ArticleGenome biology2016
Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 118 papers.
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Who cites it
118 citing papers in PubMed, 207 citations in OpenAlex.
- Effects of RIM15 deletion on yeast adaptation to synthetic spruce hydrolysate.Microbial cell factories · 2026Article
- Benzylisoquinoline Alkaloid Production in Yeast via Norlaudanosoline Improves Titer, Selectivity, and Yield.ACS synthetic biology · 2026Article
- Towards the development of a CRISPR-Cas9 based kill switch for Saccharomyces cerevisiae.Microbial cell factories · 2026Article
- Biological parts in yeast synthetic biology: from regulatory elements to predictive design platforms.FEMS yeast research · 2026Review
- Impact of CRISPRi-Mediated Titration ofACS synthetic biology · 2025Article
- Exploring CRISPR/Cas9-Mediated Gene Editing Advances in Conventional and Non-conventional Yeast Species.Applied biochemistry and biotechnology · 2025Review
- Global epistasis in budding yeast driven by many natural variants whose effects scale with fitness.Genetics · 2025Article
- Dysfunctional mitochondria trap proteins in the intermembrane space.The EMBO journal · 2025Article
- Epigenome Engineering Using dCas Systems for Biomedical Applications and Biotechnology: Current Achievements, Opportunities and Challenges.International journal of molecular sciences · 2025Review
- Unravelling fungal genome editing revolution: pathological and biotechnological application aspects.Archives of microbiology · 2025Review
- ChIP-exo and CRISPRi/a illuminate the role of Pdr1 and Yap1 in acetic acid tolerance inApplied and environmental microbiology · 2025Article
- Arrayed CRISPRi library to suppress genes required for Schizosaccharomyces pombe viability.The Journal of cell biology · 2025Article
- GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes.BMC bioinformatics · 2025Article
- Mapping the Genetic Architecture of the Adaptive Integrated Stress Response inbioRxiv : the preprint server for biology · 2024Article
- The rise and future of CRISPR-based approaches for high-throughput genomics.FEMS microbiology reviews · 2024Review
- Re-engineered guide RNA enables DNA loops and contacts modulating repression in E. coli.Nucleic acids research · 2024Article
- Robustness quantification of a mutant library screen revealed key genetic markers in yeast.Microbial cell factories · 2024Article
- Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells.Nature protocols · 2024Review
- Genome-scale analysis of interactions between genetic perturbations and natural variation.Nature communications · 2024Article
- Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals.International journal of molecular sciences · 2024Review
58 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
Abstract
backgroundGenome-scale CRISPR interference (CRISPRi) has been used in human cell lines; however, the features of effective guide RNAs (gRNAs) in different organisms have not been well characterized. Here, we define rules that determine gRNA effectiveness for transcriptional repression in Saccharomyces cerevisiae.
resultsWe create an inducible single plasmid CRISPRi system for gene repression in yeast, and use it to analyze fitness effects of gRNAs under 18 small molecule treatments. Our approach correctly identifies previously described chemical-genetic interactions, as well as a new mechanism of suppressing fluconazole toxicity by repression of the ERG25 gene. Assessment of multiple target loci across treatments using gRNA libraries allows us to determine generalizable features associated with gRNA efficacy. Guides that target regions with low nucleosome occupancy and high chromatin accessibility are clearly more effective. We also find that the best region to target gRNAs is between the transcription start site (TSS) and 200 bp upstream of the TSS. Finally, unlike nuclease-proficient Cas9 in human cells, the specificity of truncated gRNAs (18 nt of complementarity to the target) is not clearly superior to full-length gRNAs (20 nt of complementarity), as truncated gRNAs are generally less potent against both mismatched and perfectly matched targets.
conclusionsOur results establish a powerful functional and chemical genomics screening method and provide guidelines for designing effective gRNAs, which consider chromatin state and position relative to the target gene TSS. These findings will enable effective library design and genome-wide programmable gene repression in many genetic backgrounds.
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