Fig. 1: Multiplex, single cell CRISPRa screening for cell type-specific regulatory elements.

(Left) A library of gRNAs targeting candidate cis-regulatory elements (cCREs) is introduced in a multiplex fashion to a population of cells expressing CRISPRa machinery, such that each cell contains a random combination of multiple CRISPRa-mediated perturbations. (Middle) Following single cell transcriptional profiling and gRNA assignment, cells are systematically computationally partitioned into those with or without a given gRNA and tested for upregulation of neighboring genes. (Right) CRISPRa perturbations can either result in target-specific upregulation, no detectable effect (e.g., for non-targeting controls) or, at least theoretically, broad cis-upregulation of multiple genes in the vicinity of the gRNA/CRISPRa machinery. Furthermore, patterns of upregulation can either be general or cell type-specific.