Synthetic genetic array
Encyclopedia
Synthetic Genetic Array analysis (SGA) is a high-throughput
technique for exploring synthetic lethal
and synthetic sick genetic interactions (SSL
) . SGA allows for the systematic construction of double mutants using a combination of recombinant genetic techniques
, mating and selection steps. Using SGA methodology a query gene deletion mutant can be crossed to an entire genome deletion set to identify any SSL
interactions, yielding functional information of the query gene and the genes it interacts with. A large-scale application of SGA in which ~130 query genes were crossed to the set of ~5000 viable deletion mutants in yeast revealed a genetic network containing ~1000 genes and ~4000 SSL interactions . The results of this study showed that genes with similar function tend to interact with one another and genes with similar patterns of genetic interactions often encode products that tend to work in the same pathway or complex. Synthetic Genetic Array analysis was initially developed using the model organism S.cerevisiae. This method has since been extended to cover 30% of the S.cerevisiea genome . Methodology has since been developed to allow SGA analysis in S.pombe
and E.coli .
of the yeast genome (currently 4786 strains). The resulting diploids are then sporulated by transferring to a media containing reduced nitrogen. The haploid progeny are then put through a series of selection platings and incubations to select for double mutants. The double mutants are screened for SSL interactions visually or using imaging software by assessing the size of the resulting colonies.
High-throughput
High-throughput may refer to:* High-throughput computing - a computer science concept * High-throughput screening - a bioinformatics concept* Measuring data throughput - a communications concept...
technique for exploring synthetic lethal
Synthetic lethality
Synthetic lethality arises when a combination of mutations in two or more genes leads to cell death, whereas a mutation in only one of these genes does not, and by itself is said to be viable In a synthetic lethal genetic screen, it is necessary to begin with a mutation that does not kill the cell,...
and synthetic sick genetic interactions (SSL
Synthetic lethality
Synthetic lethality arises when a combination of mutations in two or more genes leads to cell death, whereas a mutation in only one of these genes does not, and by itself is said to be viable In a synthetic lethal genetic screen, it is necessary to begin with a mutation that does not kill the cell,...
) . SGA allows for the systematic construction of double mutants using a combination of recombinant genetic techniques
Recombinant DNA
Recombinant DNA molecules are DNA sequences that result from the use of laboratory methods to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in biological organisms...
, mating and selection steps. Using SGA methodology a query gene deletion mutant can be crossed to an entire genome deletion set to identify any SSL
Synthetic lethality
Synthetic lethality arises when a combination of mutations in two or more genes leads to cell death, whereas a mutation in only one of these genes does not, and by itself is said to be viable In a synthetic lethal genetic screen, it is necessary to begin with a mutation that does not kill the cell,...
interactions, yielding functional information of the query gene and the genes it interacts with. A large-scale application of SGA in which ~130 query genes were crossed to the set of ~5000 viable deletion mutants in yeast revealed a genetic network containing ~1000 genes and ~4000 SSL interactions . The results of this study showed that genes with similar function tend to interact with one another and genes with similar patterns of genetic interactions often encode products that tend to work in the same pathway or complex. Synthetic Genetic Array analysis was initially developed using the model organism S.cerevisiae. This method has since been extended to cover 30% of the S.cerevisiea genome . Methodology has since been developed to allow SGA analysis in S.pombe
Schizosaccharomyces pombe
Schizosaccharomyces pombe, also called "fission yeast", is a species of yeast. It is used as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically measure 3 to 4 micrometres in diameter and 7 to 14 micrometres in length...
and E.coli .
Background
Synthetic Genetic Array analysis was initially developed by Tong et al. in 2001 and has since been used by many groups working in a wide range of biomedical fields. SGA utilizes the entire genome yeast knock-out set created by the yeast genome deletion project .Synthetic genetic array analysis general procedure
Synthetic Genetic Array analysis is generally conducted using colony arrays on petriplates at standard densities (96, 384, 768, 1536). To perform a SGA analysis in S.cerevisae, the query gene deletion is crossed systematically with a deletion mutant array (DMA) containing every viable knockout ORFOpen reading frame
In molecular genetics, an open reading frame is a DNA sequence that does not contain a stop codon in a given reading frame.Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop...
of the yeast genome (currently 4786 strains). The resulting diploids are then sporulated by transferring to a media containing reduced nitrogen. The haploid progeny are then put through a series of selection platings and incubations to select for double mutants. The double mutants are screened for SSL interactions visually or using imaging software by assessing the size of the resulting colonies.