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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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Genetic interaction profiles and protein complexes.Distribution of pairwise Pearson correlation coefficients across 21 phenotypes for gene pairs detected by co-purification and mass spectrometry according to the DPiM dataset (Guruharsha et al., 2011) (red line) and for all other gene pairs (blue line).DOI:http://dx.doi.org/10.7554/eLife.05464.010
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fig3s2: Genetic interaction profiles and protein complexes.Distribution of pairwise Pearson correlation coefficients across 21 phenotypes for gene pairs detected by co-purification and mass spectrometry according to the DPiM dataset (Guruharsha et al., 2011) (red line) and for all other gene pairs (blue line).DOI:http://dx.doi.org/10.7554/eLife.05464.010

Mentions: In the genetic interaction map, all γ-tubulin ring complex (γTuRC) members mapped in a dense cluster surrounded by the motor proteins of the dynein/dynactin complexes as well as auxiliary regulators of the mitotic spindle (Figure 3B). Also in close proximity to the mitotic spindle we found the APC/C, which drives the metaphase-to-anaphase transition by priming several cell cycle regulators for ubiquitin-mediated degradation by the proteasome. Interestingly, the dynactin member Arp10 was found to have an ‘APC/C-like’ interaction profile, suggesting a role in supporting APC/C function. Moreover, our map showed that the APC/C is functionally linked to the proteasome via Cdc27, the motor protein Klp61F, the APC/C activator fzy (CDC20) and the ubiquitin-conjugating enzyme vih. We observed that gene pairs with high correlation coefficients are enriched for experimentally validated protein–protein interactions (Figure 3—figure supplement 2) (Guruharsha et al., 2011). Overall, the different protein complexes and functional modules were well separated in the genetic interaction map.


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)

Genetic interaction profiles and protein complexes.Distribution of pairwise Pearson correlation coefficients across 21 phenotypes for gene pairs detected by co-purification and mass spectrometry according to the DPiM dataset (Guruharsha et al., 2011) (red line) and for all other gene pairs (blue line).DOI:http://dx.doi.org/10.7554/eLife.05464.010
© Copyright Policy
Related In: Results  -  Collection

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

fig3s2: Genetic interaction profiles and protein complexes.Distribution of pairwise Pearson correlation coefficients across 21 phenotypes for gene pairs detected by co-purification and mass spectrometry according to the DPiM dataset (Guruharsha et al., 2011) (red line) and for all other gene pairs (blue line).DOI:http://dx.doi.org/10.7554/eLife.05464.010
Mentions: In the genetic interaction map, all γ-tubulin ring complex (γTuRC) members mapped in a dense cluster surrounded by the motor proteins of the dynein/dynactin complexes as well as auxiliary regulators of the mitotic spindle (Figure 3B). Also in close proximity to the mitotic spindle we found the APC/C, which drives the metaphase-to-anaphase transition by priming several cell cycle regulators for ubiquitin-mediated degradation by the proteasome. Interestingly, the dynactin member Arp10 was found to have an ‘APC/C-like’ interaction profile, suggesting a role in supporting APC/C function. Moreover, our map showed that the APC/C is functionally linked to the proteasome via Cdc27, the motor protein Klp61F, the APC/C activator fzy (CDC20) and the ubiquitin-conjugating enzyme vih. We observed that gene pairs with high correlation coefficients are enriched for experimentally validated protein–protein interactions (Figure 3—figure supplement 2) (Guruharsha et al., 2011). Overall, the different protein complexes and functional modules were well separated in the genetic interaction map.

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