CRISPR/Cas9-Mediated Knockin and Knockout in Zebrafish

Abstract

The zebrafish (Danio rerio) has emerged in recent years as a powerful vertebrate model to study neuronal circuit development and function, thanks to its relatively small size, rapid external development and translucency. These features allow the easy application of in vivo microscopy analysis and optical perturbation of neuronal function. So far, genetic manipulation in zebrafish has been limited to the generation of constitutive loss-of-function alleles and transgenic models. CRISPR/Cas9 offers unprecedented possibilities for genomic manipulation that can be exploited to study neuronal function. In the past few years, we have successfully used CRISPR/Cas9-based technology in zebrafish to achieve two goals crucial for neuronal circuit analysis by developing two CRISPR/Cas9-based approaches that overcome previous major limitations to the study of gene and neuron functions in zebrafish. The study of gene function via tissue- or cell-specific mutagenesis remains challenging in zebrafish when the study of the function of certain loci might require tight spatiotemporal control of gene inactivation, which is particularly true in studying the function of a particular gene in post mitotic neurons, when the same gene may have had an earlier developmental function. To circumvent this limitation, we developed a simple and versatile protocol to achieve tissue-specific and temporally controlled gene disruption based on Cas9 expression under the control of the Gal4/UAS binary system (Di Donato et al. 2016). This strategy allows us to induce somatic mutations in genetically labeled cell clones or single cells and to follow them in vivo via reporter gene expression. We have also been able to target endogenous genomic loci to specifically label the great variety of neuronal cell types with reporter genes such as the transcriptional activator Gal4 (Auer et al. 2014). As a result, we can specifically target the expression of fluorescent proteins, a genetically encoded calcium indicator or optogenetic actuators in defined neuronal subpopulations.