Mapping the Genetic Landscape of Human Cells

Seminal yeast studies have established the value of comprehensively mapping genetic interactions (GIs) for inferring gene function. Efforts in human cells using focused gene sets underscore the utility of this approach, but the feasibility of generating large-scale, diverse human GI maps remains unresolved. We developed a CRISPR interference platform for large-scale quantitative mapping of human GIs. We systematically perturbed 222,784 gene pairs in two cancer cell lines. The resultant maps cluster functionally related genes, assigning function to poorly characterized genes, including TMEM261, a new electron transport chain component. Individual GIs pinpoint unexpected relationships between pathways, exemplified by a specific cholesterol biosynthesis intermediate whose accumulation induces deoxynucleotide depletion, causing replicative DNA damage and a synthetic-lethal interaction with the ATR/9-1-1 DNA repair pathway. Our map provides a broad resource, establishes GI maps as a high-resolution tool for dissecting gene function, and serves as a blueprint for mapping the genetic landscape of human cells. [Display omitted] •Genetic interaction (GI) mapping enables elucidation of human gene function•Large-scale, diverse maps of 222,784 gene pairs reveal buffering and synthetic GIs•Clustering of GIs identifies novel members of functional complexes•Specific GIs can define the physiological impact of biosynthetic metabolites A large-scale genetic interaction map in human cells reveals unexpected interdependencies between core pathways and exposes potential combination therapies for cancer.