| Jun 19, 2023 |
CRISPR tool with Big Data visualization platform developed for genome editing and modification
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(Nanowerk News) The Hefei Institutes of Physical Science of the Chinese Academy of Sciences (CAS) has spearheaded the development of a novel analysis service platform named CRISPRimmunity. This interactive web server has been constructed to identify and understand crucial molecular events linked to CRISPR and the regulatory factors of genome editing systems.
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The team's results have been disseminated in the scientific journal, Nucleic Acids Research ("CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing").
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The new platform, CRISPRimmunity, has been innovatively designed for the unified analysis and prediction of CRISPR-Cas and anti-CRISPR systems. Its design incorporates specially curated databases annotated with information pertaining to recognized anti-CRISPR proteins, class II CRISPR-Cas systems, anti-CRISPR-associated proteins, CRISPR array types, HTH structural domains, and mobile genetic elements. These comprehensive resources facilitate the study of molecular events in the co-evolution of CRISPR-Cas and anti-CRISPR systems.
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To enhance the prediction accuracy, the team employed methods such as homology analysis, association analysis, and self-targeting in prophage regions. When evaluated against a dataset comprising 99 experimentally verified anti-CRISPR proteins (Acrs) and 676 non-Acrs, CRISPRimmunity demonstrated an impressive accuracy rate of 0.997.
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Moreover, the platform hosts the first-ever ab initio prediction algorithm designed specifically for class II CRISPR-Cas systems. This has enabled the identification of several hitherto unknown proteins, such as four unique Cas9s with varying PAM structural domains, a smaller Cpf1, 61 C2c10s, and three novel, unclassified V-type Cas proteins. Some of these proteins have already been experimentally confirmed for in vitro activity.
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According to the research team, CRISPRimmunity boasts numerous advantages. It's an intuitive and user-friendly web server providing a comprehensive analysis platform for CRISPR-centric research. It effectively predicts anti-CRISPR proteins, identifies novel class II CRISPR-Cas loci, and provides an evolutionary perspective on the CRISPR-Cas and anti-CRISPR systems. Unlike its contemporaries that focus solely on specific domains, CRISPRimmunity bridges the gap by introducing methods to recognize novel class II CRISPR-Cas systems.
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The platform's accessible interface offers a variety of visualization and customization options, with results presented in a machine-readable format. Moreover, it features tutorials tailored for users of varying expertise levels. It connects to the NCBI database which houses annotated data on 18,408 completely sequenced bacteria, 235 bacteria with Acr, and 208,209 human gut microorganisms, complete with details on key CRISPR-associated molecular events.
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To facilitate future experimental planning and data interpretation, users have the liberty to download or view this data. For computational biologists, a standalone version of CRISPRimmunity is also available on Github for extensive data mining.
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