Genetic interaction mapping in mammalian cells using CRISPR interference

Dan Du; Assen Roguev; David E. Gordon; Meng Chen; Si Han Chen; Michael Shales; John Paul Shen; Trey Ideker; Prashant Mali; Lei S. Qi; Nevan J. Krogan

doi:10.1038/nmeth.4286

Genetic interaction mapping in mammalian cells using CRISPR interference

Dan Du, Assen Roguev, David E. Gordon, Meng Chen, Si Han Chen, Michael Shales, John Paul Shen, Trey Ideker, Prashant Mali, Lei S. Qi, Nevan J. Krogan

Research output: Contribution to journal › Article › peer-review

115 Scopus citations

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.

Original language	English (US)
Pages (from-to)	577-580
Number of pages	4
Journal	Nature Methods
Volume	14
Issue number	6
DOIs	https://doi.org/10.1038/nmeth.4286
State	Published - May 30 2017
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/nmeth.4286

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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.",

author = "Dan Du and Assen Roguev and Gordon, {David E.} and Meng Chen and Chen, {Si Han} and Michael Shales and Shen, {John Paul} and Trey Ideker and Prashant Mali and Qi, {Lei S.} and Krogan, {Nevan J.}",

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AU - Du, Dan

AU - Roguev, Assen

AU - Gordon, David E.

AU - Chen, Meng

AU - Chen, Si Han

AU - Shales, Michael

AU - Shen, John Paul

AU - Ideker, Trey

AU - Mali, Prashant

AU - Qi, Lei S.

AU - Krogan, Nevan J.

PY - 2017/5/30

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AB - 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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Genetic interaction mapping in mammalian cells using CRISPR interference

Abstract

ASJC Scopus subject areas

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