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Science Journals RESEARCH ◥ us to formulate and quantify the general RESEARCH ARTICLE SUMMARY mechanisms of genetic suppression, which has the potential to guide the identification of modifier genes affecting the penetrance of YEAST GENETICS genetic traits, including human disease.▪ Exploring genetic suppression Genetic suppression Wild type interactions on a global scale Jolanda van Leeuwen, Carles Pons, Joseph C. Mellor, Takafumi N. Yamaguchi, Helena Friesen, John Koschwanez, Mojca Mattiazzi Ušaj, Maria Pechlaner, Mehmet Takar, Matej Ušaj,BenjaminVanderSluis,KerryAndrusiak,Pritpal Bansal, Anastasia Baryshnikova, Claire E. Boone, Jessica Cao, Atina Cote, Marinella Gebbia, Gene Horecka, Ira Horecka, Elena Kuzmin, Nicole Legro, Wendy Liang, Natascha van Lieshout, Margaret McNee, Normal fitness Reduced fitness Restored fitness (sick) (healthy) Bryan-Joseph San Luis, Fatemeh Shaeri, Ermira Shuteriqi, Song Sun, Lu Yang, Ji-Young Youn, Michael Yuen, Michael Costanzo, Anne-Claude Gingras, Patrick Aloy, Chris Oostenbrink, Andrew Murray, Todd R. Graham, Chad L. Myers,* Brenda J. Andrews,* Mapping a global suppression network Frederick P. Roth,* Charles Boone* • 1842 Literature curated suppression interactions • 195 Systematically derived INTRODUCTION: Genetic suppression oc- ping and whole-genome sequencing, we also suppression interactions curs when the phenotypic defects caused by isolated an unbiased, experimental set of ~200 - Genetic mapping a mutated gene are rescued by a mutation in spontaneous suppressor mutations that cor- - Whole genome sequencing another gene. rect the fitness defects of deletion or hypomor- on January 22, 2017 These genetic interactions can connect phic mutant alleles. Integrating these results genes that work within the same pathway yielded a global suppression network. Enrichment of suppression gene pairs or biological process, providing new ◥ The majority of suppression in- ON OUR WEBSITE colocal- GO coan- coex- same same 0164 mechanistic insights into cellular teractions identified novel gene-gene ization notation pression pathway complex fold enrich. function, or they can correct defects Read the full article connections, thus providing new in- in gene expression or protein pro- at http://dx.doi. formation about the functional wiring Mechanistic suppression classes duction. More generally, suppression org/10.1126/ diagram of a cell. Most suppression science.aag0839 interactions may play an important .................................................. pairs connected functionally related Same complex Q S role in the genetics underlying hu- genes, including genes encoding mem- Same pathway Q S man diseases, such as the diverse penetrance bers of the same pathway or complex. The Unknown of Mendelian disease variants. Our ability to functional enrichments observed for suppres- Normal fitness interpret personal genome sequences remains sion gene pairs were several times as high as Normal fitness http://science.sciencemag.org/ limited, in part, because we lack an under- those found for other types of genetic in- All mRNA stability Related pathway suppression standing of how sequence variants interact in teractions; this highlighted their discovery * Q S interactions nonadditive ways to generate profound phe- potential for assigning gene function. Our NMD notypes, including genetic suppression. systematic suppression analysis also identi- Normal fitness fied a prevalent allele-specific mechanism of RATIONALE: Genetic interactions, in which suppression, whereby growth defects of hypo- Protein stability Other Downloaded from mutations in two different genes combine to morphic alleles can be overcome by mutations Q Q functional generate an unexpected phenotype, may un- that compromise either protein or mRNA connection derlie a significant component of trait her- degradation machineries. itability. Although genetic interactions that From whole-genome sequencing of suppres- Global analysis of genetic suppression. Ge- compromise fitness, such as synthetic lethality, sor strains, we also identified additional sec- netic suppression interactions occur when the have been mapped extensively, suppression ondary mutations, the vast majority of which detrimental effects of a primary mutation can interactions have not been explored system- appeared to be random passenger mutations. be overcome by a secondary mutation. Both atically. To understand the general principles However, a small subset of genes was enriched literature-curated and experimentally derived sup- of genetic suppression and to examine the for secondary mutations, several of which pression interactions were collected and yielded extent to which these interactions reflect did not affect growth rate but rather appeared a genetic suppression network.This