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Genome-wide mapping of unexplored essential regions in the Saccharomyces cerevisiae genome: evidence for hidden synthetic lethal combinations in a genetic interaction network.

Kaboli S, Yamakawa T, Sunada K, Takagaki T, Sasano Y, Sugiyama M, Kaneko Y, Harashima S - Nucleic Acids Res. (2014)

Bottom Line: Fifty-six of the 67 regions were found to be essential for cell growth, and 49 of these carried co-lethal gene pair(s) that were not previously been detected by synthetic genetic array analysis.This result implies that regions harboring only non-essential genes contain unidentified synthetic lethal combinations at an unexpectedly high frequency, revealing a novel landscape of genetic interactions in the S. cerevisiae genome.Furthermore, this study indicates that segmental deletion might be exploited for not only revealing genome function but also breeding stress-tolerant strains.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan.

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Related in: MedlinePlus

Genome-wide mapping of deletable and undeletable regions among 110 targeted chromosomal regions. Each chromosome is represented by a gray line with the centromere shown as a black solid circle. The chromosomal lengths are drawn to scale. Based on an SGD survey, these 110 regions were selected as having at least 9 non-essential genes. The distribution of 33 deletable and 77 undeletable regions among the 110 target regions, as identified by PCD, are indicated as blue and red horizontal filled bars, respectively.
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Figure 1: Genome-wide mapping of deletable and undeletable regions among 110 targeted chromosomal regions. Each chromosome is represented by a gray line with the centromere shown as a black solid circle. The chromosomal lengths are drawn to scale. Based on an SGD survey, these 110 regions were selected as having at least 9 non-essential genes. The distribution of 33 deletable and 77 undeletable regions among the 110 target regions, as identified by PCD, are indicated as blue and red horizontal filled bars, respectively.

Mentions: To present the results in a comprehensive way, we included 1 confirmed essential region (13) and 14 confirmed non-essential regions (13,14,17,23) in the genome-wide mapping and screening. We also included three regions that were confirmed to be deletable during a prior pilot study. Karyotype analysis and phenotypic characteristics of these 18 derivatives are not shown here. Across the whole S. cerevisiae genome, 110 regions varying in content from 9 non-essential genes in the smallest region to 47 non-essential genes in the largest region and an average of 20 non-essential genes were identified (Figure 1 and Table 2).


Genome-wide mapping of unexplored essential regions in the Saccharomyces cerevisiae genome: evidence for hidden synthetic lethal combinations in a genetic interaction network.

Kaboli S, Yamakawa T, Sunada K, Takagaki T, Sasano Y, Sugiyama M, Kaneko Y, Harashima S - Nucleic Acids Res. (2014)

Genome-wide mapping of deletable and undeletable regions among 110 targeted chromosomal regions. Each chromosome is represented by a gray line with the centromere shown as a black solid circle. The chromosomal lengths are drawn to scale. Based on an SGD survey, these 110 regions were selected as having at least 9 non-essential genes. The distribution of 33 deletable and 77 undeletable regions among the 110 target regions, as identified by PCD, are indicated as blue and red horizontal filled bars, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150759&req=5

Figure 1: Genome-wide mapping of deletable and undeletable regions among 110 targeted chromosomal regions. Each chromosome is represented by a gray line with the centromere shown as a black solid circle. The chromosomal lengths are drawn to scale. Based on an SGD survey, these 110 regions were selected as having at least 9 non-essential genes. The distribution of 33 deletable and 77 undeletable regions among the 110 target regions, as identified by PCD, are indicated as blue and red horizontal filled bars, respectively.
Mentions: To present the results in a comprehensive way, we included 1 confirmed essential region (13) and 14 confirmed non-essential regions (13,14,17,23) in the genome-wide mapping and screening. We also included three regions that were confirmed to be deletable during a prior pilot study. Karyotype analysis and phenotypic characteristics of these 18 derivatives are not shown here. Across the whole S. cerevisiae genome, 110 regions varying in content from 9 non-essential genes in the smallest region to 47 non-essential genes in the largest region and an average of 20 non-essential genes were identified (Figure 1 and Table 2).

Bottom Line: Fifty-six of the 67 regions were found to be essential for cell growth, and 49 of these carried co-lethal gene pair(s) that were not previously been detected by synthetic genetic array analysis.This result implies that regions harboring only non-essential genes contain unidentified synthetic lethal combinations at an unexpectedly high frequency, revealing a novel landscape of genetic interactions in the S. cerevisiae genome.Furthermore, this study indicates that segmental deletion might be exploited for not only revealing genome function but also breeding stress-tolerant strains.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan.

Show MeSH
Related in: MedlinePlus