Nanotechnology

The CRISPR tool with a Big Data visualization platform was developed for genome editing and modification


June 19, 2023

(Nanowerk News) The Hefei Institute of Physical Sciences of the Chinese Academy of Sciences (CAS) has spearheaded the development of a new analysis service platform named CRISPRimmunity. This interactive web server has been built to identify and understand important molecular events related to CRISPR and regulatory factors of genome editing systems.

The team’s results have been published in scientific journals, Nucleic Acid Research (“CRISPRimmunity: an interactive web server for Critical Molecular events and CRISPR-related Modulators Used in the identification of Genome editing Tools”).

The new platform, CRISPRimmunity, has been innovatively designed for integrated analysis and prediction of CRISPR-Cas and anti-CRISPR systems. The design incorporates a specially curated database annotated with information relating to recognized anti-CRISPR proteins, class II CRISPR-Cas systems, anti-CRISPR related proteins, CRISPR array types, HTH structural domains, and cellular genetic elements. This comprehensive resource facilitates the study of molecular events in the co-evolution of CRISPR-Cas and anti-CRISPR systems.

To improve prediction accuracy, the team used methods such as homology analysis, association analysis, and self-targeting in forecast regions. When evaluated against a data set of 99 experimentally verified anti-CRISPR (Acrs) proteins and 676 non-Acrs, CRISPRimmunity showed an impressive accuracy rate of 0.997.

Additionally, the platform hosts the first ab initio prediction algorithm specifically designed for class II CRISPR-Cas systems. This has allowed the identification of several hitherto unknown proteins, such as four unique Cas9s with multiple PAM structural domains, the smaller Cpf1, 61 C2c10s, and three newly unclassified V-type Cas proteins. Some of these proteins have been confirmed experimentally in vitro activity.

According to the research team, CRISPRimmunity offers many advantages. It is an intuitive and user-friendly web server that provides a comprehensive analysis platform for CRISPR-centric research. It effectively predicts anti-CRISPR proteins, identifies novel CRISPR-Cas class II loci, and provides an evolutionary perspective on CRISPR-Cas and anti-CRISPR systems. Unlike its contemporaries which only focused on a specific domain, CRISPRimmunity bridged the gap by introducing a method to recognize the new class II CRISPR-Cas system.

The platform’s accessible interface offers a variety of visualization and customization options, with results presented in a machine-readable format. In addition, the tutorial feature is adapted for users of various skill levels. It is linked to the NCBI database which houses annotated data on 18,408 fully sequenced bacteria, 235 bacteria with Acr, and 208,209 human gut microorganisms, complete with details on CRISPR-associated molecular events.

To facilitate future experimental planning and data interpretation, users have the freedom to download or view this data. For computational biologists, a standalone version of CRISPRimmunity is also available available on Github for extensive data mining.





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