Large-scale F0 CRISPR screens in vivo using MIC-Drop

Saba Parvez, Zachary J. Brandt, Randall T. Peterson

Published: 2023-04-16 DOI: 10.1038/s41596-023-00821-y

CRISPR screens

MIC-Drop

zebrafish

functional genetics

biallelic mutations

AI 解读

Preparation of single-cell suspensions of mouse glomeruli for high-throughput analysis

cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA

Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins

Engineering megabase-sized genomic deletions with MACHETE (Molecular Alteration of Chromosomes with Engineered Tandem Elements)

Genome-wide pooled CRISPR screening in neurospheres

Neural cell isolation from adult macaques for high-throughput analyses and neurosphere cultures

Design and fabrication of wearable electronic textiles using twisted fiber-based threads

Nacre-inspired underwater superoleophobic films with high transparency and mechanical robustness

Quantification of organelle contact sites by split-GFP-based contact site sensors (SPLICS) in living cells

Scanorama: integrating large and diverse single-cell transcriptomic datasets

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The zebrafish is a powerful model system for studying animal development, for modeling genetic diseases, and for large-scale invivo functional genetics. Because of its ease of use and its high efficiency in targeted gene perturbation, CRISPR–Cas9 has rec
Introduction
Materials
Procedure
Troubleshooting
Timing
Anticipated results
- References
References
ACKNOWLEDGMENTS
ACKNOWLEDGMENTS

