Exploring the conservation of synthetic lethal genetic interaction networks

Communicative and Integrative Biology

Volumn 2, Issue 2, 2009, Pages 78-81

  Dixon, Scott J ^a,b   Andrews, Brenda J ^a   Boone, Charles ^a  

^a UNIVERSITY OF TORONTO   (Canada)

^b Howard Hughes Medical Institute   (United States)

Author keywords

Cerevisiae; Comparative genomics; Pombe; SGA; Synthetic lethal

Indexed keywords

EUKARYOTA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES; SCHIZOSACCHAROMYCES POMBE; SCHIZOSACCHAROMYCETACEAE;

EID: 67650646092     PISSN: None     EISSN: 19420889     Source Type: Journal    
DOI: 10.4161/cib.7501     Document Type: Article

References (36)

1. Haarer B, Viggiano S, Hibbs MA, Troyanskaya OG, Amberg DC. Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies. Genes Dev 2007; 21:148-59.
2. Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, et al. Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell 2006; 21:319-30.
3. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Pagé N, et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 2001; 294:2364-8.
4. Lehner B, Crombie C, Tischler J, Fortunato A, Fraser AG. Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways. Nat Genet 2006; 38:896-903.
5. Byrne AB, Weirauch MT, Wong V, Koeva M, Dixon SJ, Stuart JM, et al. A global analysis of genetic interactions in Caenorhabditis elegans. J Biol 2007; 6:8.
6. Davierwala AP, Haynes J, Li Z, Brost RL, Robinson MD, Yu L, et al. The synthetic genetic interaction spectrum of essential genes. Nat Genet 2005; 37:1147-52.
7. Boone C, Bussey H, Andrews BJ. Exploring genetic interactions and networks with yeast. Nat Rev Genet 2007; 8:437-49.
8. Phillips PC. Epistasis-the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 2008; 9:855-67.
9. Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, et al. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 2007; 446:806-10.
10. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, et al. Global mapping of the yeast genetic interaction network. Science 2004; 303:808-13.
11. Setty SR, Strochlic TI, Tong AH, Boone C, Burd CG. Golgi targeting of ARF-like GTPase Arl3p requires its Nalpha-acetylation and the integral membrane protein Sys1p. Nat Cell Biol 2004; 6:414-9.
12. Mayer ML, Pot I, Chang M, Xu H, Aneliunas V, Kwok T. Identification of protein complexes required for efficient sister chromatid cohesion. Mol Biol Cell 2004; 15:1736-45.
13. Chang M, Bellaoui M, Zhang C, Desai R, Morozov P, Delgado-Cruzata L, et al. RMI1/NCE4, a suppressor of genome instability, encodes a member of the RecQ helicase/Topo III complex. EMBO J 2005; 24:2024-33.
14. Hurto RL, Tong AH, Boone C, Hopper AK. Inorganic phosphate deprivation causes tRNA nuclear accumulation via retrograde transport in Saccharomyces cerevisiae. Genetics 2007; 176:841-52.
15. Pan X, Yuan DS, Xiang D, Wang X, Sookhai-Mahadeo S, Bader JS, et al. A robust toolkit for functional profiling of the yeast genome. Mol Cell 2004; 16:487-96.
16. Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, Punna T, et al. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 2005; 123:507-19.
17. Decourty L, Saveanu C, Zemam K, Hantraye F, Frachon E, Rousselle JC, et al. Linking functionally related genes by sensitive and quantitative characterization of genetic interaction profiles. Proc Natl Acad Sci USA 2008; 105:5821-6.
18. Dixon SJ, Fedyshyn Y, Koh JL, Prasad TS, Chahwan C, Chua G, et al. Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci USA 2008; 105:16653-8.
19. Collins SR, Schuldiner M, Krogan NJ, Weissman JS. A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol 2006; 7:63.
20. Mani R, St. Onge RP, Hartman JLt, Giaever G, Roth FP. Defining genetic interaction. Proc Natl Acad Sci USA 2008; 105:3461-6.
21. St. Onge RP, Mani R, Oh J, Proctor M, Fung E, Davis RW, et al. Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nat Genet 2007; 39:199-206.
22. Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, et al. High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods 2008; 5:781-7.
23. Butland G, Babu M, Díaz-Mejía JJ, Bohdana F, Phanse S, Gold B, et al. eSGA: E. coli synthetic genetic array analysis. Nat Methods 2008; 5:789-95.
24. Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, et al. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 2008; 322:405-10.
25. Roguev A, Wiren M, Weissman JS, Krogan NJ. High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe. Nat Methods 2007; 4:861-6.
26. Sharan R, Ideker T. Modeling cellular machinery through biological network comparison. Nat Biotechnol 2006; 24:427-33.
27. Kiemer L, Cesareni G. Comparative interactomics: comparing apples and pears? Trends Biotechnol 2007; 25:448-54.
28. Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, et al. The genome sequence of Schizosaccharomyces pombe. Nature 2002; 415:871-80.
29. Tischler J, Lehner B, Fraser AG. Evolutionary plasticity of genetic interaction networks. Nat Genet 2008; 40:390-1.
30. Tarailo M, Tarailo S, Rose AM. Synthetic lethal interactions identify phenotypic "interologs" of the spindle assembly checkpoint components. Genetics 2007; 177:2525-30.
31. Hedges SB. The origin and evolution of model organisms. Nat Rev Genet 2002; 3:838-49.
32. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, et al. The BioGRID Interaction Database: 2008 update. Nucleic Acids Res 2008; 36:637-40.
33. Decottignies A, Sanchez-Perez I, Nurse P. Schizosaccharomyces pombe essential genes: a pilot study. Genome Res 2003; 13:399-406.
34. Harrison R, Papp B, Pal C, Oliver SG, Delneri D. Plasticity of genetic interactions in metabolic networks of yeast. Proc Natl Acad Sci USA 2007; 104:2307-12.
35. Stuart JM, Segal E, Koller D, Kim SK. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003; 302:249-55.
36. Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, et al. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 2006; 38:285-93.