Functional Characterisation of Active Enhancers in Human Astrocytes Using a High-throughput CRISPRi Screen

We used CROP-seq to perform a high-throughput, parallel screen of 979 candidate enhancer perturbations in normal human astrocytes (NHAs), a primary cell-line. We identified the target gene(s) for 145 of these candidates, which were enriched for transcription with eRNA, transcription factor footprinting, and superenhancer annotation. Most regulatory interactions were <50kb, targeting the nearest gene in ~50% of cases, but were not typically captured by eQTL or in silico predictions. These data elucidate the regulatory network of an understudied-but-crucial brain cell-type. Overall design: Single-cell RNA-seq using 10X Chromium V3 Chemistry was performed on NHA cells stably-transduced with dCas9-KRAB, and transduced with a lentiviral library containing guide RNAs for 979 candidate enhancers, 125 positive control promoters, and 300 non-targeting negative controls