Synthetic genetic-interaction (SGI) analysis in C. elegans. (a) Two scenarios that may result in synthetic interactions are presented. The top row shows how enhancing interactions may arise when hypomorphic loss-of-function worms (mutant), which have reduced but not eliminated function of a gene, are fed RNAi that targets another gene in the same essential pathway. The lower row shows synthetic interactions that may arise when a hypomorph and a gene targeted by RNAi are in parallel pathways that regulate an essential process (X). (b) An outline of the SGI experimental approach. RNAi-inducing bacteria that target a specific C. elegans gene for knockdown (target gene A) are fed to a hypomorphic mutant (query gene B). In parallel, wild-type worms are fed the experimental RNAi-inducing bacteria (control 1), and the query mutant is fed mock RNAi-inducing bacteria (control 2). This is all done in 12-well plate format with at least three technical replicates. Over the course of several days, we estimate the number of progeny produced in each experimental and control well in a blind fashion (see text and Materials and methods). We assigned a growth score from 0–6 (0, 2 parental worms; 1, 1–10 progeny; 2, 11–50 progeny; 3, 51–100 progeny; 4, 101–200 progeny; 5, 200+ progeny; and 6, overgrown). (c) Interacting gene pairs are inferred through a difference in the population growth scores between experimental and control wells. In the example shown, a global analysis of the experimental and control query-target combinations revealed that daf-2 interacts with ist-1, and that sem-5 and sos-1 both interact with let-60.
Byrne et al. Journal of Biology 2007 6:8 doi:10.1186/jbiol58