RT Journal Article
SR Electronic
T1 Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 414870
DO 10.1101/414870
A1 Adam J. Rubin
A1 Kevin R. Parker
A1 Ansuman T. Satpathy
A1 Yanyan Qi
A1 Beijing Wu
A1 Alvin J. Ong
A1 Maxwell R. Mumbach
A1 Andrew L. Ji
A1 Daniel S. Kim
A1 Seung Woo Cho
A1 Brian J. Zarnegar
A1 William J. Greenleaf
A1 Howard Y. Chang
A1 Paul A. Khavari
YR 2018
UL http://biorxiv.org/content/early/2018/09/13/414870.abstract
AB 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.HighlightsA 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.