CRISPR-based functional genomics tools in vertebrate models

The advent of CRISPR-Cas technologies has revolutionized functional genomics by enabling precise genetic manipulations in various model organisms. In popular vertebrate models, including mice and zebrafish, CRISPR has been adapted to high-throughput mutagenesis workflows, knock-in alleles and large-scale screens, bringing us closer to understanding gene functions in development, physiology and pathology. The development of innovative technologies, such as base editors, capable of single-nucleotide modifications, and prime editors, offering precision edits without double-strand breaks, exemplifies the expanding toolkit. In addition to gene editing, transcriptional modulation, that is, CRISPR interference and CRISPR activation systems, can elucidate the mechanisms of gene regulation. Newer methods, such as MIC-Drop and Perturb-seq, which increase screening throughput in vivo, hold significant promise to improve our ability to dissect complex biological processes and mechanisms. Furthermore, CRISPR-based gene therapies for treating sickle cell disease and other monogenic diseases have already demonstrated their potential for clinical translation. Here this Review covers the transformative impact of CRISPR-based tools in vertebrate models, highlighting their utility in functional genomics research and disease modeling.