Hsu, P. D., Lander, E. S. & Zhang, F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262–1278 (2014).
Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).
Adli, M. The CRISPR tool kit for genome editing and beyond. Nat. Commun. 9, 1911 (2018).
Doudna, J. A. & Charpentier, E. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096 (2014).
Sander, J. D. & Joung, J. K. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32, 347–355 (2014).
Shalem, O., Sanjana, N. E. & Zhang, F. High-throughput functional genomics using CRISPR–Cas9. Nat. Rev. Genet. 16, 299–311 (2015).
Bock, C. et al. High-content CRISPR screening. Nat. Rev. Methods Prim. 2, 8 (2022).
Joung, J. et al. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat. Protoc. 12, 828–863 (2017).
Feldman, D. et al. Pooled genetic perturbation screens with image-based phenotypes. Nat. Protoc. 17, 476–512 (2022).
Jost, M. & Weissman, J. S. CRISPR approaches to small molecule target identification. ACS Chem. Biol. 13, 366–375 (2018).
Neggers, J. E. et al. Target identification of small molecules using large-scale CRISPR-Cas mutagenesis scanning of essential genes. Nat. Commun. 9, 502 (2018).
Kuhn, M., Santinha, A. J. & Platt, R. J. Moving from in vitro to in vivo CRISPR screens. Gene Genome Ed. 2, 100008 (2021).
Shin, U. et al. Large-scale generation and phenotypic characterization of zebrafish CRISPR mutants of DNA repair genes. DNA Repair 107, 103173 (2021).
Pei, W. et al. Guided genetic screen to identify genes essential in the regeneration of hair cells and other tissues. NPJ Regen. Med. 3, 11 (2018).
Varshney, G. K. et al. High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res. 25, 1030–1042 (2015).
Varshney, G. K. et al. A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish. Nat. Protoc. 11, 2357–2375 (2016).
Thyme, S. B. et al. Phenotypic landscape of schizophrenia-associated genes defines candidates and their shared functions. Cell 177, 478–491.e20 (2019).
Sun, Y. et al. Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9. Genome Res. 30, 118–126 (2019).
Keatinge, M. et al. CRISPR gRNA phenotypic screening in zebrafish reveals pro-regenerative genes in spinal cord injury. PLOS Genet. 17, e1009515 (2021).
Parvez, S. et al. MIC-Drop: a platform for large-scale in vivo CRISPR screens. Science 373, 1146–1151 (2021).
Patton, E. E. & Zon, L. I. The art and design of genetic screens: zebrafish. Nat. Rev. Genet. 2, 956–966 (2001).
Howe, K. et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498–503 (2013).
Kimmel, C. B., Ballard, W. W., Kimmel, S. R., Ullmann, B. & Schilling, T. F. Stages of embryonic development of the zebrafish. Dev. Dyn. 203, 253–310 (1995).
Driever, W. et al. A genetic screen for mutations affecting embryogenesis in zebrafish. Development 123, 37–46 (1996).
Haffter, P. et al. The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. Development 123, 1–36 (1996).
Eisen, J. S. Zebrafish make a big splash. Cell 87, 969–977 (1996).
Poss, K. D., Wilson, L. G. & Keating, M. T. Heart regeneration in zebrafish. Science 298, 2188–2190 (2002).
Gemberling, M., Bailey, T. J., Hyde, D. R. & Poss, K. D. The zebrafish as a model for complex tissue regeneration. Trends Genet. 29, 611–620 (2013).
Marques, I. J., Lupi, E. & Mercader, N. Model systems for regeneration: zebrafish. Development 146, dev167692 (2019).
Meshalkina, D. A. et al. Understanding zebrafish cognition. Behav. Process. 141, 229–241 (2017).
Gerlai, R. Evolutionary conservation, translational relevance and cognitive function: the future of zebrafish in behavioral neuroscience. Neurosci. Biobehav. Rev. 116, 426–435 (2020).
Kalueff, A. V. et al. Towards a comprehensive catalog of zebrafish behavior 1.0 and beyond. Zebrafish 10, 70–86 (2013).
Geng, Y. & Peterson, R. T. The zebrafish subcortical social brain as a model for studying social behavior disorders. Dis. Model. Mech. 12, dmm039446 (2019).
Bahl, A. & Engert, F. Neural circuits for evidence accumulation and decision making in larval zebrafish. Nat. Neurosci. 23, 94–102 (2020).
Nelson, J. C. & Granato, M. Zebrafish behavior as a gateway to nervous system assembly and plasticity. Development 149, dev177998 (2022).
McConnell, A. M., Noonan, H. R. & Zon, L. I. Reeling in the zebrafish cancer models. Annu. Rev. Cancer Biol. 5, 331–350 (2021).
White, R., Rose, K. & Zon, L. Zebrafish cancer: the state of the art and the path forward. Nat. Rev. Cancer 13, 624–636 (2013).
Zhang, T. & Peterson, R. T. Modeling lysosomal storage diseases in the zebrafish. Front. Mol. Biosci. 7, 82 (2020).
Campbell, P. D. & Granato, M. Zebrafish as a tool to study schizophrenia-associated copy number variants. Dis. Model. Mech. 13, dmm043877 (2020).
Grone, B. P. & Baraban, S. C. Animal models in epilepsy research: legacies and new directions. Nat. Neurosci. 18, 339–343 (2015).
Basu, S. & Sachidanandan, C. Zebrafish: a multifaceted tool for chemical biologists. Chem. Rev. 113, 7952–7980 (2013).
Hwang, W. Y. et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat. Biotechnol. 31, 227–229 (2013).
