A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.

Abstract

Functional genomics efforts face tradeoffs between number of perturbations examined and complexity of phenotypes measured. We bridge this gap with Perturb-seq, which combines droplet-based single-cell RNA-seq with a strategy for barcoding CRISPR-mediated perturbations, allowing many perturbations to be profiled in pooled format. We applied Perturb-seq to dissect the mammalian unfolded protein response (UPR) using single and combinatorial CRISPR perturbations. Two genome-scale CRISPR interference (CRISPRi) screens identified genes whose repression perturbs ER homeostasis. Subjecting ∼100 hits to Perturb-seq enabled high-precision functional clustering of genes. Single-cell analyses decoupled the three UPR branches, revealed bifurcated UPR branch activation among cells subject to the same perturbation, and uncovered differential activation of the branches across hits, including an isolated feedback loop between the translocon and IRE1α. These studies provide insight into how the three sensors of ER homeostasis monitor distinct types of stress and highlight the ability of Perturb-seq to dissect complex cellular responses.

DOI: 10.1016/j.cell.2016.11.048
010020030020162017
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@article{Adamson2016AMS, title={A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.}, author={Britt Adamson and Thomas M. Norman and Marco Jost and Min Y. Cho and James K. Nu{\~n}ez and Yuwen Chen and Jacqueline E. Villalta and Luke A Gilbert and Max A Horlbeck and Marco Y Hein and Ryan A Pak and Andrew N. Gray and Carol A. Gross and Atray Dixit and Oren Parnas and Aviv Regev and Jonathan S. Weissman}, journal={Cell}, year={2016}, volume={167 7}, pages={1867-1882.e21} }