Abstract
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.
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Acknowledgements
The authors thank J. Doudna, F. Zhang and E. Koonin for critical reading of the manuscript and helpful suggestions.
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Authors and Affiliations
Contributions
The authors contributed equally to all aspects of the article. L.V. and J.J. jointly researched background, wrote, revised and discussed the article. O.O.A. and J.S.G. jointly supervised the work.
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Competing interests
L.V., J.J., L.K., J.W, J.S.G. and O.O.A. are inventors on patent applications related to CRISPR technologies. O.O.A. and J.S.G. are co-founders of Sherlock Biosciences, Proof Diagnostics, Tome Biosciences and Doppler Bio. J.S.W. declares outside interest in 5 AM Venture, Amgen, Chroma Medicine, KSQ Therapeutics, Maze Therapeutics, Tenaya Therapeutics, Tessera Therapeutics and Third Rock Ventures.
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Nature Reviews Molecular Cell Biology thanks Quanjiang Ji, Yongsub Kim and Hao Yin for their contribution to the peer review of this work.
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Glossary
- BoxB domains
-
An RNA–protein system from phage, whereby the BoxB RNA motif binds to the N protein.
- Cas9 nickase
-
Cas9 with one of two cleavage domains inactivated, either D10A or H840A for SpCas9.
- Codon optimization
-
Alteration of the DNA sequence (that is, codon composition) without altering the amino acid sequence with the aim to maximize protein expression to achieve higher editing efficiency.
- Directed evolution
-
Mutations that optimize protein function are selected under evolutionary pressures that stems from experimental design.
- DNA deaminases
-
Enzymes that catalyse the removal of amino groups from molecules; in DNA bases, this can lead to base changes.
- Duchenne muscular dystrophy
-
X-linked and life-threatening muscular dystrophy due to mutations in the dystrophin gene.
- Integrases
-
Enzymes that catalyse the integration of a nucleic acid sequence into a target genome.
- MS2 hairpin
-
An RNA stem–loop from the MS2 bacteriophage that tightly binds to the MS2 coat protein.
- Mucopolysaccharidosis type I-Hurler (MPS I-H) syndrome
-
A life-threatening genetic disorder that leads to a reduced ability to break down glycosaminoglycans, causing toxic accumulation in multiple tissues.
- MuGam protein
-
Protein derived from the Mu bacteriophage that binds and protects DNA.
- N-of-1 trials
-
Individualized clinical trials designed to determine the efficacy and safety of interventions in single patients.
- Non-long terminal repeat retrotransposons
-
Mobile genetic elements that transpose in a copy-and-paste mechanism independently of long terminal repeats.
- OTC deficiency
-
Ornithine transcarbamylase deficiency is a rare genetic (urea cycle) disorder that leads to build-up of toxic ammonia in the blood.
- Purity
-
In the context of genome editing, purity refers to homogeneity of genetic modification outcomes.
- Site-specific recombinases
-
Enzymes that catalyse precise excision, integration or inversion of DNA sequences at specific sites within the genome.
- TALE nucleases
-
Engineered endonucleases that consist of a designed transcription activator-like effector (TALE) domain fused to the cleavage domain of a nuclease.
- Transposases
-
Enzymes that can move discrete segments of DNA from one location in the genome to a new site without using RNA intermediates.
- Transthyretin amyloidosis
-
The build-up of abnormal protein deposits (transthyretin) in vital organs, including the heart, peripheral nervous system, kidneys and eyes.
- Zinc finger nucleases
-
Engineered endonucleases that consist of a designed zinc finger DNA-binding domain fused to the cleavage domain of a nuclease.
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Villiger, L., Joung, J., Koblan, L. et al. CRISPR technologies for genome, epigenome and transcriptome editing. Nat Rev Mol Cell Biol (2024). https://doi.org/10.1038/s41580-023-00697-6
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DOI: https://doi.org/10.1038/s41580-023-00697-6
