Genetic interaction mapping in mammalian cells using CRISPR interference

Dan Du^{1

2

3}, Assen Roguev^{4

5}, David E Gordon^{4

5}, Meng Chen^{1

6}, Si-Han Chen^{4

5}, Michael Shales^{4

5}, John Paul Shen^{7

8}, Trey Ideker^{7

8}, Prashant Mali⁸, Lei S Qi^{1

2

3}, Nevan J Krogan^{4

5

6}

Affiliations

¹ Department of Bioengineering, Stanford University, Stanford, California, USA.
² Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA.
³ Stanford ChEM-H, Stanford University, Stanford, California, USA.
⁴ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA.
⁵ Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, California, USA.
⁶ J. David Gladstone Institutes, San Francisco, California, USA.
⁷ Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, California, USA.
⁸ Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.

PMID: 28481362
PMCID: PMC5584685
DOI: 10.1038/nmeth.4286

Genetic interaction mapping in mammalian cells using CRISPR interference

Dan Du et al. Nat Methods. 2017 Jun.

. 2017 Jun;14(6):577-580.

doi: 10.1038/nmeth.4286. Epub 2017 May 8.

Authors

Affiliations

¹ Department of Bioengineering, Stanford University, Stanford, California, USA.
² Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA.
³ Stanford ChEM-H, Stanford University, Stanford, California, USA.
⁴ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA.
⁵ Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, California, USA.
⁶ J. David Gladstone Institutes, San Francisco, California, USA.
⁷ Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, California, USA.
⁸ Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.

PMID: 28481362
PMCID: PMC5584685
DOI: 10.1038/nmeth.4286

Abstract

We describe a combinatorial CRISPR interference (CRISPRi) screening platform for mapping genetic interactions in mammalian cells. We targeted 107 chromatin-regulation factors in human cells with pools of either single or double single guide RNAs (sgRNAs) to downregulate individual genes or gene pairs, respectively. Relative enrichment analysis of individual sgRNAs or sgRNA pairs allowed for quantitative characterization of genetic interactions, and comparison with protein-protein-interaction data revealed a functional map of chromatin regulation.

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