Synthetic Genetic Array analysis (SGA) is a
high-throughputHigh-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 lethalSynthetic lethality and Synthetic Sickness refer to a genetic interaction where two separate strains with viable mutations result in reduced or no growth when combined in a double mutant containing both....
and synthetic sick genetic interactions (
SSLSynthetic lethality and Synthetic Sickness refer to a genetic interaction where two separate strains with viable mutations result in reduced or no growth when combined in a double mutant containing both....
) . SGA allows for the systematic construction of double mutants using a combination of
recombinant genetic techniquesRecombinant DNA is a form of DNA that does not exist naturally, which is created by combining DNA sequences that would not normally occur together...
, mating and selection steps. Using SGA methodology a query gene deletion mutant can be crossed to an entire genome deletion set to identify any
SSLSynthetic lethality and Synthetic Sickness refer to a genetic interaction where two separate strains with viable mutations result in reduced or no growth when combined in a double mutant containing both....
interactions, yielding functional information of the query gene and the genes it interacts with.
Synthetic Genetic Array analysis (SGA) is a
high-throughputHigh-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 lethalSynthetic lethality and Synthetic Sickness refer to a genetic interaction where two separate strains with viable mutations result in reduced or no growth when combined in a double mutant containing both....
and synthetic sick genetic interactions (
SSLSynthetic lethality and Synthetic Sickness refer to a genetic interaction where two separate strains with viable mutations result in reduced or no growth when combined in a double mutant containing both....
) . SGA allows for the systematic construction of double mutants using a combination of
recombinant genetic techniquesRecombinant DNA is a form of DNA that does not exist naturally, which is created by combining DNA sequences that would not normally occur together...
, mating and selection steps. Using SGA methodology a query gene deletion mutant can be crossed to an entire genome deletion set to identify any
SSLSynthetic lethality and Synthetic Sickness refer to a genetic interaction where two separate strains with viable mutations result in reduced or no growth when combined in a double mutant containing both....
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. Methodology has since been developed to allow SGA analysis in
S.pombeSchizosaccharomyces 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 is crossed systematically with a deletion mutant array (DMA) containing every viable knockout
ORFIn molecular genetics, an open reading frame is a portion of an organism's genome which contains a sequence of bases that could potentially encode a protein. The start-points and end-points of a given ORF are not equivalent to the ends of the messenger RNA , but the ends of the ORF are usually...
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.
Robotics
Due to the large number of precise replication steps in SGA analysis, robots are widely used to perform the colony manipulations. There are a few systems specifically designed for SGA analysis which greatly decrease the time to analyse a query gene. Generally these have a series of pins which are used to transfer cells to and from plates, with one system utilizing disposable pads of pins to eliminate washing cycles.