Repurposing of CAST Systems as Next-Generation Tools for Genome Engineering of Mammalian Cells

Genome editing using RNA-guided CRISPR-Cas nucleases (Clustered Regularly Interspaced Short Palindromic Repeats that associate with CRISPR associated proteins) has radically altered life sciences, enabling genome manipulation in living organisms. However, their use is limited by dependence on DNA Damage Response (DDR), which restricts genome editing to dividing cells. Further, these nucleases cannot handle DNA cargos large enough to harbour regulatory DNA circuitry, thus precluding genome engineering. In INTETOOLS, I will overcome these limitations by dissecting and repurposing CRISPR Associated Transposon (CAST) systems into genome engineering tools. CASTs are naturally occurring prokaryotic protein–RNA machineries consisting of an inactive CRISPR effector complex, which associate with Tn7 family transposons to insert large DNA cargos. Knowledge of their molecular mechanisms is scarce, which prevents their practical application in genome engineering. Accordingly, in Objective 1, I will investigate the architecture of different CASTs to obtain fundamental knowledge of their RNA-guided integration. I will then use this knowledge in Objective 2, to dissect their mechanism underpinnings whereby CRISPR-Cas complexes associate with transposition complexes to insert with nucleotide accuracy DNA cargos. This will inform Objective 3, where I will design new CAST tools that will allow RNA-guided transposition in eukaryotic genomes. These revamped CASTs will be capable of inserting large DNAs with high precision, harbouring regulatory regions into eukaryotic genomes, enabling genome engineering in eukaryotes. I will test the redesigned CASTs in mammalian cell lines and at the organismal level by rescuing the eyeless mutant phenotype in Drosophila melanogaster. INTETOOLS will catalyse a conceptual leap propelling the field into a new era of genome engineering, with major biomedical and biotechnological applications especially in synthetic biology.