@article{464614a206db46ce984e1f75e0ea2957,
title = "Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks",
abstract = "Here, we present Perturb-ATAC, a method that 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 genotype-phenotype relationships. Perturb-ATAC in human B lymphocytes uncovered regulators of chromatin accessibility, TF occupancy, and nucleosome positioning and identified a hierarchy 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. 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 strategy to dissect gene regulatory networks in development and disease.",
keywords = "ATAC-seq, CRISPR, chromatin accessibility, epigenomics, pooled screens, single-cell genomics",
author = "Rubin, {Adam J.} and Parker, {Kevin R.} and Satpathy, {Ansuman T.} and Yanyan Qi and Beijing Wu and Ong, {Alvin J.} and Mumbach, {Maxwell R.} and Ji, {Andrew L.} and Kim, {Daniel S.} and Cho, {Seung Woo} and Zarnegar, {Brian J.} and Greenleaf, {William J.} and Chang, {Howard Y.} and Khavari, {Paul A.}",
note = "Funding Information: We thank the members of the Khavari, Chang, and Greenleaf laboratories for helpful discussions. This work was supported by the Veterans Affairs Office of Research and Development (to P.A.K.), the NIH ( AR45192 and AR43799 to P.A.K., P50-HG007735 to H.Y.C. and W.J.G., and R35-CA209919 to H.Y.C.), the Parker Institute for Cancer Immunotherapy (to A.T.S. and H.Y.C.), and the Scleroderma Research Foundation (to H.Y.C.). A.J.R was supported by a Stanford Bio-X fellowship. K.R.P was supported by a Stanford graduate fellowship. A.T.S. was supported by a Parker Bridge Scholar Award from the Parker Institute for Cancer Immunotherapy and a Career Award for Medical Scientists from the Burroughs Wellcome Fund . W.J.G is a Chan Zuckerberg Biohub investigator. H.Y.C. is an investigator of the Howard Hughes Medical Institute. Funding Information: We thank the members of the Khavari, Chang, and Greenleaf laboratories for helpful discussions. This work was supported by the Veterans Affairs Office of Research and Development (to P.A.K.), the NIH (AR45192 and AR43799 to P.A.K., P50-HG007735 to H.Y.C. and W.J.G., and R35-CA209919 to H.Y.C.), the Parker Institute for Cancer Immunotherapy (to A.T.S. and H.Y.C.), and the Scleroderma Research Foundation (to H.Y.C.). A.J.R was supported by a Stanford Bio-X fellowship. K.R.P was supported by a Stanford graduate fellowship. A.T.S. was supported by a Parker Bridge Scholar Award from the Parker Institute for Cancer Immunotherapy and a Career Award for Medical Scientists from the Burroughs Wellcome Fund. W.J.G is a Chan Zuckerberg Biohub investigator. H.Y.C. is an investigator of the Howard Hughes Medical Institute. Publisher Copyright: {\textcopyright} 2018 Elsevier Inc.",
year = "2019",
month = jan,
day = "10",
doi = "10.1016/j.cell.2018.11.022",
language = "English",
volume = "176",
pages = "361--376.e17",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "1-2",
}