Quantitative high-throughput analysis of synthetic genetic interactions in Caenorhabditis elegans by RNA interference

Abstract

Biological processes are highly dynamic but the current representation of molecular networks is static and largely qualitative. To investigate the dynamic property of genetic networks, a novel quantitative high-throughput method based on RNA interference and capable of calculating the relevance of each interaction, was developed. With this approach, it will be possible to identify not only the components of a network, but also to investigate quantitatively how network and biological processes react to perturbations. As a first application of this method, the genetic interactions of a weak loss-of-function mutation in the gene efl-1/E2F with all the genes of chromosome III were investigated during embryonic development of Caenorhabditis elegans. Fifteen synthetic genetic interactions of efl-1/E2F with the genes of chromosome III were detected, measured and ranked by statistical relevance.

Fig. 1

Linear regression between automatic and manual counting of embryos of a random subset of genes of chromosome III. The data are an average of two distinct experiments and they show a strong correlation between the two methods, n = 68, R² = 0.94, p < 0.0001.

Fig. 2

RNAi gene cnx-1 in mutated strain (A0, A1) and RNAi gene cnx-1 in the wild-type (B0, B1).The images showing an enhancement of the embryonic lethality after 24 h in the mutated strain (A1): this is an example of synthetic phenotype. (A0, B0) = embryos at time 0; (A1, B1) = embryos after hour 24.

Fig. 3

Frequency distribution of embryonic lethality obtained by RNAi in the wild-type strain N2 (A) and in the mutated strain JJ1549 (B) of the full chromosome III.

Fig. 4

Linear regression between the mean percentage of embryonic lethality between the wild type strain, N2 and the mutated strain JJ1549, n = 2084, R² = 0.58, p < 0.0001. The top left triangle shows the genes with a synthetic lethality value exceeding 20%.