Mapping the Genetic Landscape of Human Cells.

Cell (2018-07-24)
Max A Horlbeck, Albert Xu, Min Wang, Neal K Bennett, Chong Y Park, Derek Bogdanoff, Britt Adamson, Eric D Chow, Martin Kampmann, Tim R Peterson, Ken Nakamura, Michael A Fischbach, Jonathan S Weissman, Luke A Gilbert
ABSTRACT

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.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Acetonitrile, anhydrous, 99.8%
Sigma-Aldrich
Adenosine 5′-triphosphate disodium salt hydrate, Grade I, ≥99%, from microbial
Sigma-Aldrich
Monoclonal Anti-β-Actin antibody produced in mouse, clone AC-15, ascites fluid
Sigma-Aldrich
Guanosine 5′-triphosphate sodium salt hydrate, ≥95% (HPLC), powder
Sigma-Aldrich
Cytidine 5′-triphosphate disodium salt, ≥95%
Sigma-Aldrich
Uridine 5′-triphosphate trisodium salt hydrate, from yeast, Type III, ≥96%
Sigma-Aldrich
Thymidine 5′-triphosphate sodium salt, ≥96%
Sigma-Aldrich
2′-Deoxyadenosine 5′-triphosphate disodium salt, ≥97%
Sigma-Aldrich
2′-Deoxycytidine 5′-triphosphate disodium salt, ≥95%
Supelco
Isopentenyl pyrophosphate trilithium salt, analytical standard
Sigma-Aldrich
2′-Deoxyguanosine 5′-triphosphate sodium salt hydrate, ≥96% (HPLC)
Sigma-Aldrich
Thymidine-13C10,15N2 5′-triphosphate disodium salt solution, ≥98 atom %, ≥95% (CP), 100 mM (in 5mM Tris HCl / H2O)
Sigma-Aldrich
Guanosine-13C10,15N5 5′-triphosphate disodium salt solution, ≥98 atom %, ≥95% (CP), 100 mM (in 5mM Tris HCl / H2O)