Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafish embryos
| Autor: | Suzan Demuynck, Aaron M. Zorn, Kris Vleminckx, Marjolein Carron, Andy Willaert, Nicole A. Edwards, Marcin Wlizla, Thomas Naert, Dieter Tulkens, Paul Coucke, Annekatrien Boel, Nikko-Ideen Shaidani, Marko E. Horb |
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| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Xenopus lcsh:Medicine Penetrance Context (language use) Computational biology Article Mice Xenopus laevis 03 medical and health sciences 0302 clinical medicine Gene Frequency Genome editing CRISPR-Associated Protein 9 Medicine and Health Sciences Animals Humans CRISPR Clustered Regularly Interspaced Short Palindromic Repeats Guide RNA lcsh:Science Frameshift Mutation Zebrafish Gene Editing Multidisciplinary biology Cas9 lcsh:R Biology and Life Sciences Mouse Embryonic Stem Cells Genetic models biology.organism_classification HEK293 Cells 030104 developmental biology Genetic engineering lcsh:Q CRISPR-Cas Systems Genetic techniques Functional genomics 030217 neurology & neurosurgery RNA Guide Kinetoplastida |
| Zdroj: | SCIENTIFIC REPORTS Scientific Reports Scientific Reports, Vol 10, Iss 1, Pp 1-12 (2020) |
| ISSN: | 2045-2322 |
| Popis: | CRISPR/Cas9 genome editing has revolutionized functional genomics in vertebrates. However, CRISPR/Cas9 edited F0 animals too often demonstrate variable phenotypic penetrance due to the mosaic nature of editing outcomes after double strand break (DSB) repair. Even with high efficiency levels of genome editing, phenotypes may be obscured by proportional presence of in-frame mutations that still produce functional protein. Recently, studies in cell culture systems have shown that the nature of CRISPR/Cas9-mediated mutations can be dependent on local sequence context and can be predicted by computational methods. Here, we demonstrate that similar approaches can be used to forecast CRISPR/Cas9 gene editing outcomes in Xenopus tropicalis, Xenopus laevis, and zebrafish. We show that a publicly available neural network previously trained in mouse embryonic stem cell cultures (InDelphi-mESC) is able to accurately predict CRISPR/Cas9 gene editing outcomes in early vertebrate embryos. Our observations can have direct implications for experiment design, allowing the selection of guide RNAs with predicted repair outcome signatures enriched towards frameshift mutations, allowing maximization of CRISPR/Cas9 phenotype penetrance in the F0 generation. |
| Databáze: | OpenAIRE |
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