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A new era in functional genomics screens

Nature Reviews Genetics volume 23, pages 89–103 (2022)Cite this article

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Abstract

The past 25 years of genomics research first revealed which genes are encoded by the human genome and then a detailed catalogue of human genome variation associated with many diseases. Despite this, the function of many genes and gene regulatory elements remains poorly characterized, which limits our ability to apply these insights to human disease. The advent of new CRISPR functional genomics tools allows for scalable and multiplexable characterization of genes and gene regulatory elements encoded by the human genome. These approaches promise to reveal mechanisms of gene function and regulation, and to enable exploration of how genes work together to modulate complex phenotypes.

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Fig. 1: Common types of CRISPR screening modalities indicating advances in CRISPR methods.
Fig. 2: Leveraging DepMap for co-correlation analysis.
Fig. 3: Combining screening modalities to broaden cell model and assay parameter space.
Fig. 4: CRISPR-based strategies to link GWAS-identified SNP variants to gene expression.
Fig. 5: Mapping genetic interactions using CRISPR.

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Acknowledgements

L.A.G. is supported by a NIH New Innovator Award (DP2 CA239597), a Pew–Stewart Scholars for Cancer Research award as well as the Goldberg–Benioff Endowed Professorship in Prostate Cancer Translational Biology.

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Authors and Affiliations

  1. Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA

    Laralynne Przybyla

  2. Laboratory for Genomics Research, University of California, San Francisco, San Francisco, CA, USA

    Laralynne Przybyla

  3. Department of Urology, University of California, San Francisco, San Francisco, CA, USA

    Luke A. Gilbert

  4. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA

    Luke A. Gilbert

  5. Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA

    Luke A. Gilbert

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The authors contributed equally to all aspects of the article.

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Correspondence to Laralynne Przybyla or Luke A. Gilbert.

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L.A.G. has filed patents on CRISPR functional genomics and is a co-founder of Chroma Medicine. The other authors declare no competing interests.

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Related links

BioGRID ORCS: https://orcs.thebiogrid.org/

Cancer Dependency Map (DepMap): https://depmap.org/portal/

Co-essentiality network analysis: http://coessentiality.net

CRISPick: https://portals.broadinstitute.org/gppx/crispick/public

CRISPRbrain: https://crisprbrain.org/

CRISP-view: http://crispview.weililab.org/

Glossary

CRISPR

(Clustered regularly interspaced short palindromic repeats). A family of DNA sequences containing short repetitions that are found in prokaryotic organisms as a form of immunity against viruses together with the Cas family of enzymes.

Genome-wide association studies

(GWAS). Large-scale genome-wide single-nucleotide polymorphism (SNP) analyses comparing genetic variants between a disease population and a control population to identify genetic loci associated with altered disease risk.

Cas9

(CRISPR-associated protein 9). An RNA-guided DNA endonuclease involved in bacterial immunity that has been co-opted for use in mammalian genetic engineering.

dCas9

(Dead Cas9). A catalytically inactive form of Cas9 generated by engineering loss-of-function mutations of the endonuclease domains (D10A and H840A).

Fluorescence-activated cell sorting

(FACS). A method for sorting cells based on their intrinsic properties such as size, shape and fluorescent intensity downstream of a reporter or fluorophore-linked antibody.

Genetic interactions

The sets of functional relationships between genes, which can be used to identify epistatic or synthetic lethal gene interactions.

Induced pluripotent stem cells

(iPS cells). Cells reprogrammed from somatic cells with the ability to self-renew by dividing as well as the ability to differentiate into any cell type in the adult organism, a property known as pluripotency.

Single-nucleotide polymorphism

(SNP). A variation in a single nucleotide in a DNA sequence.

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Przybyla, L., Gilbert, L.A. A new era in functional genomics screens. Nat Rev Genet 23, 89–103 (2022). https://doi.org/10.1038/s41576-021-00409-w

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