A map of directional genetic interactions in a metazoan cell

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.DOI: http://dx.doi.org/10.7554/eLife.05464.001

An Integrative Analysis of the InR/PI3K/Akt Network Identifies the Dynamic Response to Insulin Signaling

“…An independent screen at 60 minutes of insulin stimulus identified an additional proteins as pAkt and/or pERK regulators (data not shown), suggesting that more screens under different time points or more pathway readouts are needed to comprehensively validate the insulin network components. In addition, performing combinatorial perturbations will provide a powerful approach to identify redundancies in the network (Bakal et al, 2008; Fischer et al, 2015; Housden et al, 2015). …”

Systematic epistatic mapping of cellular processes

“…Example showing that the image-derived feature cell count did not reconstruct the genetic interaction, but the fraction of mitotic cells (mitotic index) provided this information. Figure was modified from [33] …”

“…Recent work from our laboratory has identified epistatic relationships between genes building networks reflecting temporal order of gene function in processes such as the mitotic cell cycle [33]. Epistatic relationships were reconstructed by directed genetic interactions, indicating whether one gene repressed or amplified another genes effect (Fig.…”

Decoding directional genetic dependencies through orthogonal CRISPR/Cas screens

“…In these studies, directionality could only be inferred in cases where either one of the interaction partners displays a no-loss-of-function phenotype, or both partners display opposing phenotypes 20 . However, the loss of each of two interacting genes generally has a phenotype by itself 19 and in the case of activating interactions, which are frequently found in aberrantly activated signalling cascades in cancer cells, such as MAPK signalling 23 -these phenotypes go in the same direction.…”

“…But, knowing the direction of genetic interactions can be critical for properly interpreting functional dependencies between genes, and offer rational approaches for therapeutic intervention. Yet, attempts to illuminate the direction of genetic interactions have been limited to model organisms [19][20][21][22] . In these studies, directionality could only be inferred in cases where either one of the interaction partners displays a no-loss-of-function phenotype, or both partners display opposing phenotypes 20 .…”