ArticleNucleic acids research2018
Improved sgRNA design in bacteria via genome-wide activity profiling.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed, 97 citations in OpenAlex.
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- An inducer-independent, single-plasmid CRISPR-Cas9 system for genome editing in Bacillus species.Applied microbiology and biotechnology · 2026Article
- A self-iterative orthogonal base-editing platform enables multiplex N-to-N diversification and genome-scale functional screening in Escherichia coli.Nucleic acids research · 2026Article
- AI-driven CRISPR screening: optimizing gene editing through automation and intelligent decision support.Journal of translational medicine · 2026Review
- Comprehensive profiling of CRISPR/dCas9 epigenome editors indicates a complex link between on and off target effects.Genome biology · 2026Article
- Machine learning reveals sequence and methylation determinants of SaCas9-PAM interactions in bacteria.Nucleic acids research · 2026Article
- Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli.Nucleic acids research · 2026Article
- Better data for better predictions: data curation improves deep learning for sgRNA/Cas9 prediction.PeerJ · 2026Article
- Rapid detection ofActa biochimica et biophysica Sinica · 2025Article
- Extending dynamic and operational range of the biosensor responding to l-carnitine by directed evolution.Synthetic and systems biotechnology · 2025Article
- Revolutionizing CRISPR technology with artificial intelligence.Experimental & molecular medicine · 2025Review
- GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes.BMC bioinformatics · 2025Article
- Balanced Training Sets Improve Deep Learning-Based Prediction of CRISPR sgRNA Activity.ACS synthetic biology · 2024Article
- The application of CRISPR-Cas system inHeliyon · 2024Article
- Multiplex CRISPR-Cas Genome Editing: Next-Generation Microbial Strain Engineering.Journal of agricultural and food chemistry · 2024Review
- Cell-Free Protein Expression in Polymer Materials.ACS synthetic biology · 2024Article
- CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration.Nucleic acids research · 2024Article
- Recent advances in genome-scale engineering inEngineering microbiology · 2024Review
- Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CRISPR/Cas9 is a promising tool in prokaryotic genome engineering, but its success is limited by the widely varying on-target activity of single guide RNAs (sgRNAs). Based on the association of CRISPR/Cas9-induced DNA cleavage with cellular lethality, we systematically profiled sgRNA activity by co-expressing a genome-scale library (∼70 000 sgRNAs) with Cas9 or its specificity-improved mutant in Escherichia coli. Based on this large-scale dataset, we constructed a comprehensive and high-density sgRNA activity map, which enables selecting highly active sgRNAs for any locus across the genome in this model organism. We also identified 'resistant' genomic loci with respect to CRISPR/Cas9 activity, notwithstanding the highly accessible DNA in bacterial cells. Moreover, we found that previous sgRNA activity prediction models that were trained on mammalian cell datasets were inadequate when coping with our results, highlighting the key limitations and biases of previous models. We hence developed an integrated algorithm to accurately predict highly effective sgRNAs, aiming to facilitate CRISPR/Cas9-based genome engineering, screenings and antimicrobials design in bacteria. We also isolated the important sgRNA features that contribute to DNA cleavage and characterized their key differences among wild type Cas9 and its mutant, shedding light on the biophysical mechanisms of the CRISPR/Cas9 system.
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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.