Quantitative genetic-interaction mapping in mammalian cells

Assen Roguev; Dale Talbot; Gian Luca Negri; Michael Shales; Gerard Cagney; Sourav Bandyopadhyay; Barbara Panning; Nevan J. Krogan

doi:10.1038/nmeth.2398

Quantitative genetic-interaction mapping in mammalian cells

Assen Roguev, Dale Talbot, Gian Luca Negri, Michael Shales, Gerard Cagney, Sourav Bandyopadhyay, Barbara Panning, Nevan J. Krogan

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

90 Scopus citations

Abstract

Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ∼11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape.

Original language	English
Pages (from-to)	432-437
Number of pages	6
Journal	Nature Methods
Volume	10
Issue number	5
DOIs	https://doi.org/10.1038/nmeth.2398
State	Published - May 2013
Externally published	Yes

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title = "Quantitative genetic-interaction mapping in mammalian cells",

abstract = "Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ∼11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape.",

author = "Assen Roguev and Dale Talbot and Negri, \{Gian Luca\} and Michael Shales and Gerard Cagney and Sourav Bandyopadhyay and Barbara Panning and Krogan, \{Nevan J.\}",

note = "Funding Information: We thank members of the Bandyopadhyay, Panning and Krogan laboratories for constructive discussions, J. Forrest (TTP Labtech) for providing the Acumen eX3 cytometer, J. DeRisi for allowing us access to the uPrint 3D printer, G. Tzertzinis (NEB) for providing high-concentration ShortCut RNase III, and T. Fazzio for technical advice. This work has been supported by US National Institutes of Health (GM082250, GM081879, AI090935, AI091575 to N.J.K., P50CA58207 to S.B. and GM085186 to B.P.); Defense Advanced Research Projects Agency (HR0011-11-C-0094 to N.J.K.) and University of California San Francisco Program for Breakthrough Biomedical Research to N.J.K. and B.P.",

year = "2013",

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doi = "10.1038/nmeth.2398",

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journal = "Nature Methods",

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AU - Roguev, Assen

AU - Talbot, Dale

AU - Negri, Gian Luca

AU - Shales, Michael

AU - Cagney, Gerard

AU - Bandyopadhyay, Sourav

AU - Panning, Barbara

AU - Krogan, Nevan J.

N1 - Funding Information: We thank members of the Bandyopadhyay, Panning and Krogan laboratories for constructive discussions, J. Forrest (TTP Labtech) for providing the Acumen eX3 cytometer, J. DeRisi for allowing us access to the uPrint 3D printer, G. Tzertzinis (NEB) for providing high-concentration ShortCut RNase III, and T. Fazzio for technical advice. This work has been supported by US National Institutes of Health (GM082250, GM081879, AI090935, AI091575 to N.J.K., P50CA58207 to S.B. and GM085186 to B.P.); Defense Advanced Research Projects Agency (HR0011-11-C-0094 to N.J.K.) and University of California San Francisco Program for Breakthrough Biomedical Research to N.J.K. and B.P.

PY - 2013/5

Y1 - 2013/5

N2 - Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ∼11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape.

AB - Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ∼11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape.

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JO - Nature Methods

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Quantitative genetic-interaction mapping in mammalian cells

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