Chemical genetic screening in the zebrafish embryo


Chemical genetic screening can be described as a discovery approach in which chemicals are assayed for their effects on a defined biological system. The zebrafish, Danio rerio, is a well-characterized and genetically tractable vertebrate model organism that produces large numbers of rapidly developing embryos that develop externally. These characteristics allow for flexible, rapid and scalable chemical screen design using the zebrafish. We describe a protocol for screening compounds from a chemical library for effects on early zebrafish development using an automated in situ based read-out. As screenings are carried out in the context of a complete, developing organism, this approach allows for a more comprehensive analysis of the range of a chemical's effects than that provided by, for example, a cell culture-based or in vitro biochemical assay. Using a 24-h chemical treatment, one can complete a round of screening in 6 d.

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Figure 1: In situ hybridization (ISH) for hematopoietic stem cell (HSC) markers.
Figure 2: Flow diagram showing the overview of the protocol.
Figure 3: Evidence of chemical toxicity in zebrafish embryos.


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The authors would like to thank T. North and W. Goessling for use of runx1/cmyb in situ figures. We thank S. Datta and P. Manos for informative discussions. Thanks to C. Mosimann and J. Dejong for critical reading of the manuscript. C.K.K. is supported by NIH grant 5T32CA09172-34. R.M.W. is supported by NIH grant 1K08AR055368.

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C.K.K. and R.M.W. contributed equally to this work and worked under the guidance and direction of L.Z.

Correspondence to Leonard Zon.

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Kaufman, C., White, R. & Zon, L. Chemical genetic screening in the zebrafish embryo. Nat Protoc 4, 1422–1432 (2009) doi:10.1038/nprot.2009.144

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