Mapping DNA damage-dependent genetic interactions in yeast via orgy mating and barcode fusion genetics

Diaz-Mejia, J. J.; Mellor, J. C.; Cote, A.; Balint, A.; Ho, B.; Bansal, P.; Shaeri, F.; Gebbia, M.; Weile, J.; Verby, M.; Karkhanina, A.; Zhang, Y.; Wong, C.; Rich, J.; Prendergast, D.; Gupta, G.; Ozturk, S.; Durocher, D.; Brown, G. W.; Roth, F. P.

doi:10.1101/181750

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Mapping DNA damage-dependent genetic interactions in yeast via orgy mating and barcode fusion genetics

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Abstract

Condition-dependent genetic interactions can reveal functional relationships between genes that are not evident under standard culture conditions. State-of-the-art yeast genetic interaction mapping, which relies on robotic manipulation of arrays of double mutant strains, does not scale readily to multi-condition studies. Here we describe Barcode Fusion Genetics to map Genetic Interactions (BFG-GI), by which double mutant strains generated via en masse party mating can also be monitored en masse for growth and genetic interactions. By using site-specific recombination to fuse two DNA barcodes, each representing a specific gene deletion, BFG-GI enables multiplexed quantitative tracking of double mutants via next-generation sequencing. We applied BFG-GI to a matrix of DNA repair genes under nine different conditions, including methyl methanesulfonate (MMS), 4-nitroquinoline 1-oxide (4NQO), bleomycin, zeocin, and three other DNA-damaging environments. BFG-GI recapitulated known genetic interactions and yielded new condition-dependent genetic interactions. We validated and further explored a subnetwork of condition-dependent genetic interactions involving MAG1, SLX4, and genes encoding the Shu complex, and inferred that loss of the Shu complex leads to a decrease in the activation or activity of the checkpoint protein kinase Rad53.

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Diaz-Mejia, J. J., Mellor, J. C., Cote, A., Balint, A., Ho, B., Bansal, P., Shaeri, F., Gebbia, M., Weile, J., Verby, M., Karkhanina, A., Zhang, Y., Wong, C., Rich, J., Prendergast, D., Gupta, G., Ozturk, S., Durocher, D., Brown, G. W., Roth, F. P.. 2017-08-31. Mapping DNA damage-dependent genetic interactions in yeast via orgy mating and barcode fusion genetics. https://doi.org/10.1101/181750

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