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

Cell. 2016 Dec 15;167(7):1867-1882.e21. doi: 10.1016/j.cell.2016.11.048.


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.

Keywords: CRIPSRi; CRISPR; Single-cell RNA-seq; cell-to-cell heterogeneity; genome-scale screening; single-cell genomics; unfolded protein response.

MeSH terms

  • Animals
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Endoribonucleases
  • Feedback
  • Humans
  • Models, Molecular
  • Protein Serine-Threonine Kinases
  • RNA, Guide, CRISPR-Cas Systems / metabolism
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods*
  • Transcription, Genetic
  • Unfolded Protein Response


  • RNA, Guide, CRISPR-Cas Systems
  • ERN1 protein, human
  • Protein Serine-Threonine Kinases
  • Endoribonucleases