Genome engineering in the nematode C. elegans

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Project Summary CRISPR offers the promise of total control over genes in model organisms, such as the nematode C. elegans. To make this a reality, we need functional tags on all proteins that we can use as handles to influence the biology of any cell. However, each individual edit requires unique reagents and takes experienced worm geneticists 6 weeks or more to create. To edit many genes with diverse tags one gene at a time is just not practical. The goals of this project are to make CRISPR genome modifications simple, inexpensive and with increased throughput. We propose a series of multiplexed genome engineering methods that will accelerate gene tagging in C. elegans 10- to 100-fold. First, we propose to optimize cassette exchange methods using diverse recombinases that will allow geneticists to alter one gene with many diverse tags. Second, we propose to develop a multiplexed CRISPR strategy that will allow groups to modify many genes within a single editing experiment. Third, we will develop software and reagent libraries required to modify all genes in the genome. • Aim 1. One gene: recombinase-mediated cassette exchange. We will characterize the germline activity of a diverse set of recombinases and develop cassette exchange methods for rapidly integrating transgenes or tags anywhere in the genome. • Aim 2. Many genes: multiplex CRISPR. Current methods require a unique injection cocktail for each unique gene modification. We will develop a multiplex CRISPR strategy in which the reagents for tagging many unique genes are injected simultaneously to generate many edited worm strains, each with a single edited target. • Aim 3. All genes: software and molecular reagents. To tag the proteome, reagents cannot be efficiently designed one-at-a-time, by hand. We will write software that identifies optimal tagging locations and designs the required reagents, and we will build build a cost-effective pooled molecular workflow to build genome editing reagents. C. elegans shares most of the genes mutated in human genetic diseases; as a simple, compact and rapidly developing animal, it is an attractive platform to study these genes. In the future, the genome engineering pipelines developed here could be used to insert a swappable tagging site in every protein-coding gene in the C. elegans genome, making it possible to easily add any tag to any gene. Such a strain collection would be a boon for cell biologists and geneticists, enabling new inroads in studying how cells work and how to fix them when disease processes cause them to malfunction.