Genetic Interactions in Yeast

Genetic interactions report on how the presence of one mutation alters the phenotypic outcome of a second mutation, and can be used to identify genes that function in related or parallel pathways. We have developed a large-scale, quantitative approach for measuring genetic interactions, called E-MAP (Epistatic Miniarray Profile). E-MAPs are comprised of quantitative measurements of genetic interactions between pairs of mutations within large sets of genes. We have generated E-MAPs for most processes in budding yeast and fission yeast. These studies have led to a wealth of functional insights into these organisms and on the evolution of genetic interactomes.

 

Our initial E-MAP studies used deletions and knockdowns of non-essential and essential genes, respectively. However, many important proteins are multi-functional, and a limitation to this work was that secondary functions of proteins tend to be obscured by the central function. To address the next level of complexity, we developed an advance of the E-MAP analysis, termed point-mutant E-MAP (pE-MAP), which allows us to examine multifunctional gene function at a residue-level resolution. We applied this technique to functionally dissect RNA polymerase II and histones H3 and H4 in budding yeast. In addition to discovering connections between individual residues and cellular processes, we discovered a relationship between spatial proximity and genetic similarity of the mutated residues. Based on this observation, we are currently exploring the applications of our technique as a tool for structure-function analysis.

 

In a further advance of E-MAP technology, we have developed Triple Mutant Analysis (TMA), which allows for investigation of genetic interactions in triple mutants. This approach is particularly useful for revealing functional redundancies that could not be uncovered by standard double mutant genetic interactions.