A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation

• Published in: Cell metabolism Vol. 24; no. 6; pp. 875 - 885
• Main Authors: Arroyo, Jason D., Jourdain, Alexis A., Calvo, Sarah E., Ballarano, Carmine A., Doench, John G., Root, David E., Mootha, Vamsi K.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 13-12-2016
• Subjects: 16S RNA; Cell Death - drug effects; Cell Death - genetics; Clustered Regularly Interspaced Short Palindromic Repeats - genetics; CRISPR; death screen; Galactose - pharmacology; Genes, Mitochondrial; Genome; Glucose - pharmacology; HEK293 Cells; HeLa Cells; Humans; K562 Cells; Mitochondria; Mitochondria - drug effects; Mitochondria - metabolism; mitochondrial ribosome; neugrin; Oxidative Phosphorylation; OXPHOS; Phenotype; Protein Biosynthesis - drug effects; pseudouridine; pseudouridylation; Reproducibility of Results; RNA, Ribosomal, 16S - genetics; synthetic lethality; CRISPR; Mitochondria; death screen; neugrin; synthetic lethality; OXPHOS; pseudouridylation; pseudouridine; 16S RNA; mitochondrial ribosome
• ISSN: 1550-4131; 1932-7420
• DOI: 10.1016/j.cmet.2016.08.017

Oxidative phosphorylation (OXPHOS) is the major pathway for ATP production in humans. Deficiencies in OXPHOS can arise from mutations in either mitochondrial or nuclear genomes and comprise the largest collection of inborn errors of metabolism. At present we lack a complete catalog of human genes and pathways essential for OXPHOS. Here we introduce a genome-wide CRISPR “death screen” that actively selects dying cells to reveal human genes required for OXPHOS, inspired by the classic observation that human cells deficient in OXPHOS survive in glucose but die in galactose. We report 191 high-confidence hits essential for OXPHOS, including 72 underlying known OXPHOS diseases. Our screen reveals a functional module consisting of NGRN, WBSCR16, RPUSD3, RPUSD4, TRUB2, and FASTKD2 that regulates the mitochondrial 16S rRNA and intra-mitochondrial translation. Our work yields a rich catalog of genes required for OXPHOS and, more generally, demonstrates the power of death screening for functional genomic analysis.
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•Death screening is a new method that actively selects and sequences dead cells•A high-quality catalog of genes essential for human OXPHOS is reported•NGRN, WBSCR16, RPUSD3, RPUSD4, TRUB2, and FASTKD2 form a 16S rRNA regulatory module
Arroyo et al. introduce CRISPR “death screening” and apply it to systematically identify human genes essential for oxidative phosphorylation. Among the hits, they reveal how five new genes encode a functional module that regulates mitochondrial 16S rRNA and intra-mitochondrial translation.