Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks, bioRxiv, 2018-09-17

SummaryHere 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-associatedcis-regulatory elements. Perturb-ATAC in primary human epidermal cells revealed three sequential modules ofcis-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<jatslist list-type=order><jatslist-item>A new method for simultaneous measurement of CRISPR perturbations and chromatin state in single cells.<jatslist-item><jatslist-item>Perturb-ATAC reveals regulatory factors that controlcis-element accessibility,trans-factor occupancy, and nucleosome positioning.<jatslist-item><jatslist-item>Perturb-ATAC reveals regulatory modules of coordinatedtrans-factor activity in B lymphoblasts.<jatslist-item><jatslist-item>Keratinocyte differentiation is orchestrated by synergistic activities of co-binding TFs oncis-elements.<jatslist-item>

biorxiv genomics 100-200-users 2018

 

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