmed short DNA substitution and insertion in various loci in the zebrafish genome. Whereas the nickase-based PE is advantageous for nucleotide substitutions, we find that the nuclease-based PE can be used to insert short DNA fragments precisely with high efficiency. To further evaluate our approach, we inserted a nuclear localisation signal into a reporter transgene to incorporate longer fragments by prime editing. These gene modifications were transmitted to the next generation. We demonstrate that PE-mediated prime editing can efficiently manipulate genome information in zebrafish without using exogenous donor DNA.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2025.04.23.650248
- https://www.biorxiv.org/content/biorxiv/early/2025/04/23/2025.04.23.650248.full.pdf
- OA Status
- green
- References
- 68
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4409750049
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4409750049Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2025.04.23.650248Digital Object Identifier
- Title
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Optimised genome editing for precise DNA insertion and substitution using Prime Editors in zebrafishWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-04-23Full publication date if available
- Authors
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Yosuke Ono, Martin Peterka, Michael I. Love, A.R. Bhandari, Euan Gordon, Jonathan S. Ball, Charles R. Tyler, Steve Rees, Mohammad Bohlooly‐Y, Marcello Maresca, Steffen ScholppList of authors in order
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https://doi.org/10.1101/2025.04.23.650248Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2025/04/23/2025.04.23.650248.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2025/04/23/2025.04.23.650248.full.pdfDirect OA link when available
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Substitution (logic), Zebrafish, Prime (order theory), Computational biology, Genome, Genetics, DNA, Biology, Computer science, Programming language, Gene, Mathematics, CombinatoricsTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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68Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.loci | 88 |
| abstract_inverted_index.next | 149 |
| abstract_inverted_index.that | 104, 153 |
| abstract_inverted_index.this | 21 |
| abstract_inverted_index.tool | 9 |
| abstract_inverted_index.used | 110 |
| abstract_inverted_index.were | 145 |
| abstract_inverted_index.with | 44, 117 |
| abstract_inverted_index.Here, | 69 |
| abstract_inverted_index.Prime | 38 |
| abstract_inverted_index.These | 142 |
| abstract_inverted_index.donor | 167 |
| abstract_inverted_index.fused | 43 |
| abstract_inverted_index.prime | 140, 155 |
| abstract_inverted_index.short | 51, 81, 113 |
| abstract_inverted_index.using | 20, 37, 165 |
| abstract_inverted_index.(PEs), | 40 |
| abstract_inverted_index.animal | 65 |
| abstract_inverted_index.become | 6 |
| abstract_inverted_index.enable | 47 |
| abstract_inverted_index.genome | 2, 32, 62, 160 |
| abstract_inverted_index.insert | 112 |
| abstract_inverted_index.longer | 137 |
| abstract_inverted_index.models | 66 |
| abstract_inverted_index.random | 26 |
| abstract_inverted_index.signal | 130 |
| abstract_inverted_index.Editors | 39 |
| abstract_inverted_index.Whereas | 93 |
| abstract_inverted_index.editing | 3, 63, 156 |
| abstract_inverted_index.further | 121 |
| abstract_inverted_index.genome. | 56, 92 |
| abstract_inverted_index.nuclear | 128 |
| abstract_inverted_index.perform | 79 |
| abstract_inverted_index.popular | 8 |
| abstract_inverted_index.precise | 31, 61 |
| abstract_inverted_index.rapidly | 5 |
| abstract_inverted_index.reverse | 45 |
| abstract_inverted_index.system, | 22 |
| abstract_inverted_index.utilise | 71 |
| abstract_inverted_index.various | 87 |
| abstract_inverted_index.without | 164 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.Advanced | 34 |
| abstract_inverted_index.However, | 19, 57 |
| abstract_inverted_index.editing. | 141 |
| abstract_inverted_index.evaluate | 122 |
| abstract_inverted_index.inserted | 126 |
| abstract_inverted_index.modified | 17 |
| abstract_inverted_index.nickase- | 73 |
| abstract_inverted_index.proteins | 42 |
| abstract_inverted_index.reporter | 133 |
| abstract_inverted_index.studying | 11 |
| abstract_inverted_index.approach, | 124 |
| abstract_inverted_index.deletions | 29 |
| abstract_inverted_index.exogenous | 166 |
| abstract_inverted_index.fragments | 115, 138 |
| abstract_inverted_index.functions | 13 |
| abstract_inverted_index.insertion | 85 |
| abstract_inverted_index.precisely | 116 |
| abstract_inverted_index.restricts | 30 |
| abstract_inverted_index.transgene | 134 |
| abstract_inverted_index.zebrafish | 91, 163 |
| abstract_inverted_index.generating | 15 |
| abstract_inverted_index.insertions | 27 |
| abstract_inverted_index.manipulate | 159 |
| abstract_inverted_index.nucleotide | 100 |
| abstract_inverted_index.organisms. | 18 |
| abstract_inverted_index.programmed | 48, 80 |
| abstract_inverted_index.stochastic | 23 |
| abstract_inverted_index.CRISPR/Cas9 | 35 |
| abstract_inverted_index.PE-mediated | 154 |
| abstract_inverted_index.application | 59 |
| abstract_inverted_index.demonstrate | 152 |
| abstract_inverted_index.efficiency. | 119 |
| abstract_inverted_index.efficiently | 158 |
| abstract_inverted_index.generation. | 150 |
| abstract_inverted_index.genetically | 16 |
| abstract_inverted_index.incorporate | 136 |
| abstract_inverted_index.information | 161 |
| abstract_inverted_index.integration | 24, 49 |
| abstract_inverted_index.transmitted | 146 |
| abstract_inverted_index.advantageous | 98 |
| abstract_inverted_index.challenging. | 68 |
| abstract_inverted_index.localisation | 129 |
| abstract_inverted_index.substitution | 83 |
| abstract_inverted_index.technologies | 36 |
| abstract_inverted_index.manipulation. | 33 |
| abstract_inverted_index.modifications | 53, 144 |
| abstract_inverted_index.nickase-based | 95 |
| abstract_inverted_index.nuclease-based | 76, 106 |
| abstract_inverted_index.substitutions, | 101 |
| abstract_inverted_index.transcriptase, | 46 |
| abstract_inverted_index.CRISPR/Cas9-mediated | 1 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 11 |
| citation_normalized_percentile.value | 0.13796324 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |