ADVANCING GENE-EDITING NUCLEASES FOR DIVERSE ZEBRAFISH APPLICATIONS

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Development of CRISPR/Cas9 technology has transformed our ability to edit the genomes of numerous organisms. Today, almost any investigator can practice the basic genome editing technologies, thanks to the broad distribution of open-source CRISPR reagents. Still, the full potential of the field has not been reached. Further innovation is likely to deliver major new advances, enabling application to a wide range of important biomedical problems. Several potential future advances are particularly exciting, including: 1) developments that will make drug discovery more efficient, 2), developments combining genome editing tools with diverse molecular technologies to create novel diagnostics and biosensors, and 3) developments enabling efficient, genome-wide screens to discover gene functions. Work in these areas will undoubtedly lead to advances in our ability to understand, diagnose, and treat human genetic disorders. Collaboration between the Peterson, Yeh, and Joung labs over the past decade has resulted in several key advances in genome editing, including the first use of TALENs to edit the zebrafish genome, the first use of CRISPR/Cas9 to modify the genome of any animal, and the first engineering of Cas9 to alter PAM specificity. These advances have collectively been cited thousands of times and become tools used around the world. We propose to develop three novel technologies that are connected by their use of CRISPR/Cas9-based components and by their potential to augment the utility of the zebrafish as a model organism. Plans include: Aim 1. To develop a technology for instantaneous visual genotyping. We will use the ΦC31 DNA integrase system to insert fluorescent markers into CRISPR/Cas9-generated mutants, a different color for each gene copy. This will enable rapid identification and sorting of wild-type, heterozygous, and homozygous mutants from a mixed population, with potential applications ranging from genetic studies to drug screening. Aim 2. To create a DNA proximity split-reporter system. We will establish a reporter system in which two CRISPR guide RNAs, when targeted to two DNA sequences located near each other, will induce quantifiable luminescence. Development of this platform will enable numerous future applications including mapping 3D chromosome structure and diagnosing chromosomal organization defects. Aim 3. To develop a system enabling high-throughput CRISPR library screening in zebrafish. The platform will enable rapid injection of libraries of sgRNAs along with target-identifying tags, followed by selection of animals exhibiting phenotypes of interest. The identity of the causative gene disruptions will be obtained by recovery of the implanted tags. Upon completing these aims, this project will have an impact on biomedical research broadly by providing new tools and methodologies for targeted genome manipulation.