ArticleNature communications2022
Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Genomic evidence of ecological flexibility and cross-niche CRISPR spacerome targeting phage-plasmid hybrids in Latilactobacillus curvatus.BMC genomics · 2026Article
- Pangenomics of Limosilactobacillus fermentum reveals genomic diversity and bacteriocin activity against Staphylococcus aureus and Escherichia coli.Scientific reports · 2026Article
- Uncovering Cas9 PAM diversity through metagenomic mining and machine learning.Nature communications · 2026Article
- Customizing CRISPR-Cas PAM specificity with protein language models.Nature biotechnology · 2026Article
- Reprogramming CRISPR-Cas enzymes for customized genome editing.Nature biotechnology · 2026Article
- Integrating CRISPR/Cas technology with clinical trials: Principles, progress and challenges.Asian journal of pharmaceutical sciences · 2025Review
- MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.Genome biology · 2025Article
- Crosstalk between three CRISPR-Cas types enables primed type VI-A adaptation in Listeria seeligeri.Cell host & microbe · 2025Article
- Article
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- Article
- CasGen: A Regularized Generative Model for CRISPR Cas Protein Design with Classification and Margin-Based Optimization.bioRxiv : the preprint server for biology · 2025Article
- Engineering of CRISPR-Cas PAM recognition using deep learning of vast evolutionary data.bioRxiv : the preprint server for biology · 2025Article
- Article
- Progress and opportunities of foundation models in bioinformatics.Briefings in bioinformatics · 2024Review
- CoCas9 is a compact nuclease from the human microbiome for efficient and precise genome editing.Nature communications · 2024Article
- Eukaryotic-driven directed evolution of Cas9 nucleases.Genome biology · 2024Article
- An optimized SpCas9 high-fidelity variant for direct protein delivery.Molecular therapy : the journal of the American Society of Gene Therapy · 2023Article
- Seven technologies to watch in 2023.Nature · 2023Article
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Authors and funding
12 authors.
Funding
Abstract
The identification of the protospacer adjacent motif (PAM) sequences of Cas9 nucleases is crucial for their exploitation in genome editing. Here we develop a computational pipeline that was used to interrogate a massively expanded dataset of metagenome and virome assemblies for accurate and comprehensive PAM predictions. This procedure allows the identification and isolation of sequence-tailored Cas9 nucleases by using the target sequence as bait. As proof of concept, starting from the disease-causing mutation P23H in the RHO gene, we find, isolate and experimentally validate a Cas9 which uses the mutated sequence as PAM. Our PAM prediction pipeline will be instrumental to generate a Cas9 nuclease repertoire responding to any PAM requirement.
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