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Structures, mechanisms and applications of RNA-centric CRISPR–Cas13

Nature Chemical Biology (2024)Cite this article

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Abstract

Prokaryotes are equipped with a variety of resistance strategies to survive frequent viral attacks or invading mobile genetic elements. Among these, CRISPR–Cas surveillance systems are abundant and have been studied extensively. This Review focuses on CRISPR–Cas type VI Cas13 systems that use single-subunit RNA-guided Cas endonucleases for targeting and subsequent degradation of foreign RNA, thereby providing adaptive immunity. Notably, distinct from single-subunit DNA-cleaving Cas9 and Cas12 systems, Cas13 exhibits target RNA-activated substrate RNase activity. This Review outlines structural, biochemical and cell biological studies toward elucidation of the unique structural and mechanistic principles underlying surveillance effector complex formation, precursor CRISPR RNA (pre-crRNA) processing, self-discrimination and RNA degradation in Cas13 systems as well as insights into suppression by bacteriophage-encoded anti-CRISPR proteins and regulation by endogenous accessory proteins. Owing to its programmable ability for RNA recognition and cleavage, Cas13 provides powerful RNA targeting, editing, detection and imaging platforms with emerging biotechnological and therapeutic applications.

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Fig. 1: Three stages of CRISPR–Cas13 adaptive immunity: adaptation, expression and interference.
Fig. 2: Functional module organization of CRISPR type VI Cas13 loci.
Fig. 3: Mechanisms of crRNA recognition and maturation in type VI-A systems.
Fig. 4: Mechanisms of target RNA recognition in type VI-A systems.
Fig. 5: Mechanism of self–non-self-discrimination in type VI-A systems.
Fig. 6: Modulation mechanisms of type VI systems involving anti-CRISPRs and accessory proteins.
Fig. 7: Active Cas13-based RNA-targeting technologies.
Fig. 8: dCas13-based RNA manipulation technologies.

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Acknowledgements

H.Y. was supported by grants from the CAS project for Young Scientists in Basic research (YSBR-009), the Strategic Priority Research Program of the Chinese Academy of Science (XDB0570300), the National Key R&D Program of China (2023YFA0915600), the Natural Science Foundation of China (32171266 and 31971135), the Shanghai Rising-Star Program (20QA1410700) and the National Natural Science Foundation of Shanghai (22ZR1468900). D.J.P. was supported by funds from the NIH (GM129430, GM145888 and AI141507), the Maloris Foundation and Memorial Sloan-Kettering Cancer Center Core grant P30 CA008748.

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  1. Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China

    Hui Yang

  2. Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA

    Dinshaw J. Patel

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H.Y. wrote the initial draft and prepared the figures of the review. D.J.P. provided input and assistance in completing the review.

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Yang, H., Patel, D.J. Structures, mechanisms and applications of RNA-centric CRISPR–Cas13. Nat Chem Biol (2024). https://doi.org/10.1038/s41589-024-01593-6

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