ArticleGenome biology2021
PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 48 citations in OpenAlex.
- A rapid, sensitive, and field-deployable RAA-EsCas13d platform for detection of porcine adenovirus type 3.Microbiology spectrum · 2026Article
- Computational tool choice impacts CRISPR spacer-protospacer detection.Bioinformatics (Oxford, England) · 2026Article
- The complexity of multiple CRISPR arrays in strains with (co-occurring) CRISPR systems.microLife · 2026Article
- An overview of CRISPR-artificial intelligence theranostics: Current and emerging applications.Biomaterials translational · 2026Review
- Characterization of CRISPR-Cas systems in the Haemophilus genus CRISPR-Cas in Haemophilus spp.Genetics and molecular biology · 2026Article
- An evolutionary approach to predict the orientation of CRISPR arrays.PLoS computational biology · 2025Article
- Crosstalk between three CRISPR-Cas types enables primed type VI-A adaptation in Listeria seeligeri.Cell host & microbe · 2025Article
- Recent applications, future perspectives, and limitations of the CRISPR-Cas system.Molecular therapy. Nucleic acids · 2025Review
- Phage susceptibility to a minimal, modular synthetic CRISPR-Cas system inPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- A type III-associated Cas6 functions as a negative regulator of type I-B CRISPR-Cas system in Thermus thermophilus.Communications biology · 2025Article
- Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons.Nature communications · 2024Article
- Characterization ofmSphere · 2024Article
- Development and implementation of a Type I-C CRISPR-based programmable repression system formBio · 2024Article
- Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment.PLoS computational biology · 2023Article
- A novel Queuovirinae lineage of Pseudomonas aeruginosa phages encode dPreQ0 DNA modifications with a single GA motif that provide restriction and CRISPR Cas9 protection in vitro.Nucleic acids research · 2023Article
- A predicted CRISPR-mediated symbiosis between uncultivated archaea.Nature microbiology · 2023Article
- Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis.Microbiome · 2023Article
- Cas4/1 dual nuclease activities enable prespacer maturation and directional integration in a type I-G CRISPR-Cas system.bioRxiv : the preprint server for biology · 2023Article
- A Novel Anti-CRISPR AcrIE9.2 Is Associated with Dissemination ofAntimicrobial agents and chemotherapy · 2023Article
- The biology and type I/III hybrid nature of type I-D CRISPR-Cas systems.The Biochemical journal · 2023Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe adaptive CRISPR-Cas immune system stores sequences from past invaders as spacers in CRISPR arrays and thereby provides direct evidence that links invaders to hosts. Mapping CRISPR spacers has revealed many aspects of CRISPR-Cas biology, including target requirements such as the protospacer adjacent motif (PAM). However, studies have so far been limited by a low number of mapped spacers in the database.
resultsBy using vast metagenomic sequence databases, we map approximately one-third of more than 200,000 unique CRISPR spacers from a variety of microbes and derive a catalog of more than two hundred unique PAM sequences associated with specific CRISPR-Cas subtypes. These PAMs are further used to correctly assign the orientation of CRISPR arrays, revealing conserved patterns between the last nucleotides of the CRISPR repeat and PAM. We could also deduce CRISPR-Cas subtype-specific preferences for targeting either template or coding strand of open reading frames. While some DNA-targeting systems (type I-E and type II systems) prefer the template strand and avoid mRNA, other DNA- and RNA-targeting systems (types I-A and I-B and type III systems) prefer the coding strand and mRNA. In addition, we find large-scale evidence that both CRISPR-Cas adaptation machinery and CRISPR arrays are shared between different CRISPR-Cas systems. This could lead to simultaneous DNA and RNA targeting of invaders, which may be effective at combating mobile genetic invaders.
conclusionsThis study has broad implications for our understanding of how CRISPR-Cas systems work in a wide range of organisms for which only the genome sequence is known.
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