global network cellular function, we harnessed the powerful to delay the onset of the stationary phase. This was enriched for functional relationships and de- Saccharomyces genetics of the budding yeast delay suggests that they are selected for under fined distinct mechanistic classes of genetic cerevisiae to assemble a global network of gen- laboratory growth conditions because they suppression. etic suppression interactions. increase cell abundance within a propagat- ing population. RESULTS: By analyzing hundreds of pub- The list of author affiliations is available in the full article online. lished papers, we assembled a network of CONCLUSION: A global network of genetic *Corresponding author. Email: cmyers@cs.umn.edu (C.L.M.); genetic suppression interactions involving suppression interactions highlights the major brenda.andrews@utoronto.ca (B.J.A.); fritz.roth@utoronto.ca (F.P.R); charlie.boone@utoronto.ca (C.B.) ~1300 different yeast genes and ~1800 unique potential for systematic studies of suppression Cite this article as J. van Leeuwen et al., Science 354, interactions. Through automated genetic map- to map cellular function. Our findings allowed aag0839 (2016). DOI: 10.1126/science.aag0839 SCIENCE sciencemag.org 4NOVEMBER2016• VOL 354 ISSUE 6312 599 RESEARCH ◥ and (ii) functional suppressors in which a muta- RESEARCH ARTICLE tion in a second gene functionally compensates for the defect associated with the primary muta- tion (8). Here, our major goal was to investigate YEAST GENETICS the general principles of functional suppression by assembling a global network of these inter- actions, which should provide new mechanistic Exploring genetic suppression insights about protein function and enable the ordering of components of biological pathways. interactions on a global scale A network of literature-curated suppression interactions Jolanda van Leeuwen,1* Carles Pons,2,3* Joseph C. Mellor,1,4† 1,4,5 1 6 To capture existing suppression interactions in Takafumi N. Yamaguchi, Helena Friesen, John Koschwanez, Saccharomyces cerevisiae, we examined ~6000 š 1 7 8 š 1 Mojca Mattiazzi U aj, Maria Pechlaner, Mehmet Takar, Matej U aj, potential interactions in ~1700 published papers 2 1,5 1,4 Benjamin VanderSluis, ‡ Kerry Andrusiak, Pritpal Bansal, derived from the BioGRID’s “synthetic rescue” 9 1 1 1,4 Anastasia Baryshnikova, Claire E. Boone, Jessica Cao, Atina Cote, data set (9). From each interaction, we annotated 1,4 1 1 1,5 1 Marinella Gebbia, Gene Horecka, Ira Horecka, Elena Kuzmin, Nicole Legro, the type of suppressor mutation (e.g., spontane- Wendy Liang,1 Natascha van Lieshout,1,4,5 Margaret McNee,1 Bryan-Joseph San Luis,1 ous mutation or deletion allele); the type of mu- Fatemeh Shaeri,1,4 Ermira Shuteriqi,1 Song Sun,1 Lu Yang,1 Ji-Young Youn,4 tation that is being suppressed, which we refer to Michael Yuen,1 Michael Costanzo,1 Anne-Claude Gingras,4,5 Patrick Aloy,3,10 as a “query” mutation; and the use of specific Chris Oostenbrink,7 Andrew Murray,6 Todd R. Graham,8 Chad L. Myers,2,11§ conditions (e.g., a drug or specialized carbon Brenda J. Andrews,1,5§ Frederick P. Roth,1,4,5,11,12§ Charles Boone1,5,11§ source). Suppression interactions that were in- tragenic, involved a specific phenotype other Genetic suppression occurs when the phenotypic defects caused by a mutation in a particular than growth, or included more than two genes gene are rescued by a mutation in a second gene. To explore the principles of genetic were excluded from the final data set. We also suppression, we examined both literature-curated and unbiased experimental data, involving removed suppression interactions derived from on January 22, 2017 systematic genetic mapping and whole-genome sequencing, to generate a large-scale high-throughput experiments or dosage inter- suppression network among yeast genes. Most suppression pairs identified novel relationships actions in which either the query or the suppressor among functionally related genes, providing new insights into the functional wiring diagram was overexpressed. The resulting literature-curated of the cell. In addition to suppressor mutations, we identified frequent secondary mutations, network encompassed 1304 genes and 1842 unique in a subset of genes, that likely cause a delay in the onset of stationary phase, which appears suppression interactions (table S1). We visual- to promote their enrichment within a propagating population. These findings allow us to ized this network using a force-directed layout formulate and quantify general mechanisms of genetic suppression. (10), so that query genes that share a common suppressor tend to be positioned together (Fig. 1B). Most query genes (69%) are suppressed by lthough causative variants have been iden- est growing single mutant, to
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