In a systematic genomics approach, we will produce a genetic interaction map for the model eukryotic cell, Saccharomyces cerevisiae. The completion of the genome sequence of S. cerevisiae led to the development of a complete and systematic set of """"""""Yeast KnockOut"""""""" mutations (the YKO collection). This study defined about 15% of yeast cells as being essential for growth. However, existing methods have not addressed two of the most important unanswered questions About eukaryotic genomes: 1) What pairs of genes interact in a cell? 2) What is the extent of functional redundancy? We know from haphazard small- scale analyses that there are many cases of duplicated genes in which neither single gene is essential, but the double mutant is lethal. Thus much more than 15% of the genome is likely to play an essential role. Also, the patterns of which gene pairs are essential in combination will provide crucial new information on the essential regulatory and metabolic pathways of eukaryotic cells. The proposed project will define genetic conditions under which many genes of known or unknown function are required for viability. Two general approaches will be used: one that generates double mutants using a high-throughput meiotic strategy with a growth readout, and one that generates them using a DNA-mediated transformation strategy with a growth readout, and one that generates them using a DNA-mediated transformation strategy using a microarray readout.. The synthetic lethal results we obtain will be made available through a database we develop. We will also identify or develop bioinformatic tools, as needed to analyze them these new types of data in the context of other gene properties, such as encoded protein similarity and known or proposed function. Similar tools are already available for analyzing two-hybrid interactions and their networks. As part of this effort, we will also make available physical resources that will support the screening of synthetic phenotypes other than lethality. These will enhance the ability of the research community to discover genetic interactions defined by criteria that provide focus on specific biological pathways. The ultimate goal is complete map (a """"""""wiring diagram"""""""" of all the genetic interactions of eukaryotic cells. Because yeast and human genes are often conserved in structure and function, many parts of this wiring diagram will be directly applicable to studies of human gene function and dysfunction.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG002432-02
Application #
6620766
Study Section
Genome Study Section (GNM)
Program Officer
Feingold, Elise A
Project Start
2002-02-06
Project End
2005-01-31
Budget Start
2003-02-01
Budget End
2004-01-31
Support Year
2
Fiscal Year
2003
Total Cost
$1,754,329
Indirect Cost
Name
Johns Hopkins University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21218
Darby, Miranda M; Serebreni, Leo; Pan, Xuewen et al. (2012) The Saccharomyces cerevisiae Nrd1-Nab3 transcription termination pathway acts in opposition to Ras signaling and mediates response to nutrient depletion. Mol Cell Biol 32:1762-75
Pan, Xuewen; Reissman, Stefanie; Douglas, Nick R et al. (2010) Trivalent arsenic inhibits the functions of chaperonin complex. Genetics 186:725-34
Li, Fuyang; Dong, Junchao; Pan, Xuewen et al. (2008) Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates. Mol Cell 30:325-35
Lin, Yu-yi; Qi, Yan; Lu, Jin-ying et al. (2008) A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Genes Dev 22:2062-74
Peyser, Brian D; Irizarry, Rafael; Spencer, Forrest A (2008) Statistical analysis of fitness data determined by TAG hybridization on microarrays. Methods Mol Biol 416:369-81
Meluh, Pamela B; Pan, Xuewen; Yuan, Daniel S et al. (2008) Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray. Methods Mol Biol 416:221-47
Pan, Xuewen; Yuan, Daniel S; Ooi, Siew-Loon et al. (2007) dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. Methods 41:206-21
Zurita-Martinez, Sara A; Puria, Rekha; Pan, Xuewen et al. (2007) Efficient Tor signaling requires a functional class C Vps protein complex in Saccharomyces cerevisiae. Genetics 176:2139-50
Yuan, Daniel S; Irizarry, Rafael A (2006) High-resolution spatial normalization for microarrays containing embedded technical replicates. Bioinformatics 22:3054-60
Pan, Xuewen; Ye, Ping; Yuan, Daniel S et al. (2006) A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124:1069-81

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