title: Genome-wide requirements for resistance to functionally distinct DNA-damaging agents.
abstract: The mechanistic and therapeutic differences in the cellular response to DNA-damaging compounds are not completely understood, despite intense study. To expand our knowledge of DNA damage, we assayed the effects of 12 closely related DNA-damaging agents on the complete pool of approximately 4,700 barcoded homozygous deletion strains of Saccharomyces cerevisiae. In our protocol, deletion strains are pooled together and grown competitively in the presence of compound. Relative strain sensitivity is determined by hybridization of PCR-amplified barcodes to an oligonucleotide array carrying the barcode complements. These screens identified genes in well-characterized DNA-damage-response pathways as well as genes whose role in the DNA-damage response had not been previously established. High-throughput individual growth analysis was used to independently confirm microarray results. Each compound produced a unique genome-wide profile. Analysis of these data allowed us to determine the relative importance of DNA-repair modules for resistance to each of the 12 profiled compounds. Clustering the data for 12 distinct compounds uncovered both known and novel functional interactions that comprise the DNA-damage response and allowed us to define the genetic determinants required for repair of interstrand cross-links. Further genetic analysis allowed determination of epistasis for one of these functional groups.
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: William
authors.initials: W
authors.lastname: Lee
authors.forename: Robert P
authors.initials: RP
authors.lastname: St Onge
authors.forename: Michael
authors.initials: M
authors.lastname: Proctor
authors.forename: Patrick
authors.initials: P
authors.lastname: Flaherty
authors.forename: Michael I
authors.initials: MI
authors.lastname: Jordan
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
authors.forename: Ronald W
authors.initials: RW
authors.lastname: Davis
authors.forename: Corey
authors.initials: C
authors.lastname: Nislow
authors.forename: Guri
authors.initials: G
authors.lastname: Giaever
mesh_terms: D000935:Antifungal Agents / Q000494:pharmacology; D016000:Cluster Analysis; D004249:DNA Damage / Q000187:drug effects / Q000235:genetics*; D004260:DNA Repair / Q000235:genetics; D004351:Drug Resistance / Q000235:genetics*; D004843:Epistasis, Genetic; D016681:Genome, Fungal; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017384:Sequence Deletion
chemical_list: D000935:Antifungal Agents