Burger, A. et al. Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes. Development 143, 2025–2037 (2016).
Gagnon, J. A. et al. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One 9, e98186 (2014).
Shah, A. N., Davey, C. F., Whitebirch, A. C., Miller, A. C. & Moens, C. B. Rapid reverse genetic screening using CRISPR in zebrafish. Nat. Methods 12, 535–540 (2015).
Jao, L.-E., Wente, S. R. & Chen, W. Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc. Natl Acad. Sci. USA 110, 13904–13909 (2013).
Wu, R. S. et al. A rapid method for directed gene knockout for screening in G0 zebrafish. Dev. Cell 46, 112–125.e4 (2018).
Kroll, F. et al. A simple and effective F0 knockout method for rapid screening of behaviour and other complex phenotypes. eLife 10, e59683 (2021).
Hoshijima, K. et al. Highly efficient CRISPR-Cas9-based methods for generating deletion mutations and F0 embryos that lack gene function in zebrafish. Dev. Cell 51, 645–657.e4 (2019).
Long, L. et al. Regulation of transcriptionally active genes via the catalytically inactive Cas9 in C. elegans and D. rerio. Cell Res. 25, 638–641 (2015).
Dong, X. et al. Zebrafish Znfl1 proteins control the expression of hoxb1b gene in the posterior neuroectoderm by acting upstream of pou5f3 and sall4 genes. J. Biol. Chem. 292, 13045–13055 (2017).
Ghanta, K. S., Ishidate, T. & Mello, C. C. Microinjection for precision genome editing in Caenorhabditis elegans. STAR Protoc. 2, 100748 (2021).
Stepicheva, N. A. & Song, J. L. High throughput microinjections of sea urchin zygotes. J. Vis. Exp. 2014, e50841 (2014).
Peng, P. et al. CRISPR-Cas9 mediated genome editing in Drosophila. Bio. Protoc. 9, e3141 (2019).
Nakayama, T. et al. Cas9-based genome editing in Xenopus tropicalis. Methods Enzymol. 546, 355–375 (2014).
Wang, H. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153, 910–918 (2013).
Schubert, S., Keddig, N., Hanel, R. & Kammann, U. Microinjection into zebrafish embryos (Danio rerio) - a useful tool in aquatic toxicity testing? Environ. Sci. Eur. 26, 32 (2014).
McKee, R. A. & Wingert, R. A. Nephrotoxin microinjection in zebrafish to model acute kidney injury. J. Vis. Exp. 2016, 10.3791/54241 (2016).
Amsterdam, A. et al. A large-scale insertional mutagenesis screen in zebrafish. Genes Dev. 13, 2713–2724 (1999).
Gaiano, N. et al. Insertional mutagenesis and rapid cloning of essential genes in zebrafish. Nature 383, 829–832 (1996).
Amsterdam, A. et al. Identification of 315 genes essential for early zebrafish development. Proc. Natl Acad. Sci. USA 101, 12792–12797 (2004).
Golling, G. et al. Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development. Nat. Genet. 31, 135–140 (2002).
Fuentes, R., Letelier, J., Tajer, B., Valdivia, L. E. & Mullins, M. C. Fishing forward and reverse: advances in zebrafish phenomics. Mech. Dev. 154, 296–308 (2018).
Sander, J. D. et al. Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat. Biotechnol. 29, 697–698 (2011).
Huang, P. et al. Heritable gene targeting in zebrafish using customized TALENs. Nat. Biotechnol. 29, 699–700 (2011).
Doyon, Y. et al. Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat. Biotechnol. 26, 702–708 (2008).
Foley, J. E. et al. Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by Oligomerized Pool ENgineering (OPEN). PLoS One 4, e4348 (2009).
Bradford, Y. M. et al. Zebrafish information network, the knowledgebase for Danio rerio research. Genetics 220, iyac016 (2022).
Mullins, M. C., Acedo, J. N., Priya, R., Solnica-Krezel, L. & Wilson, S. W. The zebrafish issue: 25 years on. Development 148, dev200343 (2021).
Jin, X. et al. In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. Science 370, eaaz6063 (2020).
Trubiroha, A. et al. A rapid CRISPR/Cas-based mutagenesis assay in zebrafish for identification of genes involved in thyroid morphogenesis and function. Sci. Rep. 8, 5647 (2018).
Klatt Shaw, D. & Mokalled, M. H. Efficient CRISPR/Cas9 mutagenesis for neurobehavioral screening in adult zebrafish. G3 (Bethesda) 11, jkab089 (2021).
Labun, K. et al. CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Res. 47, W171–W174 (2019).
Moreno-Mateos, M. A. et al. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat. Methods 12, 982–988 (2015).
Concordet, J.-P. & Haeussler, M. CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic Acids Res. 46, W242–W245 (2018).
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).
Quick, R. E., Buck, L. D., Parab, S., Tolbert, Z. R. & Matsuoka, R. L. Highly efficient synthetic CRISPR RNA/Cas9-based mutagenesis for rapid cardiovascular phenotypic screening in F0 zebrafish. Front. Cell Dev. Biol. 9, 735598 (2021).
Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 33, 187–197 (2015).
Košir, A. B. et al. Droplet volume variability as a critical factor for accuracy of absolute quantification using droplet digital PCR. Anal. Bioanal. Chem. 409, 6689–6697 (2017).

Large-scale F0 CRISPR screens in vivo using MIC-Drop

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