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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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An epistatic network of mitotic genes.(A) Graph showing data-derived epistatic interactions of genes that are key regulators of cell cycle events, including polo, and members of the γTuRC, SAC, APC/C, the dynein/dynactin complex, sister chromatid cohesion complexes and cytokinesis genes. Blue arrows show alleviating epistatic interactions and red arrows show aggravating epistatic interactions. Exemplarily, the underlying data is shown for epistatic interactions. (B) Epistatic network of complexes that regulate mitotic events, as derived from the epistatic interactions between the members of the complexes.DOI:http://dx.doi.org/10.7554/eLife.05464.014
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fig5: An epistatic network of mitotic genes.(A) Graph showing data-derived epistatic interactions of genes that are key regulators of cell cycle events, including polo, and members of the γTuRC, SAC, APC/C, the dynein/dynactin complex, sister chromatid cohesion complexes and cytokinesis genes. Blue arrows show alleviating epistatic interactions and red arrows show aggravating epistatic interactions. Exemplarily, the underlying data is shown for epistatic interactions. (B) Epistatic network of complexes that regulate mitotic events, as derived from the epistatic interactions between the members of the complexes.DOI:http://dx.doi.org/10.7554/eLife.05464.014

Mentions: Next, we studied the directional genetic interactions of key regulators of the cell cycle (Figure 5A). The mitosis master regulator polo was observed as alleviating epistatic to components that are required for the initial mitotic phases, including the γTuRC, which serves as the structural basis of the mitotic spindle. In contrast, the ubiquitin-conjugating enzyme vih showed directional interactions to components that are active at later stages. Depletion of γTuRC members aggravated the cellular phenotype of the spindle assembly checkpoint (SAC). Dynein/dynactin motor proteins mediated a chain of directional epistatic interactions between the SAC and the APC/C. Moreover, whereas SAC knockdown had an aggravating effect on the phenotype of condensin/cohesion, the latter relied on a functional APC/C. The phenotypes of cytokinesis regulators including sti, pav, tum, Rho1 or scra were strongly dependent on APC/C as well as on dynein/dynactin motor proteins. Our data also showed that vih, the ubiquitin-ligase APC/C, as well as cytokinesis executers regulated the phenotype of the SCF ubiquitin-ligase core component Skp2. In contrast, Elongin-B, another ubiquitin-ligase core component, itself regulated the phenotype of the SAC, condensin/cohesin components and cytokinesis regulators. This unbiased mapping and automated inference of directional epistatic interactions, made possible by the multivariate phenotyping approach, revealed a detailed circuit diagram of regulatory, temporal and causal relationships of complexes that function during the M-phase of the cell cycle (Figure 5B).10.7554/eLife.05464.014Figure 5.An epistatic network of mitotic genes.


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)

An epistatic network of mitotic genes.(A) Graph showing data-derived epistatic interactions of genes that are key regulators of cell cycle events, including polo, and members of the γTuRC, SAC, APC/C, the dynein/dynactin complex, sister chromatid cohesion complexes and cytokinesis genes. Blue arrows show alleviating epistatic interactions and red arrows show aggravating epistatic interactions. Exemplarily, the underlying data is shown for epistatic interactions. (B) Epistatic network of complexes that regulate mitotic events, as derived from the epistatic interactions between the members of the complexes.DOI:http://dx.doi.org/10.7554/eLife.05464.014
© Copyright Policy
Related In: Results  -  Collection

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

fig5: An epistatic network of mitotic genes.(A) Graph showing data-derived epistatic interactions of genes that are key regulators of cell cycle events, including polo, and members of the γTuRC, SAC, APC/C, the dynein/dynactin complex, sister chromatid cohesion complexes and cytokinesis genes. Blue arrows show alleviating epistatic interactions and red arrows show aggravating epistatic interactions. Exemplarily, the underlying data is shown for epistatic interactions. (B) Epistatic network of complexes that regulate mitotic events, as derived from the epistatic interactions between the members of the complexes.DOI:http://dx.doi.org/10.7554/eLife.05464.014
Mentions: Next, we studied the directional genetic interactions of key regulators of the cell cycle (Figure 5A). The mitosis master regulator polo was observed as alleviating epistatic to components that are required for the initial mitotic phases, including the γTuRC, which serves as the structural basis of the mitotic spindle. In contrast, the ubiquitin-conjugating enzyme vih showed directional interactions to components that are active at later stages. Depletion of γTuRC members aggravated the cellular phenotype of the spindle assembly checkpoint (SAC). Dynein/dynactin motor proteins mediated a chain of directional epistatic interactions between the SAC and the APC/C. Moreover, whereas SAC knockdown had an aggravating effect on the phenotype of condensin/cohesion, the latter relied on a functional APC/C. The phenotypes of cytokinesis regulators including sti, pav, tum, Rho1 or scra were strongly dependent on APC/C as well as on dynein/dynactin motor proteins. Our data also showed that vih, the ubiquitin-ligase APC/C, as well as cytokinesis executers regulated the phenotype of the SCF ubiquitin-ligase core component Skp2. In contrast, Elongin-B, another ubiquitin-ligase core component, itself regulated the phenotype of the SAC, condensin/cohesin components and cytokinesis regulators. This unbiased mapping and automated inference of directional epistatic interactions, made possible by the multivariate phenotyping approach, revealed a detailed circuit diagram of regulatory, temporal and causal relationships of complexes that function during the M-phase of the cell cycle (Figure 5B).10.7554/eLife.05464.014Figure 5.An epistatic network of mitotic genes.

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