ArticleProceedings of the National Academy of Sciences of the United States of America2023
A genome-wide optical pooled screen reveals regulators of cellular antiviral responses.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
29 citing papers in PubMed, 36 citations in OpenAlex.
- A one-week automated genome-wide optical pooled screen using OttoSeq.Genome biology · 2026Article
- Brieflow: an integrated computational pipeline for high-throughput analysis of optical pooled screening data.Nature communications · 2026Article
- Progress and new challenges in image-based profiling.Molecular systems biology · 2026Review
- From CRISPR functional genomics to synthetic interventions: engineering antiviral strategies.Journal of virology · 2026Review
- The one-week automated genome-wide optical pooled screen.bioRxiv : the preprint server for biology · 2026Article
- Article
- Reimagining the Synthetic Biology DBTL Cycle with Machine Learning.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A pooled Cell Painting CRISPR screening platform enables de novo inference of gene function by self-supervised deep learning.Nature communications · 2025Article
- CRISPR with Transcriptional Readout reveals influenza transcription is modulated by NELF and can precipitate an interferon response.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Optical pooled screening for the discovery of regulators of the alternative lengthening of telomeres pathway.Methods (San Diego, Calif.) · 2025Article
- Article
- Single-cell image-based screens identify host regulators of Ebola virus infection dynamics.Nature microbiology · 2025Article
- NIS-Seq enables cell-type-agnostic optical perturbation screening.Nature biotechnology · 2025Article
- High-content image-based pooled screens reveal regulators of synaptogenesis.Cell reports · 2025Article
- CROPseq-multi: a universal solution for multiplexed perturbation in high-content pooled CRISPR screens.bioRxiv : the preprint server for biology · 2025Article
- MORPH Predicts the Single-Cell Outcome of Genetic Perturbations Across Conditions and Data Modalities.bioRxiv : the preprint server for biology · 2025Article
- Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView.Nature biotechnology · 2025Article
- Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap.Nature biotechnology · 2025Article
- CRISPR with Transcriptional Readout reveals influenza transcription is modulated by NELF and can precipitate an interferon response.bioRxiv : the preprint server for biology · 2025Article
- Cellular RNA interacts with MAVS to promote antiviral signaling.Science (New York, N.Y.) · 2024Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The infection of mammalian cells by viruses and innate immune responses to infection are spatiotemporally organized processes. Cytosolic RNA sensors trigger nuclear translocation of the transcription factor interferon regulatory factor 3 (IRF3) and consequent induction of host immune responses to RNA viruses. Previous genetic screens for factors involved in viral sensing did not resolve changes in the subcellular localization of host or viral proteins. Here, we increased the throughput of our optical pooled screening technology by over fourfold. This allowed us to carry out a genome-wide CRISPR knockout screen using high-resolution multiparameter imaging of cellular responses to Sendai virus infection coupled with in situ cDNA sequencing by synthesis (SBS) to identify 80,408 single guide RNAs (sgRNAs) in 10,366,390 cells-over an order of magnitude more genomic perturbations than demonstrated previously using an in situ SBS readout. By ranking perturbations using human-designed and deep learning image feature scores, we identified regulators of IRF3 translocation, Sendai virus localization, and peroxisomal biogenesis. Among the hits, we found that ATP13A1, an ER-localized P5A-type ATPase, is essential for viral sensing and is required for targeting of mitochondrial antiviral signaling protein (MAVS) to mitochondrial membranes where MAVS must be localized for effective signaling through retinoic acid-inducible gene I (RIG-I). The ability to carry out genome-wide pooled screens with complex high-resolution image-based phenotyping dramatically expands the scope of functional genomics approaches.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.