A map of directional genetic interactions in a metazoan cell.
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.
Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Bernd
http://orcid.org/0000-0001-9437-2099
B
Fischer
Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Thomas
T
Sandmann
Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Thomas
T
Horn
Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Maximilian
M
Billmann
Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Varun
V
Chaudhary
Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Wolfgang
W
Huber
Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Michael
M
Boutros
D000465:Algorithms; D000818:Animals; D002460:Cell Line; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D029721:Drosophila Proteins / Q000235:genetics* / Q000378:metabolism; D004331:Drosophila melanogaster / Q000166:cytology / Q000235:genetics* / Q000378:metabolism; D004843:Epistasis, Genetic; D053263:Gene Regulatory Networks; D045325:HCT116 Cells; D006801:Humans; D008856:Microscopy, Fluorescence; D010641:Phenotype; D034622:RNA Interference; D015203:Reproducibility of Results; D015398:Signal Transduction / Q000235:genetics; D059010:Single-Cell Analysis / Q000379:methods; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D018631:ras Proteins / Q000235:genetics / Q000378:metabolism
D002868:Chromosomal Proteins, Non-Histone; D029721:Drosophila Proteins; C445179:SWI-SNF-B chromatin-remodeling complex; D014157:Transcription Factors; D018631:ras Proteins
D. melanogaster; chromosomes; epistasis; evolutionary biology; genes; genetic interactions; genomics; image-based phenotyping