Epistasis Blog

From the Artificial Intelligence Innovation Lab at Cedars-Sinai Medical Center (www.epistasis.org)

Thursday, September 20, 2018

The complex underpinnings of genetic background effects

A nice new paper on epistasis is yeast.

Mullis MN, Matsui T, Schell R, Foree R, Ehrenreich IM. The complex underpinnings of genetic background effects. Nat Commun. 2018 Sep 17;9(1):3548. [PubMed]

Genetic interactions between mutations and standing polymorphisms can cause mutations to show distinct phenotypic effects in different individuals. To characterize the genetic architecture of these so-called background effects, we genotype 1411 wild-type and mutant yeast cross progeny and measure their growth in 10 environments. Using these data, we map 1086 interactions between segregating loci and 7 different gene knockouts. Each knockout exhibits between 73 and 543 interactions, with 89% of all interactions involving higher-order epistasis between a knockout and multiple loci. Identified loci interact with as few as one knockout and as many as all seven knockouts. In mutants, loci interacting with fewer and more knockouts tend to show enhanced and reduced phenotypic effects, respectively. Cross-environment analysis reveals that most interactions between the knockouts and segregating loci also involve the environment. These results illustrate the complicated interactions between mutations, standing polymorphisms, and the environment that cause background effects.

Saturday, September 01, 2018

Analysis of Epistasis in Natural Traits Using Model Organisms

A nice new essay in Trends in Genetics

Campbell RF, McGrath PT, Paaby AB. Analysis of Epistasis in Natural Traits Using Model Organisms. Trends Genet. 2018 [PubMed]


Identification of statistical epistasis in natural populations remains challenging due to the relationship between allele frequency and statistical power.

Artificial populations have been constructed in model organisms to detect statistical epistasis between two regions of the genome; however, it is difficult to use these results to understand how epistasis operates in natural populations.

Studies of focal perturbations in defined genetic backgrounds suggests that natural selection can influence the types of nonadditive relationships that exist.