4.7 Review

The double life of CRISPR-Cas13

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Review Microbiology

Alternative functions of CRISPR-Cas systems in the evolutionary arms race

Prarthana Mohanraju et al.

Summary: CRISPR-Cas systems not only play a role in adaptive immunity, but also control gene expression, serve as tools for virus attacks and transposon navigation, and allow pathogenic bacteria to evade the human immune system. Understanding the diverse functions of CRISPR-Cas systems is crucial for the development of CRISPR-based applications.

NATURE REVIEWS MICROBIOLOGY (2022)

Article Multidisciplinary Sciences

Targeted gene silencing in the nervous system with CRISPR-Cas13

Jackson E. Powell et al.

Summary: Cas13 nucleases are programmable RNA-targeting CRISPR effector proteins that can silence target gene expression in mammalian cells. By delivering RfxCas13d to the mouse spinal cord and brain, neurodegeneration-associated genes can be effectively silenced, offering a versatile platform for gene knockdown in the nervous system.

SCIENCE ADVANCES (2022)

Article Biochemistry & Molecular Biology

CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells

Yuxi Ai et al.

Summary: CRISPR/Cas13 effectors have gained attention as tools for detecting and depleting target RNAs. However, their specificity in eukaryotic cells has been debated due to the potential for collateral damage caused by the exposed nuclease domains. This study highlights the need for caution when designing and interpreting Cas13-based knockdown experiments.

NUCLEIC ACIDS RESEARCH (2022)

Article Microbiology

A target expression threshold dictates invader defense and prevents autoimmunity by CRISPR-Cas13

Elena Vialetto et al.

Summary: CRISPR-Cas systems need to provide robust immunity against foreign genetic material without causing cytotoxic autoimmunity. This study reveals that target transcript expression levels exceeding a threshold are essential for inducing autoimmunity in RNA-targeting CRISPR-Cas systems. Target expression levels serve as an additional criterion for immune defense, preventing autoimmunity and distinguishing pathogenic from benign invaders.

CELL HOST & MICROBE (2022)

Article Biochemistry & Molecular Biology

Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy

Parinaz Fozouni et al.

Summary: This study developed an amplification-free CRISPR-Cas13a assay for direct detection of SARS-CoV-2, showing rapid, highly sensitive, and mobile phone-based readout capabilities.
Article Biochemical Research Methods

Screening for functional circular RNAs using the CRISPR-Cas13 system

Siqi Li et al.

Summary: The study demonstrates that CRISPR-RfxCas13d can effectively discriminate circRNAs from mRNAs and has identified important circRNAs involved in cell growth, such as the pro-proliferative circFAM120A and the regulatory circMan1a2 in mouse embryo preimplantation development.

NATURE METHODS (2021)

Article Biotechnology & Applied Microbiology

Treatment of influenza and SARS-CoV-2 infections via mRNA-encoded Cas13a in rodents

Emmeline L. Blanchard et al.

Summary: Cas13a delivered to the lung of mice and hamsters inhibits replication of influenza virus and SARS-CoV-2, suggesting that Cas13a-mediated targeting of pathogenic viruses can mitigate respiratory infections. The study successfully reduced viral RNA levels in the lung tissue of animals, demonstrating the efficacy of Cas13a in targeting RNA viruses.

NATURE BIOTECHNOLOGY (2021)

Article Biochemical Research Methods

Programmable RNA editing with compact CRISPR-Cas13 systems from uncultivated microbes

Chunlong Xu et al.

Summary: The study identified two compact CRISPR-Cas families, Cas13X and Cas13Y, for RNA interference experiments and RNA base editing. These untapped bacterial defense systems can function efficiently in mammalian cells, potentially useful for RNA-editing-based research.

NATURE METHODS (2021)

Article Virology

Efficient RNA Virus Targeting via CRISPR/CasRx in Fish

Qing Wang et al.

Summary: The study successfully engineered a highly effective CasRx system for fish virus interference by targeting the red-spotted grouper nervous necrosis virus (RGNNV) with synthetic mRNA coding for CasRx, resulting in significant interference with virus infections both in vitro and in vivo.

JOURNAL OF VIROLOGY (2021)

Article Multidisciplinary Sciences

Programmable RNA targeting with the single-protein CRISPR effector Cas7-11

Ahsen Ozcan et al.

Summary: The study revealed that Cas7-11 from class 1 CRISPR-Cas systems is a single-protein effector with RNA interference capability. It can process pre-CRISPR RNA into mature crRNA with high specificity, and has potential applications in RNA knockdown and editing in mammalian cells. The findings provide a basis for developing new programmable RNA-targeting tools that are free of collateral activity and cell toxicity.

NATURE (2021)

Article Multidisciplinary Sciences

The gRAMP CRISPR-Cas effector is an RNA endonuclease complexed with a caspase-like peptidase

Sam P. B. van Beljouw et al.

