Synthetic Genetic Array (SGA) Analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe

Baryshnikova, Anastasia; Costanzo, Michael; Dixon, Scott J.; Vizeacoumar, Franco J.; Myers, Chad L.; Andrews, Brenda; Boone, Charles

doi:10.1016/s0076-6879(10)70007-0

Cited by 198 publications

(225 citation statements)

References 65 publications

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“…In an effort to parse key effectors driving the altered DDR kinetics and genomic instability seen upon Sec8 depletion, we queried available synthetic genetic array (SGA) data from yeast for genetic interactions with exocyst mutants. Analysis of the SGA resource using pairwise correlation coefficients allows for clustering of significant (r ϭ Ͼ0.1) biological relationships (61). Among the exocyst mutants that were not single-gene lethal (62,63), we identified a functional cluster centered on Sec3 that contained additional subunits of the exocyst and the histone acetyltransferase HPA2, which suggests that the exocyst complex participates in the regulation of histone modification (Fig.…”

Section: Resultsmentioning

confidence: 96%

Role of the Exocyst Complex Component Sec6/8 in Genomic Stability

Torres

Pandita

Kulak

et al. 2015

Molecular and Cellular Biology

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The exocyst is a heterooctomeric complex well appreciated for its role in the dynamic assembly of specialized membrane domains. Accumulating evidence indicates that this macromolecular machine also serves as a physical platform that coordinates regulatory cascades supporting biological systems such as host defense signaling, cell fate, and energy homeostasis. The isolation of multiple components of the DNA damage response (DDR) as exocyst-interacting proteins, together with the identification of Sec8 as a suppressor of the p53 response, suggested functional interactions between the exocyst and the DDR. We found that exocyst perturbation resulted in resistance to ionizing radiation (IR) and accelerated resolution of DNA damage. This occurred at the expense of genomic integrity, as enhanced recombination frequencies correlated with the accumulation of aberrant chromatid exchanges. Sec8 perturbation resulted in the accumulation of ATF2 and RNF20 and the promiscuous accumulation of DDR-associated chromatin marks and Rad51 repairosomes. Thus, the exocyst supports DNA repair fidelity by limiting the formation of repair chromatin in the absence of DNA damage. The faithful repair of DNA damage is integral to the maintenance of the genome and suppression of oncogenesis (1). This relationship has motivated intense efforts to elaborate the composition and mechanism of action of core DNA repair machinery as well as peripheral molecular systems that modulate this machinery to suppress genomic instability (2-5). With respect to the latter, emerging evidence implicates multiple regulatory layers that link activation of the DNA damage response (DDR), repair pathway choice, and resolution of the DDR to chromatin organization (6-9), RNA metabolism (10, 11), and autophagy (12)(13)(14). By extrapolation, the coordinated response of cellular processes to DNA damage is necessary for efficient DNA repair, and perturbations of these pathways can lead to genomic instability and development of neoplastic disease.The exocyst (also known as the Sec6/8 complex) is a conserved heterooctomeric protein complex, which includes Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo84, and Exo70. The holocomplex is well appreciated for its role in the dynamic trafficking of secretory vesicles to specialized membrane domains such as the basolateral membrane of polarized epithelial cells (15) and abscission planes in dividing cells (16) and to lamellipodia and growth cones of migrating cells and differentiating neurons (17, 18). Accumulating evidence indicates that exocyst subcomplexes, and their regulation by Ras and Rho family GTPases, also selectively participate in the assembly and activation of signal transduction events that mediate host defense, autophagy, cell growth, and oncogene signaling (19-23). An overarching implication is that the exocyst and its subcomplexes serve as physical platforms that coordinate organellar assembly with the activation of attendant regulatory cascades required for the execution of distinct cell biological programs.Here, we ...

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Section: Resultsmentioning

confidence: 96%

Role of the Exocyst Complex Component Sec6/8 in Genomic Stability

Torres

Pandita

Kulak

et al. 2015

Molecular and Cellular Biology

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“…Because the spindle checkpoint and cell cycle regulation are highly conserved between yeast and humans (15), we used synthetic genetic array (SGA) technology (16,17) to screen the haploid deletion MATa library (4,541 strains) for candidate genes whose deletion kills Mad2-overexpressing yeast cells. Deletion mutant strains carrying pGAL-MAD2 were spotted onto dextrose or galactose plates.…”

Section: Resultsmentioning

confidence: 99%

Synthetic genetic array screen identifies PP2A as a therapeutic target in Mad2-overexpressing tumors

Bian

Kitagawa

Bansal

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Significance The spindle checkpoint is required for proper chromosome segregation. Mitotic arrest deficiency 2 (Mad2), a component of the spindle checkpoint, is overexpressed in many cancer cells. This phenotype can be used to specifically kill Mad2-overexpressing tumor cells. Because the spindle checkpoint pathway is highly conserved between yeast and humans, we performed a screen to identify mutants in which Mad2 overexpression kills yeast cells. The screen revealed that Mad2 overexpression induced lethality in 13 gene deletions. Among the human homologs of the 13 candidate genes, a gene encoding protein phosphatase 2 (PP2A) significantly inhibited the growth of Mad2-overexpressing tumor cells. These results indicate that PP2A can be a specific therapeutic target in Mad2-overexpressing tumors.

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“…A resistant (R) cell response is distinguished from sensitivity (S). (Baryshnikova et al, 2010) indicating relatedness between ORFs YLR143w and YBR246w and diphthamide synthesis genes DPH1, DPH2, DPH4 and DPH5. (B) Phenotypic clustering (Carette et al, 2009) and phenotypic scores, in relation to dipthamide mutant dph1, between YBR246w and DPH5 genes as well as YLR143w and DPH4 suggest both ORFs to be related to DPH1 and to the diphthamide modification pathway.…”

Section: Posttranslational Biosynthesis Of Diphthamide On Ef2mentioning

confidence: 99%

“…Based on synthetic genetic interaction data deposited at the genetic interaction database (GID; University of Toronto, Canada) (Baryshnikova et al, 2010) and the significance of the phenotypic correlation scores, both budding yeast ORFs are predicted to have EF2-related functions (Fig. 9).…”

Section: Posttranslational Biosynthesis Of Diphthamide On Ef2mentioning

confidence: 99%