iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast.
Systematic screens for genetic interactions are a cornerstone of both network and systems biology. However, most screens have been limited to characterizing interaction networks in a single environment. Moving beyond this static view of the cell requires a major technological advance to increase the throughput and ease of replication in these assays. Here, we introduce iSeq-a platform to build large double barcode libraries and rapidly assay genetic interactions across environments. We use iSeq in yeast to measure fitness in three conditions of nearly 400 clonal strains, representing 45 possible single or double gene deletions, including multiple replicate strains per genotype. We show that iSeq fitness and interaction scores are highly reproducible for the same clonal strain across replicate cultures. However, consistent with previous work, we find that replicates with the same putative genotype have highly variable genetic interaction scores. By whole-genome sequencing 102 of our strains, we find that segregating variation and de novo mutations, including aneuploidy, occur frequently during strain construction, and can have large effects on genetic interaction scores. Additionally, we uncover several new environment-dependent genetic interactions, suggesting that barcode-based genetic interaction assays have the potential to significantly expand our knowledge of genetic interaction networks.
Department of Genetics, Stanford School of Medicine, California 94305.
Mia
0000-0002-0836-2458
M
Jaffe
Department of Genetics, Stanford School of Medicine, California 94305.
Gavin
0000-0002-1692-4983
G
Sherlock
The Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York 11794 sasha.levy@stonybrook.edu.|Department of Biochemistry & Cell Biology, Stony Brook University, New York 11794.
Sasha F
0000-0002-0923-1636
SF
Levy
D000782:Aneuploidy; D004843:Epistasis, Genetic; D015966:Gene Expression Regulation, Fungal / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics*; D059647:Gene-Environment Interaction; D005838:Genotype; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D049490:Systems Biology / Q000379:methods*
DNA barcoding; Saccharomyces cerevisiae; genetic interactions; systems biology; whole genome sequencing