High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9.


The use of CRISPR/Cas9 as a genome-editing tool in various model organisms has radically changed targeted mutagenesis. Here, we present a high-throughput targeted mutagenesis pipeline using CRISPR/Cas9 technology in zebrafish that will make possible both saturation mutagenesis of the genome and large-scale phenotyping efforts. We describe a cloning-free single-guide RNA (sgRNA) synthesis, coupled with streamlined mutant identification methods utilizing fluorescent PCR and multiplexed, high-throughput sequencing. We report germline transmission data from 162 loci targeting 83 genes in the zebrafish genome, in which we obtained a 99% success rate for generating mutations and an average germline transmission rate of 28%. We verified 678 unique alleles from 58 genes by high-throughput sequencing. We demonstrate that our method can be used for efficient multiplexed gene targeting. We also demonstrate that phenotyping can be done in the F1 generation by inbreeding two injected founder fish, significantly reducing animal husbandry and time. This study compares germline transmission data from CRISPR/Cas9 with those of TALENs and ZFNs and shows that efficiency of CRISPR/Cas9 is sixfold more efficient than other techniques. We show that the majority of published "rules" for efficient sgRNA design do not effectively predict germline transmission rates in zebrafish, with the exception of a GG or GA dinucleotide genomic match at the 5' end of the sgRNA. Finally, we show that predicted off-target mutagenesis is of low concern for in vivo genetic studies.

DOI: 10.1101/gr.186379.114

7 Figures and Tables

Citations per Year

793 Citations

Semantic Scholar estimates that this publication has 793 citations based on the available data.

See our FAQ for additional information.

Cite this paper

@article{Varshney2015HighthroughputGT, title={High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9.}, author={Gaurav K Varshney and Wuhong Pei and Matthew C LaFave and Jennifer Idol and Lisha Xu and Viviana Gallardo and Blake Carrington and Kevin Bishop and MaryPat Jones and Mingyu Li and Ursula Harper and Sunny C Huang and Anupam Prakash and Wenbiao Chen and Raman Sood and Johan Ledin and Shawn M Burgess}, journal={Genome research}, year={2015}, volume={25 7}, pages={1030-42} }