Cited by 1,193Endoplasmic Reticulum Stress and DiseaseSingle-cell and spatial transcriptomicsCRISPR and Genetic Engineering

The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.

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

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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.

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Metadata

Authors
Adamson, B., Norman, T. M., Jost, M., Cho, M. Y., Nuñez, J. K., Chen, Y., Villalta, J. E., Gilbert, L. A., Horlbeck, M. A., Hein, M. Y., Pak, R. A., Gray, A. N., Gross, C. A., Dixit, A., Parnas, O., Regev, A., & Weissman, J. S.
Affiliations
  • Howard Hughes Medical Institute (US)
  • University of California, San Francisco (US)
  • Broad Institute (US)
Corresponding author
Weissman, Jonathan S.
Venue
Cell
Publisher
Elsevier BV
Published
2016-12
Volume
167
Issue
7
Pages
1867-1882.e21
ISSN
0092-8674 (ISSN-L)
OpenAlex
W2562947047
Cited by
1,193
References
46
Citations by year
2026: 201 · 2025: 157 · 2024: 125 · 2023: 103 · 2022: 122 · 2021: 111 · 2020: 102 · 2019: 104 · 2018: 94 · 2017: 71 · 2016: 2
FWCI
38.26
Type
journal article
Language
en
Open access
Locations
  • Cell (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-nd)
  • eScholarship (California Digital Library) (submittedVersion)
  • PMC
Funders
  • Howard Hughes Medical Institute
  • National Institutes of Health (5rm1hg006193-10)
  • National Institute on Aging (R01AG041826)
  • National Institute on Drug Abuse (R01DA036858)
  • National Human Genome Research Institute (RM1‐HG006193, P50HG006193)
  • National Cancer Institute (K99CA204602, U01CA168370, R00CA204602)
  • National Institute of General Medical Sciences (F32GM116331, T32GM007618, R01GM102790, P50GM102706, R35GM118061)
  • National Institute of Biomedical Imaging and Bioengineering (T32EB009383)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Endoplasmic Reticulum Stress and Disease
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
Keywords
unfolded protein response, Perturb-seq, CRISPR screen, CRISPR interference, endoplasmic reticulum homeostasis, IRE1α, translocon, feedback loops
MeSH terms
RNA, Guide, CRISPR-Cas Systems, Animals, Endoribonucleases, Feedback, Humans, Models, Molecular, Transcription, Genetic, Protein Serine-Threonine Kinases, Sequence Analysis, RNA, Unfolded Protein Response, Single-Cell Analysis, Clustered Regularly Interspaced Short Palindromic Repeats

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