A global genetic interaction network maps a wiring diagram of cellular function
Authors: Costanzo Michael , VanderSluis Benjamin , Koch Elizabeth N. , Baryshnikova Anastasia , Pons Carles , Tan Guihong , Wang Wen , Usaj Matej , Hanchard Julia , Lee Susan D. , Pelechano Vicent , Styles Erin B. , Billmann Maximilian , van Leeuwen Jolanda , van Dyk Nydia , Lin Zhen-Yuan , Kuzmin Elena , Nelson Justin , Piotrowski Jeff S. , Srikumar Tharan , Bahr Sondra , Chen Yiqun , Deshpande Raamesh , Kurat Christoph F. , Li Sheena C. , Li Zhijian , Usaj Mojca Mattiazzi , Okada Hiroki , Pascoe Natasha , San Luis Bryan-Joseph , Sharifpoor Sara , Shuteriqi Emira , Simpkins Scott W. , Snider Jamie , Suresh Harsha Garadi , Tan Yizhao , Zhu Hongwei , Malod-Dognin Noel , Janjic Vuk , Przulj Natasa , Troyanskaya Olga G. , Stagljar Igor , Xia Tian , Ohya Yoshikazu , Gingras Anne-Claude , Raught Brian , Boutros Michael , Steinmetz Lars M. , Moore Claire L. , Rosebrock Adam P. , Caudy Amy A. , Myers Chad L. , Andrews Brenda , Boone Charles 
Published: September 2016

INTRODUCTION

Genetic interactions occur when mutations in two or more genes combine to generate an unexpected phenotype. An extreme negative or synthetic lethal genetic interaction occurs when two mutations, neither lethal individually, combine to cause cell death. Conversely, positive genetic interactions occur when two mutations produce a phenotype that is less severe than expected. Genetic interactions identify functional relationships between genes and can be harnessed for biological discovery and therapeutic target identification. They may also explain a considerable component of the undiscovered genetics associated with human diseases. Here, we describe construction and analysis of a comprehensive genetic interaction network for a eukaryotic cell.

RATIONALE

Genome sequencing projects are providing an unprecedented view of genetic variation. However, our ability to interpret genetic information to predict inherited phenotypes remains limited, in large part due to the extensive buffering of genomes, making most individual eukaryotic genes dispensable for life. To explore the extent to which genetic interactions reveal cellular function and contribute to complex phenotypes, and to discover the general principles of genetic networks, we used automated yeast genetics to construct a global genetic interaction network.

RESULTS

We tested most of the ~6000 genes in the yeast
Saccharomyces cerevisiae
for all possible pairwise genetic interactions, identifying nearly 1 million interactions, including ~550,000 negative and ~350,000 positive interactions, spanning ~90% of all yeast genes. Essential genes were network hubs, displaying five times as many interactions as nonessential genes. The set of genetic interactions or the genetic interaction profile for a gene provides a quantitative measure of function, and a global network based on genetic interaction profile similarity revealed a hierarchy of modules reflecting the functional architecture of a cell. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections associated with defects in cell cycle progression or cellular proteostasis. Importantly, the global network illustrates how coherent sets of negative or positive genetic interactions connect protein complex and pathways to map a functional wiring diagram of the cell.

CONCLUSION

A global genetic interaction network highlights the functional organization of a cell and provides a resource for predicting gene and pathway function. This network emphasizes the prevalence of genetic interactions and their potential to compound phenotypes associated with single mutations. Negative genetic interactions tend to connect functionally related genes and thus may be predicted using alternative functional information. Although less functionally informative, positive interactions may provide insights into general mechanisms of genetic suppression or resiliency. We anticipate that the ordered topology of the global genetic network, in which genetic interactions connect coherently within and between protein complexes and pathways, may be exploited to decipher genotype-to-phenotype relationships.

A global network of genetic interaction profile similarities.

(
Left
) Genes with similar genetic interaction profiles are connected in a global network, such that genes exhibiting more similar profiles are located closer to each other, whereas genes with less similar profiles are positioned farther apart. (
Right
) Spatial analysis of functional enrichment was used to identify and color network regions enriched for similar Gene Ontology bioprocess terms.