Pairwise and higher-order genetic interactions during the evolution of a tRNA

A central question in genetics and evolution is the extent to which the outcomes of mutations change depending on the genetic context in which they occur(1-3). Pairwise interactions between mutations have been systematically mapped within(4-8) and between(19) genes, and have been shown to contribute substantially to phenotypic variation among individuals'. However, the extent to which genetic interactions themselves are stable or dynamic across genotypes is unclear(21,22). Here we quantify more than 45,000 genetic interactions between the same 87 pairs of mutations across more than 500 closely related genotypes of a yeast tRNA. Notably, all pairs of mutations interacted in at least 9% of genetic backgrounds and all pairs switched from interacting positively to interacting negatively in different genotypes (false discovery rate < 0.1). Higher-order interactions are also abundant and dynamic across genotypes. The epistasis in this tRNA means that all individual mutations switch from detrimental to beneficial, even in closely related genotypes. As a consequence, accurate genetic prediction requires mutation effects to be measured across different genetic backgrounds and the use of higher-order epistatic terms.