ArticlemSystems2019
Bioinformatics Identification of Anti-CRISPR Loci by Using Homology, Guilt-by-Association, and CRISPR Self-Targeting Spacer Approaches.
Article in mSystems, 2019. 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, 53 citations in OpenAlex.
- Regulation of anti-CRISPR operons by structurally distinct families of Aca proteins.Communications biology · 2025Article
- AcrDB update: Predicted 3D structures of anti-CRISPRs in human gut viromes.Protein science : a publication of the Protein Society · 2025Article
- Article
- Unlocking the potential of CRISPR tools and databases for precision genome editing.Frontiers in plant science · 2025Review
- Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors.Nature biotechnology · 2024Article
- dbAPIS: a database of anti-prokaryotic immune system genes.Nucleic acids research · 2024Article
- Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system inmSphere · 2023Article
- Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems.Nucleic acids research · 2023Article
- Anti-CRISPR Discovery: Using Magnets to Find Needles in Haystacks.Journal of molecular biology · 2023Review
- In Silico Approaches for Prediction of Anti-CRISPR Proteins.Journal of molecular biology · 2023Review
- Widespread CRISPR repeat-like RNA regulatory elements in CRISPR-Cas systems.bioRxiv : the preprint server for biology · 2023Article
- Phage Encounters Recorded in CRISPR Arrays in the GenusViruses · 2022Article
- AcaFinder: Genome Mining for Anti-CRISPR-Associated Genes.mSystems · 2022Article
- Article
- Isolation, characterization and complete genome analysis of a novel bacteriophage vB_EfaS-SRH2 against Enterococcus faecalis isolated from periodontitis patients.Scientific reports · 2022Article
- Prophage integration into CRISPR loci enables evasion of antiviral immunity in Streptococcus pyogenes.Nature microbiology · 2021Article
- Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2.The Journal of biological chemistry · 2021Article
- Digging into the lesser-known aspects of CRISPR biology.International microbiology : the official journal of the Spanish Society for Microbiology · 2021Review
- Crystal structure of the anti-CRISPR repressor Aca2.Journal of structural biology · 2021Article
- Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein.Nucleic acids research · 2021Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Anti-CRISPR (Acr) loci/operons encode Acr proteins and Acr-associated (Aca) proteins. Forty-five Acr families have been experimentally characterized inhibiting seven subtypes of CRISPR-Cas systems. We have developed a bioinformatics pipeline to identify genomic loci containing Acr homologs and/or Aca homologs by combining three computational approaches: homology, guilt-by-association, and self-targeting spacers. Homology search found thousands of Acr homologs in bacterial and viral genomes, but most are homologous to AcrIIA7 and AcrIIA9. Investigating the gene neighborhood of these Acr homologs revealed that only a small percentage (23.0% in bacteria and 8.2% in viruses) of them have neighboring Aca homologs and thus form Acr-Aca operons. Surprisingly, although a self-targeting spacer is a strong indicator of the presence of Acr genes in a genome, a large percentage of Acr-Aca loci are found in bacterial genomes without self-targeting spacers or even without complete CRISPR-Cas systems. Additionally, for Acr homologs from genomes with self-targeting spacers, homology-based Acr family assignments do not always agree with the self-targeting CRISPR-Cas subtypes. Last, by investigating Acr genomic loci coexisting with self-targeting spacers in the same genomes, five known subtypes (I-C, I-E, I-F, II-A, and II-C) and five new subtypes (I-B, III-A, III-B, IV-A, and V-U4) of Acrs were inferred. Based on these findings, we conclude that the discovery of new anti-CRISPRs should not be restricted to genomes with self-targeting spacers and loci with Acr homologs. The evolutionary arms race of CRISPR-Cas systems and anti-CRISPR systems may have driven the adaptive and rapid gain and loss of these elements in closely related genomes.
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