Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks

Summary Here we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by assay of transposase-accessible chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ∼4,300 single cells, encompassing more than 63 unique genotype-phenotype relationships. Perturb-ATAC in human B lymphocytes uncovered regulators of chromatin accessibility, TF occupancy, and nucleosome positioning, and identified a hierarchical organization of TFs that govern B cell state, variation, and disease-associated cis -regulatory elements. Perturb-ATAC in primary human epidermal cells revealed three sequential modules of cis -elements that specify keratinocyte fate, orchestrated by the TFs JUNB, KLF4, ZNF750, CEBPA, and EHF. Combinatorial deletion of all pairs of these TFs uncovered their epistatic relationships and highlighted genomic co-localization as a basis for synergistic interactions. Thus, Perturb-ATAC is a powerful and general strategy to dissect gene regulatory networks in development and disease. Highlights A new method for simultaneous measurement of CRISPR perturbations and chromatin state in single cells. Perturb-ATAC reveals regulatory factors that control cis -element accessibility, trans -factor occupancy, and nucleosome positioning. Perturb-ATAC reveals regulatory modules of coordinated trans -factor activity in B lymphoblasts. Keratinocyte differentiation is orchestrated by synergistic activities of co-binding TFs on cis -elements.