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Genomic profiling of drug sensitivities via induced haploinsufficiency

Abstract

Lowering the dosage of a single gene from two copies to one copy in diploid yeast results in a heterozygote that is sensitized to any drug that acts on the product of this gene. This haploinsufficient phenotype thereby identifies the gene product of the heterozygous locus as the likely drug target. We exploited this finding in a genomic approach to drug-target identification. Genome sequence information was used to generate molecularly tagged heterozygous yeast strains that were pooled, grown competitively in drug and analysed for drug sensitivity using high-density oligonucleotide arrays. Individual heterozygous strain analysis verified six known drug targets. Parallel analysis identified the known target and two hypersensitive loci in a mixed culture of 233 strains in the presence of the drug tunicamycin. Our discovery that both drug target and hypersensitive loci exhibit drug-induced haploinsufficiency may have important consequences in pharmacogenomics and variable drug toxicity observed in human populations.

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Figure 1: Tunicamycin sensitivity of alg7/ALG7.
Figure 2: Benomyl sensitivity of tub1/TUB1.
Figure 3: Heterozygote deletion construct.
Figure 4: Growth of 12 heterozygous strains in 0.
Figure 5: Tunicamycin sensitivity profiling for 233 heterozygous yeast strains.
Figure 6: Halo assays of tunicamycin-sensitive strains.

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Acknowledgements

We thank Affymetrix for their help with all aspects of the oligonucleotide array technology used here. Specifically, M. Mittmann and D. Morris for oligonucleotide selection and chip design; E. Gentalen for array synthesis; and D. Lockhart for helpful discussions. We thank C. Nislow and I. Herskowitz for critical reading and helpful comments on the manuscript and all members of the S. cerevisiae Deletion Consortium for their efforts. Supported by a grant from Rhone-Poulenc Rorer and NIH grant H600198.

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Correspondence to Guri Giaever.

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Giaever, G., Shoemaker, D., Jones, T. et al. Genomic profiling of drug sensitivities via induced haploinsufficiency . Nat Genet 21, 278–283 (1999). https://doi.org/10.1038/6791

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