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Not all predicted CRISPR–Cas systems are equal: isolated cas genes and classes of CRISPR like elements
BACKGROUND: The CRISPR–Cas systems in prokaryotes are RNA-guided immune systems that target and deactivate foreign nucleic acids. A typical CRISPR–Cas system consists of a CRISPR array of repeat and spacer units, and a locus of cas genes. The CRISPR and the cas locus are often located next to each o...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5294841/ https://www.ncbi.nlm.nih.gov/pubmed/28166719 http://dx.doi.org/10.1186/s12859-017-1512-4 |
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author | Zhang, Quan Ye, Yuzhen |
author_facet | Zhang, Quan Ye, Yuzhen |
author_sort | Zhang, Quan |
collection | PubMed |
description | BACKGROUND: The CRISPR–Cas systems in prokaryotes are RNA-guided immune systems that target and deactivate foreign nucleic acids. A typical CRISPR–Cas system consists of a CRISPR array of repeat and spacer units, and a locus of cas genes. The CRISPR and the cas locus are often located next to each other in the genomes. However, there is no quantitative estimate of the co-location. In addition, ad-hoc studies have shown that some non-CRISPR genomic elements contain repeat-spacer-like structures and are mistaken as CRISPRs. RESULTS: Using available genome sequences, we observed that a significant number of genomes have isolated cas loci and/or CRISPRs. We found that 11%, 22% and 28% of the type I, II and III cas loci are isolated (without CRISPRs in the same genomes at all or with CRISPRs distant in the genomes), respectively. We identified a large number of genomic elements that superficially reassemble CRISPRs but don’t contain diverse spacers and have no companion cas genes. We called these elements false-CRISPRs and further classified them into groups, including tandem repeats and Staphylococcus aureus repeat (STAR)-like elements. CONCLUSION: This is the first systematic study to collect and characterize false-CRISPR elements. We demonstrated that false-CRISPRs could be used to reduce the false annotation of CRISPRs, therefore showing them to be useful for improving the annotation of CRISPR–Cas systems. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-017-1512-4) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5294841 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-52948412017-02-09 Not all predicted CRISPR–Cas systems are equal: isolated cas genes and classes of CRISPR like elements Zhang, Quan Ye, Yuzhen BMC Bioinformatics Research Article BACKGROUND: The CRISPR–Cas systems in prokaryotes are RNA-guided immune systems that target and deactivate foreign nucleic acids. A typical CRISPR–Cas system consists of a CRISPR array of repeat and spacer units, and a locus of cas genes. The CRISPR and the cas locus are often located next to each other in the genomes. However, there is no quantitative estimate of the co-location. In addition, ad-hoc studies have shown that some non-CRISPR genomic elements contain repeat-spacer-like structures and are mistaken as CRISPRs. RESULTS: Using available genome sequences, we observed that a significant number of genomes have isolated cas loci and/or CRISPRs. We found that 11%, 22% and 28% of the type I, II and III cas loci are isolated (without CRISPRs in the same genomes at all or with CRISPRs distant in the genomes), respectively. We identified a large number of genomic elements that superficially reassemble CRISPRs but don’t contain diverse spacers and have no companion cas genes. We called these elements false-CRISPRs and further classified them into groups, including tandem repeats and Staphylococcus aureus repeat (STAR)-like elements. CONCLUSION: This is the first systematic study to collect and characterize false-CRISPR elements. We demonstrated that false-CRISPRs could be used to reduce the false annotation of CRISPRs, therefore showing them to be useful for improving the annotation of CRISPR–Cas systems. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-017-1512-4) contains supplementary material, which is available to authorized users. BioMed Central 2017-02-06 /pmc/articles/PMC5294841/ /pubmed/28166719 http://dx.doi.org/10.1186/s12859-017-1512-4 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Zhang, Quan Ye, Yuzhen Not all predicted CRISPR–Cas systems are equal: isolated cas genes and classes of CRISPR like elements |
title | Not all predicted CRISPR–Cas systems are equal: isolated cas genes and classes of CRISPR like elements |
title_full | Not all predicted CRISPR–Cas systems are equal: isolated cas genes and classes of CRISPR like elements |
title_fullStr | Not all predicted CRISPR–Cas systems are equal: isolated cas genes and classes of CRISPR like elements |
title_full_unstemmed | Not all predicted CRISPR–Cas systems are equal: isolated cas genes and classes of CRISPR like elements |
title_short | Not all predicted CRISPR–Cas systems are equal: isolated cas genes and classes of CRISPR like elements |
title_sort | not all predicted crispr–cas systems are equal: isolated cas genes and classes of crispr like elements |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5294841/ https://www.ncbi.nlm.nih.gov/pubmed/28166719 http://dx.doi.org/10.1186/s12859-017-1512-4 |
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