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Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation
Open accessAbstract
The bacterial CRISPR-Cas9 system has emerged as a multifunctional platform for sequence-specific regulation of gene expression. This Review describes the development of technologies based on nuclease-deactivated Cas9, termed dCas9, for RNA-guided genomic transcription regulation, both by repression through CRISPR interference (CRISPRi) and by activation through CRISPR activation (CRISPRa). We highlight different uses in diverse organisms, including bacterial and eukaryotic cells, and summarize current applications of harnessing CRISPR-dCas9 for multiplexed, inducible gene regulation, genome-wide screens and cell fate engineering. We also provide a perspective on future developments of the technology and its applications in biomedical research and clinical studies.
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“Novel strategies of Cas9-based transcription modulators rapidly appeared prompted by the fusion of dCas9 or gRNA to different activator or repressor elements, with multiple degrees of modulation and specificity, and enabling single or multiplexed transcriptional control [74,75,76].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [76]
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“Therefore, catalytically inactive dCas-9 can be used to activate (CRISPRa) or silence (CRISPRi) the expression of a specific gene of interest.50”
From Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing (2021) · cites this paper as [50]
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“One general challenge for these CRISPR methods involves the specificity and efficiency of gRNAs (reviewed in [94]).”
From Mapping gene regulatory networks from single-cell omics data (2018) · cites this paper as [94]
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“As all four methods are based on CRISPR/CAS9, in principle, any CRISPR-based perturbations could be used, including knockouts and transcriptional- or epigenetic-based repression or activation (e.g. CRISPRi, CRISPRa [94]).”
From Mapping gene regulatory networks from single-cell omics data (2018) · cites this paper as [94]
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Metadata
- Authors
- Dominguez, A. A., Lim, W. A., & Qi, L. S.
- Affiliations
- Stanford University (US)
- QB3 (US)
- Corresponding author
- Lim, Wendell A.
- Qi, Lei S.
- Venue
- Nature Reviews Molecular Cell Biology
- Published
- 2015-12-16
- Volume
- 17
- Issue
- 1
- Pages
- 5-15
- ISSN
- 1471-0072 (ISSN-L)
- 1471-0080
- PMC
- PMC4922510
- OpenAlex
- W2204875887
- Cited by
- 832
- References
- 91
- Citations by year
- 2026: 39 · 2025: 41 · 2024: 58 · 2023: 65 · 2022: 78 · 2021: 81 · 2020: 95 · 2019: 105 · 2018: 106 · 2017: 96 · 2016: 63 · 2015: 2
- FWCI
- 8.63
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Molecular Cell Biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (DP5OD017887)
- National Institute on Drug Abuse (R01DA036858)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- CRISPR/Cas9, dCas9, CRISPR interference, CRISPR activation, gene expression inhibition, gene activation, genome-wide screen
- MeSH terms
- Animals, Humans, Models, Genetic, Transcription, Genetic, Genome, RNA Editing, Genomics, CRISPR-Cas Systems
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