CRISPRcombo SIGNED

Project "CRISPRcombo" data sheet

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 Project objective

A ubiquitous yet poorly understood theme pervading biology is redundancy, wherein seemingly equivalent components drive shared processes. In cases from development to pathogenesis, untangling the ensuing web of potential genetic interactions can be virtually impossible with conventional techniques. CRISPR technologies, with their propensity for multiplexing, are well poised to address this challenge. However, current CRISPR-based screens have not exceeded more than two targets at a time. Here, I will achieve a major leap forward for CRISPR-based screens and dissecting redundancy by harnessing a core yet underexplored part of CRISPR: CRISPR arrays. CRISPR arrays naturally form the immunological memory of CRISPR-Cas systems and produce multiple targeting gRNAs processed from a single transcript. The arrays are highly compact, genetically stable, and can encode hundreds of gRNAs. However, the repetitive “repeats” within each array have hampered their construction and widespread adoption. My group recently made a breakthrough with the modular one-pot assembly of long arrays and array libraries. This capability grants us the unique opportunity to develop the first high-throughput, CRISPR-based screens that readily scale to many gene targets at a time. In parallel, our first assembled arrays highlighted technical constraints to designing robust and highly active arrays. I posit that native CRISPR arrays have faced similar limitations and thus can inform the design of array libraries. I thus propose to 1) Develop design rules for CRISPR arrays yielding only intended and uniformly abundant guide RNAs. 2) Elucidate and exploit why CRISPR arrays are genetically stable. 3) Perform scalable combinatorial screens using redundancy by small RNAs in E. coli as a compelling case study. If successful, this project will reveal unexplored properties of CRISPR arrays and, for the first time, achieve scalable combinatorial screens for interrogating redundancy throughout biology.