ArticleNature microbiology2024
CRISPRi-TnSeq maps genome-wide interactions between essential and non-essential genes in bacteria.
Article in Nature microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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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.
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Who cites it
14 citing papers in PubMed.
- A genome-wide CRISPRi screen identifies homologous recombination pathway as potential target for broad-spectrum antibiotic adjuvants.Journal of advanced research · 2026Article
- Applications of transposon-insertion sequencing for understanding bacterial physiology.Microbial genomics · 2026Review
- CRISPRi-mediatedAntimicrobial agents and chemotherapy · 2026Article
- Unravelling the unique essential genes ofMicrobial genomics · 2026Article
- Article
- Elucidating the roles of essential genes in autotrophic metabolism and cell morphology of Clostridium ljungdahlii by CRISPRi.Applied microbiology and biotechnology · 2026Article
- Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance inmSystems · 2026Article
- Comprehensive genomics, systems, and structural assessment for novel target identification in penicillin-resistantFrontiers in bioinformatics · 2026Article
- CRISPRi-mediated validation of candidatebioRxiv : the preprint server for biology · 2025Article
- Genetic tools for engineering Zymomonas mobilis, Cereibacter sphaeroides and Novosphingobium aromaticivorans to improve production of bioenergy compounds.Microbial cell factories · 2025Review
- Identifying essential genes inJournal of bacteriology · 2025Article
- Hierarchical metabolic engineering for rewiring cellular metabolism.FEMS microbiology reviews · 2025Review
- Engineering Microbial Consortia as Living Materials: Advances and Prospectives.ACS synthetic biology · 2024Review
- Transcription modulation of pathogenic streptococcal and enterococcal species using CRISPRi technology.PLoS pathogens · 2024Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Genetic interactions identify functional connections between genes and pathways, establishing gene functions or druggable targets. Here we use CRISPRi-TnSeq, CRISPRi-mediated knockdown of essential genes alongside TnSeq-mediated knockout of non-essential genes, to map genome-wide interactions between essential and non-essential genes in Streptococcus pneumoniae. Transposon-mutant libraries constructed in 13 CRISPRi strains enabled screening of ~24,000 gene pairs. This identified 1,334 genetic interactions, including 754 negative and 580 positive interactions. Network analyses show that 17 non-essential genes pleiotropically interact with more than half the essential genes tested. Validation experiments confirmed that a 7-gene subset protects against perturbations. Furthermore, we reveal hidden redundancies that compensate for essential gene loss, relationships between cell wall synthesis, integrity and cell division, and show that CRISPRi-TnSeq identifies synthetic and suppressor-type relationships between both functionally linked and disparate genes and pathways. Importantly, in species where CRISPRi and Tn-Seq are established, CRISPRi-TnSeq should be straightforward to implement.
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Registered trials
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