High-throughput functional genomics using CRISPR-Cas9
Open accessAbstract
Forward genetic screens are powerful tools for the discovery and functional annotation of genetic elements. Recently, the RNA-guided CRISPR (clustered regularly interspaced short palindromic repeat)-associated Cas9 nuclease has been combined with genome-scale guide RNA libraries for unbiased, phenotypic screening. In this Review, we describe recent advances using Cas9 for genome-scale screens, including knockout approaches that inactivate genomic loci and strategies that modulate transcriptional activity. We discuss practical aspects of screen design, provide comparisons with RNA interference (RNAi) screening, and outline future applications and challenges.
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DNA barcoding has largely limited pooled screens to assessing effects on cell fitness.
“This has limited pooled screens largely to vetting genes for their potential impact on cell fitness”
From Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens (2018) · cites this paper as Shalem et al., 2015
Three distinct bacterial CRISPR systems have been identified; Type I, II and III, and it is the Type II system that has mainly been adapted for use in artificial gene regulation and genome editing.
“So far three distinct bacterial CRISPR systems have been identified; Type I, II and III, and it is the Type II system that has mainly been adapted for use in artificial gene regulation and genome editing (Kim and Kim 2014; Shalem, Sanjana and Zhang 2015).”
From <i>Candida glabrata</i> : new tools and technologies—expanding the toolkit (2015) · cites this paper as Shalem, Sanjana and Zhang 2015
The most commonly used CRISPR Type II system consists of a gRNA and an endonuclease, the CRISPR-associated (Cas) nuclease, Cas9, which cleaves the targeted chromosomal DNA in a site-specific manner triggering endogenous DNA repair systems resulting in genome modification.
“The most commonly used CRISPR Type II system consists of a gRNA and an endonuclease, the CRISPR-associated (Cas) nuclease, Cas9, which cleaves the targeted chromosomal DNA in a site-specific manner triggering endogenous DNA repair systems resulting in genome modification (for an in-depth review, see Doudna and Charpentier 2014; Kim and Kim 2014; Shalem, Sanjana and Zhang 2015).”
From <i>Candida glabrata</i> : new tools and technologies—expanding the toolkit (2015) · cites this paper as Shalem, Sanjana and Zhang 2015
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Self-citation
- Authors
- Shalem, O., Sanjana, N. E., & Zhang, F.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Shalem, Ophir
- Zhang, Feng
- Venue
- Nature Reviews Genetics
- Published
- 2015-04-09
- Volume
- 16
- Issue
- 5
- Pages
- 299-311
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- PMC
- PMC4503232
- OpenAlex
- W2026592619
- Cited by
- 1,233
- References
- 130
- Citations by year
- 2026: 71 · 2025: 91 · 2024: 103 · 2023: 85 · 2022: 101 · 2021: 105 · 2020: 121 · 2019: 117 · 2018: 131 · 2017: 145 · 2016: 123 · 2015: 37 · 2014: 1 · 2013: 1
- FWCI
- 14.12
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- PMC
- Funders
- Klarman Family Foundation
- Simons Center for the Social Brain, Massachusetts Institute of Technology
- National Institute of Mental Health (DP1MH100706)
- National Human Genome Research Institute (K99HG008171)
- National Institute of Neurological Disorders and Stroke (R01NS073124)
- National Center for Chronic Disease Prevention and Health Promotion (DP1‑MH100706)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Keywords
- CRISPR/Cas9, genome-wide screen, guide RNA library, forward genetic screen, gene knockout, transcriptional regulation, phenotypic screening, screen design, functional genomics
- MeSH terms
- Animals, Genetic Testing, Humans, Models, Genetic, Gene Library, Genomics, RNA Interference, Mice, Gene Knockout Techniques, High-Throughput Nucleotide Sequencing, CRISPR-Cas Systems
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