AsCpf1. Homo sapiens

Perturbing multiple genomic loci is a useful approach to understanding cellular interactions and pathways. Current approaches are limited by the complexity introduced by using multiple Cas9 enzymes. Acidaminococcus Cpf1 (AsCpf1, Cas12a) is an alternative CRISPR enzyme which has the ability to process multiple guides under one promoter, thereby simplifying the targeting of multiple loci. While rules for designing guides for SpCas9 have been developed and continue to improve, design rules for Cpf1 guides are not well characterized. Here we use machine learning models to develop design rules for Cpf1. By varying the direct repeat sequences between these guides we reduce the possibility of recombination in the multiplexed constructs. We also examine the effect of reordering these arrays by targeting BCL2L1 and MCL1, a known synthetically lethal pair. Using the optimized array, we perform a combinatorial screen of synthetically lethal pairs.