ReviewNature protocols2022
CRISPRi-seq for genome-wide fitness quantification in bacteria.
Review in Nature protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
52 citing papers in PubMed, 95 citations in OpenAlex.
- A c-di-AMP receptor mediates epithelial adhesion of Lactiplantibacillus plantarum.Nature communications · 2026Article
- Targeting the Energy-Coupling Factor Transporters: A Novel Antibiotic Drug Target inJournal of medicinal chemistry · 2026Article
- A programmableApplied and environmental microbiology · 2026Article
- Multi-omics and artificial intelligence for precision drug discovery and potential clinical applications.Signal transduction and targeted therapy · 2026Review
- CaRPOOL: a pooled calcium‑recording CRISPR screening platform identifies CCR7 as a modulator of cellular osmomechanosensing.Cell communication and signaling : CCS · 2026Article
- CRISPRi-based functional genomic screening identifies genes essential for CHScience advances · 2026Article
- PRICE: direct and robust detection of microRNAs at single-nucleotide resolution.Nature communications · 2026Article
- A platform for CRISPRi-seq inmBio · 2026Article
- Pneumococcal S protein coordinates cell wall modification and repair to resist host antimicrobials.Nature microbiology · 2026Article
- High-throughput chemical genomic screening: a step-by-step workflow from plate to phenotype.mSystems · 2025Article
- Applications of Genome-wide Screening of CRISPR/Cas9 Knockout Library in Identifying Novel Molecular Targets for Xenobiotics.Environment & health (Washington, D.C.) · 2025Review
- Multi-omics profiling reveals atypical sugar utilization and a key membrane composition regulator in Streptococcus pneumoniae.Nature communications · 2025Article
- A CRISPRi Gene Regulation System for Bifidobacteria.Microbial biotechnology · 2025Article
- CRISPRi-seq in Haemophilus influenzae reveals genome-wide and medium-specific growth determinants.PLoS pathogens · 2025Article
- A programmable, selection-free CRISPR interference system iniScience · 2025Article
- Cell splitting in Staphylococcus aureus is controlled by an adaptor protein facilitating degradation of a peptidoglycan hydrolase.PLoS genetics · 2025Article
- Review
- Genome-wide antibiotic-CRISPRi profiling identifies LiaR activation as a strategy to resensitize fluoroquinolone-resistant Streptococcus pneumoniae.Nature communications · 2025Article
- Article
- Make-or-break prime editing for genome engineering in Streptococcus pneumoniae.Nature communications · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CRISPR interference (CRISPRi) is a powerful tool to link essential and nonessential genes to specific phenotypes and to explore their functions. Here we describe a protocol for CRISPRi screenings to assess genome-wide gene fitness in a single sequencing step (CRISPRi-seq). We demonstrate the use of the protocol in Streptococcus pneumoniae, an important human pathogen; however, the protocol can easily be adapted for use in other organisms. The protocol includes a pipeline for single-guide RNA library design, workflows for pooled CRISPRi library construction, growth assays and sequencing steps, a read analysis tool (2FAST2Q) and instructions for fitness quantification. We describe how to make an IPTG-inducible system with small libraries that are easy to handle and cost-effective and overcome bottleneck issues, which can be a problem when using similar, transposon mutagenesis-based methods. Ultimately, the procedure yields a fitness score per single-guide RNA target for any given growth condition. A genome-wide screening can be finished in 1 week with a constructed library. Data analysis and follow-up confirmation experiments can be completed in another 2-3 weeks.
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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.