Dead-Seq: Discovering Synthetic Lethal Interactions from Dead Cells Genomics

Abstract

Pooled genetic screens have revolutionized the field of functional genomics, yet perturbations that decrease fitness, such as those leading to synthetic lethality, have remained difficult to quantify at the genomic level. We and colleagues previously developed "death screening," a protocol based on the purification of dead cells in genetic screens, and used it to identify a set of genes necessary for mitochondrial gene expression, translation, and oxidative phosphorylation (OXPHOS), thus offering new possibilities for the diagnosis of mitochondrial disorders. Here, we describe Dead-Seq, a refined protocol for death screening that is compatible with most pooled screening protocols, including genome-wide CRISPR/Cas9 screening. Dead-Seq converts negative-selection screens into positive-selection screens and generates high-quality data directly from dead cells, at limited sequencing costs.

Keywords: Annexin V; Apoptosis; Auxotrophy; Drop-out screen; Galactose; Genome-wide screening; MACS; Metabolism; Mitochondria; Mitochondrial translation; Necroptosis; ORFeome; RNAi; Synthetic lethality; Systems genetics; sgRNA; shRNA.