title: Genomic phenotyping of the essential and non-essential yeast genome detects novel pathways for alkylation resistance.
abstract: BACKGROUND
  A myriad of new chemicals has been introduced into our environment and exposure to these agents can damage cells and induce cytotoxicity through different mechanisms, including damaging DNA directly. Analysis of global transcriptional and phenotypic responses in the yeast S. cerevisiae provides means to identify pathways of damage recovery upon toxic exposure.
  
  
  RESULTS
  Here we present a phenotypic screen of S. cerevisiae in liquid culture in a microtiter format. Detailed growth measurements were analyzed to reveal effects on ~5,500 different haploid strains that have either non-essential genes deleted or essential genes modified to generate unstable transcripts. The pattern of yeast mutants that are growth-inhibited (compared to WT cells) reveals the mechanisms ordinarily used to recover after damage. In addition to identifying previously-described DNA repair and cell cycle checkpoint deficient strains, we also identified new functional groups that profoundly affect MMS sensitivity, including RNA processing and telomere maintenance.
  
  
  CONCLUSIONS
  We present here a data-driven method to reveal modes of toxicity of different agents that impair cellular growth. The results from this study complement previous genomic phenotyping studies as we have expanded the data to include essential genes and to provide detailed mutant growth analysis for each individual strain. This eukaryotic testing system could potentially be used to screen compounds for toxicity, to identify mechanisms of toxicity, and to reduce the need for animal testing.
authors: Biological Engineering Department, Center for Environmental Health Sciences, Biology Department, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors: J Peter
authors: JP
authors: Svensson
authors: Laia Quirós
authors: LQ
authors: Pesudo
authors: Rebecca C
authors: RC
authors: Fry
authors: Yeyejide A
authors: YA
authors: Adeleye
authors: Paul
authors: P
authors: Carmichael
authors: Leona D
authors: LD
authors: Samson
mesh_terms: D000478:Alkylation; D018929:Cell Culture Techniques; D004249:DNA Damage; D004260:DNA Repair / Q000235:genetics*; D005800:Genes, Fungal; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D009153:Mutagens / Q000494:pharmacology; D010641:Phenotype; D060066:Protein Interaction Maps; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D018675:Toxicity Tests
chemical_list: D009153:Mutagens