ArticleNature communications2018
Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
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Who cites it
146 citing papers in PubMed.
- Determination of Gene-Level Fitness Contributions Across the Mucin-Utilization Network of Bacteroides thetaiotaomicron.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Interrogating the Escherichia coli Epitranscriptome Via CRISPR Interference and Nanopore Native RNA Sequencing.MicrobiologyOpen · 2026Article
- A programmableApplied and environmental microbiology · 2026Article
- Cross-Strain Transferability of CRISPRi Systems and Design Rules from Laboratory to ClinicalACS synthetic biology · 2026Article
- CRISPRi-based functional genomic screening identifies genes essential for CHScience advances · 2026Article
- Systematic CRISPRi screening reveals genetic modulators ofbioRxiv : the preprint server for biology · 2026Article
- Article
- Integrated transcriptomic and metabolomic analyses uncover novel genetic targets for enhanced l-tryptophan production inSynthetic and systems biotechnology · 2026Article
- CRISPRi Screening Identifies EssentialInternational journal of molecular sciences · 2026Article
- Cross-strain transferability of CRISPRi systems and design rules from laboratory to clinicalbioRxiv : the preprint server for biology · 2026Article
- Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli.Nucleic acids research · 2026Article
- Design of CRISPRi-Based Synthetic Gene Circuits in Bacteria.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Regulatory time-kill sequencing maps antibiotic-specific transcriptional control ofFrontiers in microbiology · 2026Article
- Systematic genome-wide mapping of host determinants of bacteriophage infectivity.Cell systems · 2025Article
- Comprehensive genetic interaction analysis of the Bacillus subtilis envelope using double-CRISPRi.Cell systems · 2025Article
- Analysis of essential genes inJournal of bacteriology · 2025Article
- CRISPRi-seq in Haemophilus influenzae reveals genome-wide and medium-specific growth determinants.PLoS pathogens · 2025Article
- Extending dynamic and operational range of the biosensor responding to l-carnitine by directed evolution.Synthetic and systems biotechnology · 2025Article
- Advanced Strategies in Phage Research: Innovations, Applications, and Challenges.Microorganisms · 2025Review
- CRISPRi screening revealsmSystems · 2025Article
86 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
To fully exploit the microbial genome resources, a high-throughput experimental platform is needed to associate genes with phenotypes at the genome level. We present here a novel method that enables investigation of the cellular consequences of repressing individual transcripts based on the CRISPR interference (CRISPRi) pooled screening in bacteria. We identify rules for guide RNA library design to handle the unique structure of prokaryotic genomes by tiling screening and construct an E. coli genome-scale guide RNA library (~60,000 members) accordingly. We show that CRISPRi outperforms transposon sequencing, the benchmark method in the microbial functional genomics field, when similar library sizes are used or gene length is short. This tool is also effective for mapping phenotypes to non-coding RNAs (ncRNAs), as elucidated by a comprehensive tRNA-fitness map constructed here. Our results establish CRISPRi pooled screening as a powerful tool for mapping complex prokaryotic genetic networks in a precise and high-throughput manner.
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