Trigenic Synthetic Genetic Array (τ-SGA) Technique for Complex Interaction Analysis

Rapid, scalable, combinatorial genome engineering by marker-less enrichment and recombination of genetically engineered loci in yeast

A major challenge to rationally building multi-gene processes in yeast arises due to the combinatorics of combining all of the individual edits into the same strain. Here, we present a precise and multi-site genome editing approach that combines all edits without selection markers using CRISPR-Cas9. We demonstrate a highly efficient gene drive that selectively eliminates specific loci by integrating CRISPR-Cas9-mediated double-strand break (DSB) generation and homology-directed recombination with yeast sexual assortment. The method enables marker-less enrichment and recombination of genetically engineered loci (MERGE). We show that MERGE converts single heterologous loci to homozygous loci at ∼100% efficiency, independent of chromosomal location. Furthermore, MERGE is equally efficient at converting and combining multiple loci, thus identifying compatible genotypes. Finally, we establish MERGE proficiency by engineering a fungal carotenoid biosynthesis pathway and most of the human α-proteasome core into yeast. Therefore, MERGE lays the foundation for scalable, combinatorial genome editing in yeast.

Synthetic lethal gene pairs: Experimental approaches and predictive models

Synthetic lethality (SL) refers to a genetic interaction in which the simultaneous perturbation of two genes leads to cell or organism death, whereas viability is maintained when only one of the pair is altered. The experimental exploration of these pairs and predictive modeling in computational biology contribute to our understanding of cancer biology and the development of cancer therapies. We extensively reviewed experimental technologies, public data sources, and predictive models in the study of synthetic lethal gene pairs and herein detail biological assumptions, experimental data, statistical models, and computational schemes of various predictive models, speculate regarding their influence on individual sample- and population-based synthetic lethal interactions, discuss the pros and cons of existing SL data and models, and highlight potential research directions in SL discovery.