Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents

Lee, William; St.Onge, Robert P.; Proctor, Michael; Flaherty, Patrick; Jordan, Michael I.; Arkin, Adam P.; Davis, Ronald W.; Nislow, Corey; Giaever, Guri

doi:10.1371/journal.pgen.0010024

Title: Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents

Journal Article · Fri Aug 19 00:00:00 EDT 2005 · PLoS Genetics

DOI: https://doi.org/10.1371/journal.pgen.0010024 · OSTI ID:1627261

Lee, William ^[1]; St.Onge, Robert P. ^[2]; Proctor, Michael ^[2]; Flaherty, Patrick ^[3]; Jordan, Michael I. ^[4]; Arkin, Adam P. ^[5]; Davis, Ronald W. ^[6]; Nislow, Corey ^[2]; Giaever, Guri ^[2]

Stanford Univ., CA (United States). School of Medicine. Dept. of Genetics; DOE/OSTI
Stanford Univ., CA (United States). School of Medicine. Stanford Genome Technology Center. Dept. of Biochemistry
Univ. of California, Berkeley, CA (United States). Dept. of electrical Engineering and Computer Science; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division
Univ. of California, Berkeley, CA (United States). Dept. of Statistics. Division of Computer Science
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering. Howard Hughes Medical Inst.
Stanford Univ., CA (United States). School of Medicine. Dept. of Genetics; Stanford Univ., CA (United States). School of Medicine. Stanford Genome Technology Center. Dept. of Biochemistry

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 ;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 DNAdamage-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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1627261

Journal Information:: PLoS Genetics, Journal Name: PLoS Genetics Journal Issue: 2 Vol. 1; ISSN 1553-7404

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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