ArticleNucleic acids research2014
Expanding the catalog of cas genes with metagenomes.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
20 citing papers in PubMed, 31 citations in OpenAlex.
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- Design, potential and limitations of conjugation-based antibacterial strategies.Microbial biotechnology · 2024Review
- Complete Genome Sequence and Pan-Genome Analysis ofMicroorganisms · 2023Article
- Antimicrobial resistance expansion in pathogens: a review of current mitigation strategies and advances towards innovative therapy.JAC-antimicrobial resistance · 2023Review
- Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering.Microbial biotechnology · 2023Article
- The Application of the CRISPR-Cas System in Antibiotic Resistance.Infection and drug resistance · 2022Review
- Genome editing technologies: CRISPR, LEAPER, RESTORE, ARCUT, SATI, and RESCUE.EXCLI journal · 2021Review
- Genomic Analysis of Molecular Bacterial Mechanisms of Resistance to Phage Infection.Frontiers in microbiology · 2021Article
- CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data.NAR genomics and bioinformatics · 2020Article
- Targeted assemblies of cas1 suggest CRISPR-Cas's response to soil warming.The ISME journal · 2020Article
- Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic GenusPathogens (Basel, Switzerland) · 2019Article
- CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog.Cell host & microbe · 2019Article
- Interspaced Repeat Sequences Confer the Regulatory Functions of AtXTH10, Important for Root Growth in Arabidopsis.Plants (Basel, Switzerland) · 2019Article
- CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea.Database : the journal of biological databases and curation · 2019Article
- Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements.BMC bioinformatics · 2017Article
- Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data.RNA (New York, N.Y.) · 2016Article
- CRISPRDetect: A flexible algorithm to define CRISPR arrays.BMC genomics · 2016Article
- Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.Nature communications · 2016Article
- Identification of diversity-generating retroelements in human microbiomes.International journal of molecular sciences · 2014Article
- CRISPR adaptive immune systems of Archaea.RNA biology · 2014Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The CRISPR (clusters of regularly interspaced short palindromic repeats)-Cas adaptive immune system is an important defense system in bacteria, providing targeted defense against invasions of foreign nucleic acids. CRISPR-Cas systems consist of CRISPR loci and cas (CRISPR-associated) genes: sequence segments of invaders are incorporated into host genomes at CRISPR loci to generate specificity, while adjacent cas genes encode proteins that mediate the defense process. We pursued an integrated approach to identifying putative cas genes from genomes and metagenomes, combining similarity searches with genomic neighborhood analysis. Application of our approach to bacterial genomes and human microbiome datasets allowed us to significantly expand the collection of cas genes: the sequence space of the Cas9 family, the key player in the recently engineered RNA-guided platforms for genome editing in eukaryotes, is expanded by at least two-fold with metagenomic datasets. We found genes in cas loci encoding other functions, for example, toxins and antitoxins, confirming the recently discovered potential of coupling between adaptive immunity and the dormancy/suicide systems. We further identified 24 novel Cas families; one novel family contains 20 proteins, all identified from the human microbiome datasets, illustrating the importance of metagenomics projects in expanding the diversity of cas genes.
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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.