Linking functionally related genes by sensitive and quantitative characterization of genetic interaction profiles

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 15, 2008, Pages 5821-5826

  Decourty, Laurence ^a   Saveanu, Cosmin ^a   Zemam, Kenza ^a   Hantraye, Florence ^a   Frachon, Emmanuel ^b   Rousselle, Jean Claude ^c   Fromont Racine, Micheline ^a   Jacquier, Alain ^a  

^a CNRS   (France)

^b Plate Forme de Production de Protéines Recombinantes et d'Anticorps   (France)

^c Plate Forme Protéomique   (France)

Author keywords

Epistasis; Functional genomics; Genetic screen; mRNA decapping; Saccharomyces cerevisiae

Indexed keywords

ARTICLE; FUNCTIONAL GENOMICS; FUNGAL STRAIN; GENE CLUSTER; GENE DELETION; GENE INTERACTION; GENE MAPPING; GENE MUTATION; GENETIC EPISTASIS; GENETIC LINKAGE; GENETIC SCREENING; GENOTYPE; MOLECULAR PHYLOGENY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; RNA DEGRADATION; RNA INTERFERENCE; SACCHAROMYCES CEREVISIAE;

GENE LIBRARY; GENE REGULATORY NETWORKS; GENES, FUNGAL; GENOME, FUNGAL; MUTATION; SACCHAROMYCES CEREVISIAE; YEASTS;

SACCHAROMYCES CEREVISIAE;

EID: 44449135980     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0710533105     Document Type: Article

References (25)

1. Tong AH, et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294:2364-2368.
2. Ooi SL, Shoemaker DD, Boeke JD (2003) DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. Nat Genet 35:277-286.
3. Pan X, et al. (2004) A robust toolkit for functional profiling of the yeast genome. Mol Cell 16:487-496.
4. Tong AH, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303:808-813.
5. Collins SR, et al. (2007) Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446:806-810.
6. Segre D, Deluna A, Church GM, Kishony R (2005) Modular epistasis in yeast metabolism. Nat Genet 37:77-83.
7. Schuldiner M, et al. (2005) Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123:507-519.
8. Winzeler EA, et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901-906.
9. Frachon E, Bondet V, Munier-Lehmann H, Bellalou J (2006) Multiple microfermentor battery: A versatile tool for use with automated parallel cultures of microorganisms producing recombinant proteins and for optimization of cultivation protocols. Appl Environ Microbiol 72:5225-5231.
10. Kshirsagar M, Parker R (2004) Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces cerevisiae. Genetics 166:729-739.
11. Badis G, Saveanu C, Fromont-Racine M, Jacquier A (2004) Targeted mRNA degradation by deadenylation-independent decapping. Mol Cell 15:5-15.
12. Dong S, et al. (2007) YRA1 autoregulation requires nuclear export and cytoplasmic Edc3p-mediated degradation of its pre-mRNA. Mol Cell 25:559-573.
13. Fleischer TC, et al. (2006) Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Genes Dev 20:1294-1307.
14. Anantharaman V, Aravind L (2004) Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability. BMC Genomics 5:45.
15. Albrecht M, Lengauer T (2004) Novel Sm-like proteins with long C-terminal tails and associated methyltransferases. FEBS Lett 569:18-26.
16. Muhlrad D, Parker R (2005) The yeast EDC1 mRNA undergoes deadenylation-independent decapping stimulated by Not2p, Not4p, and Not5p. EMBO J 24:1033-1045.
17. Rigaut G, et al. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17:1030-1032.
18. Barbee SA, et al. (2006) Staufen- and FMRP-containing neuronal RNPs are structurally and functionally related to somatic P bodies. Neuron 52:997-1009.
19. Decker CJ, Parker R (1993) A turnover pathway for both stable and unstable mRNAs in yeast: evidence for a requirement for deadenylation. Genes Dev 7:1632-1643.
20. Anderson JS, Parker RP (1998) The 3′ to 5′ degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3′ to 5′ exonucleases of the exosome complex. EMBO J 17:1497-1506.
21. Collins SR, et al. (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 6:439-450.
22. Myers CL, et al. (2006) Finding function: evaluation methods for functional genomic data. BMC Genomics 7:187.
23. Berger AB, et al. (2007) Hmo1 is required for TOR-dependent regulation of ribosomal protein gene transcription. Mol Cell Biol 27:8015-8026.
24. Stark C, et al. (2006) BioGRID: A general repository for interaction datasets. Nucleic Acids Res 34:D535-D539.
25. Belli G, et al. (1998) An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast. Nucleic Acids Res 26:942-947.