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A map of directional genetic interactions in a metazoan cell.

Fischer B, Sandmann T, Horn T, Billmann M, Chaudhary V, Huber W, Boutros M - Elife (2015)

Bottom Line: Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease.The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules.Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations.

View Article: PubMed Central - PubMed

Affiliation: Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

ABSTRACT
Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale. Here, we used combinatorial RNA interference and automated single-cell phenotyping to generate a large genetic interaction map for 21 phenotypic features of Drosophila cells. We devised a method that combines genetic interactions on multiple phenotypes to reveal directional relationships. This network reconstructed the sequence of protein activities in mitosis. Moreover, it revealed that the Ras pathway interacts with the SWI/SNF chromatin-remodelling complex, an interaction that we show is conserved in human cancer cells. Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations.

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Ras-induced cell growth requires SWI/SNF complex function.Cell viability of parental HCT116 KRAS mutant cells (KRASG13D/+) and isogenic HCT116 KRAS wild type cells (KRASKO/+).DOI:http://dx.doi.org/10.7554/eLife.05464.016
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fig6s1: Ras-induced cell growth requires SWI/SNF complex function.Cell viability of parental HCT116 KRAS mutant cells (KRASG13D/+) and isogenic HCT116 KRAS wild type cells (KRASKO/+).DOI:http://dx.doi.org/10.7554/eLife.05464.016

Mentions: Next, we tested whether human KRAS-mutant cancer cells might specifically depend on the SWI/SNF complex. We investigated this by knockdown of SWI/SNF complex members in the colon cancer cell line HCT116, which harbours an activating KRAS G13D mutation (KRASG13D/+), and in a derived cell line in which the mutant KRAS allele was deleted (KRASKO/+). Whereas there was no difference in cell growth between the two isogenic cell lines (Figure 6—figure supplement 1), knockdown of individual SWI/SNF members SMARCA4, SMARCB1 and ARID1A caused a significant decrease in viability selectively in the context of constitutively active KRAS (Figure 6F). Together, this indicates that SWI/SNF complex members genetically interact with activated Ras signalling.


A map of directional genetic interactions in a metazoan cell.

Fischer B, Sandmann T, Horn T, Billmann M, Chaudhary V, Huber W, Boutros M - Elife (2015)

Ras-induced cell growth requires SWI/SNF complex function.Cell viability of parental HCT116 KRAS mutant cells (KRASG13D/+) and isogenic HCT116 KRAS wild type cells (KRASKO/+).DOI:http://dx.doi.org/10.7554/eLife.05464.016
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384530&req=5

fig6s1: Ras-induced cell growth requires SWI/SNF complex function.Cell viability of parental HCT116 KRAS mutant cells (KRASG13D/+) and isogenic HCT116 KRAS wild type cells (KRASKO/+).DOI:http://dx.doi.org/10.7554/eLife.05464.016
Mentions: Next, we tested whether human KRAS-mutant cancer cells might specifically depend on the SWI/SNF complex. We investigated this by knockdown of SWI/SNF complex members in the colon cancer cell line HCT116, which harbours an activating KRAS G13D mutation (KRASG13D/+), and in a derived cell line in which the mutant KRAS allele was deleted (KRASKO/+). Whereas there was no difference in cell growth between the two isogenic cell lines (Figure 6—figure supplement 1), knockdown of individual SWI/SNF members SMARCA4, SMARCB1 and ARID1A caused a significant decrease in viability selectively in the context of constitutively active KRAS (Figure 6F). Together, this indicates that SWI/SNF complex members genetically interact with activated Ras signalling.

Bottom Line: Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease.The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules.Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations.

View Article: PubMed Central - PubMed

Affiliation: Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

ABSTRACT
Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale. Here, we used combinatorial RNA interference and automated single-cell phenotyping to generate a large genetic interaction map for 21 phenotypic features of Drosophila cells. We devised a method that combines genetic interactions on multiple phenotypes to reveal directional relationships. This network reconstructed the sequence of protein activities in mitosis. Moreover, it revealed that the Ras pathway interacts with the SWI/SNF chromatin-remodelling complex, an interaction that we show is conserved in human cancer cells. Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations.

Show MeSH
Related in: MedlinePlus