Summary: The study presents a novel type III-E effector, Sb-gRAMP, which uses CRISPR RNA to guide target RNA recognition and cleavage, and potentially gains viral immunity through target RNA-induced protease activity.

SCIENCE (2021)

Article Biotechnology & Applied Microbiology

Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying functional circRNAs

Yang Zhang et al.

Summary: By using the CRISPR/Cas13d tool and optimizing the design strategy, the specificity of circRNA silencing is significantly enhanced and validated in parallel screenings. Utilizing CRISPR/Cas13d for high-throughput study of functional circRNAs proves to be an effective approach.

GENOME BIOLOGY (2021)

Article Medicine, Research & Experimental

Rapid design and development of CRISPR-Cas13a targeting SARS-CoV-2 spike protein

Lin Wang et al.

Summary: This study proposes a potential anti-SARS-CoV-2 strategy based on the CRISPR-Cas13a system, identifying a specific RNA segment of the spike protein and designing an efficient crRNA sequence for cleavage. It provides a rapid design pipeline for an antiviral tool against SARS-CoV-2 and introduces a novel approach for anti-virus study.

THERANOSTICS (2021)

Review Microbiology

Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants

Kira S. Makarova et al.

NATURE REVIEWS MICROBIOLOGY (2020)

Article Biochemistry & Molecular Biology

Development of CRISPR as an Antiviral Strategy to Combat SARS-CoV-2 and Influenza

Timothy R. Abbott et al.

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CasRx-mediated RNA targeting prevents choroidal neovascularization in a mouse model of age-related macular degeneration

Changyang Zhou et al.

NATIONAL SCIENCE REVIEW (2020)

Article Biotechnology & Applied Microbiology

Massively parallel Cas13 screens reveal principles for guide RNA design

Hans-Hermann Wessels et al.

NATURE BIOTECHNOLOGY (2020)

Article Cell Biology

CRISPR-Cas13d Induces Efficient mRNA Knockdown in Animal Embryos

Gopal Kushawah et al.

DEVELOPMENTAL CELL (2020)

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Programmable RNA Targeting Using CasRx in Flies

Anna Buchman et al.

CRISPR JOURNAL (2020)

Article Engineering, Biomedical

Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA

Maturada Patchsung et al.

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A New Tool for CRISPR-Cas13a-Based Cancer Gene Therapy

Jinliang Gao et al.

MOLECULAR THERAPY-ONCOLYTICS (2020)

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A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila

Nhan Huynh et al.

GENOME BIOLOGY (2020)

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Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage

Alexander J. Meeske et al.

NATURE (2019)

Article Biochemistry & Molecular Biology

Programmable RNA-Guided RNA Effector Proteins Built from Human Parts

Simone Rauch et al.

Article Biochemistry & Molecular Biology

Programmable Inhibition and Detection of RNA Viruses Using Cas13

Catherine A. Freije et al.

MOLECULAR CELL (2019)

Article Biotechnology & Applied Microbiology

CRISPR-Cas13d mediates robust RNA virus interference in plants

Ahmed Mahas et al.

GENOME BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors

Silvana Konermann et al.

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Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

Lovorka Stojic et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Implementation of the CRISPR-Cas13a system in fission yeast and its repurposing for precise RNA editing

Xinyun Jing et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

Field-deployable viral diagnostics using CRISPR-Cas13

Cameron Myhrvold et al.

SCIENCE (2018)

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Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6

Jonathan S. Gootenberg et al.

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Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d

Cheng Zhang et al.

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Targeted m(6)A Reader Proteins To Study Epitranscriptomic Regulation of Single RNAs

Simone Rauch et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

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RNA Guide Complementarity Prevents Self-Targeting in Type VI CRISPR Systems

Alexander J. Meeske et al.

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RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a

Akshay Tambe et al.

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RNA virus interference via CRISPR/Cas13a system in plants

Rashid Aman et al.

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RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes

Alexandra East-Seletsky et al.

MOLECULAR CELL (2017)

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RNA targeting with CRISPR-Cas13

Omar O. Abudayyeh et al.

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Diversity and evolution of class 2 CRISPR-Cas systems

Sergey Shmakov et al.

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Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme

Gavin J. Knott et al.

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RNA editing with CRISPR-Cas13

David B. T. Cox et al.

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Nucleic acid detection with CRISPR-Cas13a/C2c2

Jonathan S. Gootenberg et al.

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Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme

Gavin J. Knott et al.

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The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a

Liang Liu et al.

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Aviad Tsherniak et al.

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Two Distant Catalytic Sites Are Responsible for C2c2 RNase Activities

Liang Liu et al.

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Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection

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Bacteria differently regulate mRNA abundance to specifically respond to various stresses

Alexander Bartholomaeus et al.

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Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems

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C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

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Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

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Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

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CRISPR-Cas immunity in prokaryotes

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