title: Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray.
abstract: Comprehensive collections of open reading frame (ORF) deletion mutant strains exist for the budding yeast Saccharomyces cerevisiae. With great prescience, these strains were designed with short molecular bar codes or TAGs that uniquely mark each deletion allele, flanked by shared priming sequences. These features have enabled researchers to handle yeast mutant collections as complex pools of approximately 6000 strains. The presence of any individual mutant within a pool can be assessed indirectly by measuring the relative abundance of its corresponding TAG(s) in genomic DNA prepared from the pool. This is readily accomplished by wholesale polymerase chain reaction (PCR) amplification of the TAGs using fluorescent oligonucleotide primers that recognize the common flanking sequences, followed by hybridization of the labeled PCR products to a TAG oligonucleotide microarray. Here we describe a method-diploid-based synthetic lethality analysis by microarray (dSLAM)-whereby such pools can be manipulated to rapidly construct and assess the fitness of 6000 double-mutant strains in a single experiment. Analysis of double-mutant strains is of growing importance in defining the spectrum of essential cellular functionalities and in understanding how these functionalities interrelate.
authors.affiliation: Department of Molecular Biology and Genetics, The High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors.forename: Pamela B
authors.initials: PB
authors.lastname: Meluh
authors.forename: Xuewen
authors.initials: X
authors.lastname: Pan
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Yuan
authors.forename: Carol
authors.initials: C
authors.lastname: Tiffany
authors.forename: Ou
authors.initials: O
authors.lastname: Chen
authors.forename: Sharon
authors.initials: S
authors.lastname: Sookhai-Mahadeo
authors.forename: Xiaoling
authors.initials: X
authors.lastname: Wang
authors.forename: Brian D
authors.initials: BD
authors.lastname: Peyser
authors.forename: Rafael
authors.initials: R
authors.lastname: Irizarry
authors.forename: Forrest A
authors.initials: FA
authors.lastname: Spencer
authors.forename: Jef D
authors.initials: JD
authors.lastname: Boeke
mesh_terms: D017353:Gene Deletion; D020869:Gene Expression Profiling / Q000379:methods; D015966:Gene Expression Regulation, Fungal / Q000235:genetics / Q000502:physiology*; D005804:Genes, Lethal; D016681:Genome, Fungal; D009154:Mutation / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics*