Analysis of Gene Function Through RNAi Screens in C. elegans

To what extent is our phenotype predictable from our genotype? This is one of the central problems of modern medical genetics.  The two key goals of our research are to be able to predict the effect of any single inherited mutation on our overall phenotype and to understand how mutations in multiple genes combine phenotypically.  To attempt to address these questions, we work in C. elegans where we can carry out systematic surveys of gene function in the intact animal using RNAi screening.  To date over 50 such genome-scale RNAi screens have been carried out in the worm, identifying genes that participate in a wide range of developmental processes from germ line function to vulval development to synaptic transmission. However, the loss of function phenotype of any gene is often acutely sensitive to genetic background — in the context of medical genetics, two individuals inheriting the same disease-associated allele may have very different disease risks due to other variation in their genomes. Studying systematically how genetic background affects perturbed phenotypes is the focus of my presentation as this will be critical for our ability to predict disease risk in individuals. I will present data from an ongoing study where we examine the RNAi phenotypes of over 2000 genes in a large panel of natural isolates of C. elegans. These isolates have a level of genetic variation similar to that seen in human populations and represent the entire global genetic diversity in the worm population.  Furthermore, many of these isolates have been completely sequenced — we thus have the chance to examine systematically how loss of function phenotypes change within a species, and to what extent phenotypic variation is predictable from genetic variation.  We find that while most genes have the same loss-of-function phenotype in all isolates studied, there are also many examples of genes strong variation in loss-of-function phenotype between different isolates.  Furthermore, genes whose phenotype varies between any two strains often fall into similar functional classes suggesting that each isolate has subtly altered genetic networks which have different levels of requirement for specific pathways and molecular machineries.  This is the first such systematic study of natural variation in loss-of-function phenotypes for any species and I will discuss the implications for human genetic disease and predictability of disease risk.