Research Article

Systematic analysis of complex genetic interactions

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Science  20 Apr 2018:
Vol. 360, Issue 6386, eaao1729
DOI: 10.1126/science.aao1729

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Trigenic interactions in yeast link bioprocesses

To dissect the genotype-phenotype landscape of a cell, it is necessary to understand interactions between genes. Building on the digenic protein-protein interaction network, Kuzmin et al. created a trigenic landscape of yeast by using a synthetic genetic array (see the Perspective by Walhout). Triple-mutant analyses indicated that the majority of genes with trigenic associations functioned within the same biological processes. These converged on networks identified in the digenic interaction landscape. Although the overall effects were weaker for trigenic than for digenic interactions, trigenic interactions were more likely to bridge biological processes in the cell.

Science, this issue p. eaao1729; see also p. 269

Structured Abstract

INTRODUCTION

Genetic interactions occur when mutations in different genes combine to result in a phenotype that is different from expectation based on those of the individual mutations. Negative genetic interactions occur when a combination of mutations leads to a fitness defect that is more exacerbated than expected. For example, synthetic lethality occurs when two mutations, neither of which is lethal on its own, generate an inviable double mutant. Alternatively, positive genetic interactions occur when genetic perturbations combine to generate a double mutant with a greater fitness than expected. Global digenic interaction studies have been useful for understanding the functional wiring diagram of the cell and may also provide insight into the genotype-to-phenotype relationship, which is important for tracking the missing heritability of human health and disease. Here we describe a network of higher-order trigenic interactions and explore its implications.

RATIONALE

Variation in phenotypic outcomes in different individuals is caused by genetic determinants that act as modifiers. Modifier loci are prevalent in human populations, but knowledge regarding how variants interact to modulate phenotype in different individuals is lacking. Similarly, in yeast, traits including conditional essentiality—in which certain genes are essential in one genetic background but nonessential in another—often result from an interplay of multiple modifier loci. Because complex modifiers may underlie the genetic basis of physiological states found in natural populations, it is critical to understand the landscape of higher-order genetic interactions.

RESULTS

To survey trigenic interactions, we designed query strains that sampled key features of the global digenic interaction network: (i) digenic interaction strength, (ii) average number of digenic interactions, and (iii) digenic interaction profile similarity. In total, we tested ~400,000 double and ~200,000 triple mutants for fitness defects and identified ~9500 digenic and ~3200 trigenic negative interactions. Although trigenic interactions tend to be weaker than digenic interactions, they were both enriched for functional relationships. About one-third of trigenic interactions identified “novel” connections that were not observed in our digenic control network, whereas the remaining approximately two-thirds of trigenic interactions “modified” a digenic interaction, suggesting that the global digenic interaction network is important for understanding the trigenic interaction network. Despite their functional enrichment, trigenic interactions also bridged distant bioprocesses. We estimate that the global trigenic interaction network is ~100 times as large as the global digenic network, highlighting the potential for complex genetic interactions to affect the biology of inheritance.

CONCLUSION

The extensive network of trigenic interactions and their ability to generate functionally diverse phenotypes suggest that higher-order genetic interactions may play a key role in the genotype-to-phenotype relationship, genome size, and speciation.

Systematic analysis of trigenic interactions.

We surveyed for trigenic interactions and found that they are ~100 times as prevalent as digenic interactions, often modify a digenic interaction, and connect functionally related genes as well as genes in more diverse bioprocesses (multicolored nodes). PPI, protein-protein interaction.

Abstract

To systematically explore complex genetic interactions, we constructed ~200,000 yeast triple mutants and scored negative trigenic interactions. We selected double-mutant query genes across a broad spectrum of biological processes, spanning a range of quantitative features of the global digenic interaction network and tested for a genetic interaction with a third mutation. Trigenic interactions often occurred among functionally related genes, and essential genes were hubs on the trigenic network. Despite their functional enrichment, trigenic interactions tended to link genes in distant bioprocesses and displayed a weaker magnitude than digenic interactions. We estimate that the global trigenic interaction network is ~100 times as large as the global digenic network, highlighting the potential for complex genetic interactions to affect the biology of inheritance, including the genotype-to-phenotype relationship.

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