SCRaMbLEing of a Synthetic Yeast Chromosome with Clustered Essential Genes Reveals Synthetic Lethal Interactions

Genome-scale gene knockout is an important approach to the study of global genetic interactions. SCRaMbLEing of synthetic yeast chromosomes provides an efficient way to generate random deletion mutants. Here, we demonstrate the use of SCRaMbLE to explore synthetic lethal interactions. First, all essential genes of yeast chromosome III (chrIII) were clustered in a centromeric plasmid. We found that three types of reorganized clustered chrIII essential genes had similar transcriptional levels. Further, SCRaMbLEing of synthetic chromosome III (synIII) with supplementary clustered essential genes enables deletion of large chromosomal regions. Investigation of 141 SCRaMbLEd strains revealed varied deletion frequencies of synIII chromosomal regions. Among the no deletion detected regions, a hidden synthetic lethal interaction was revealed in the region of synIII 82-88 kb. This study shows that SCRaMbLE with clustered essential genes enhances streamlining of synthetic yeast chromosome and provides a novel strategy to uncover complex genetic interactions.