Identifying transcription factor functions and targets by phenotypic activation

Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12045-50. doi: 10.1073/pnas.0605140103. Epub 2006 Jul 31.


Mapping transcriptional regulatory networks is difficult because many transcription factors (TFs) are activated only under specific conditions. We describe a generic strategy for identifying genes and pathways induced by individual TFs that does not require knowledge of their normal activation cues. Microarray analysis of 55 yeast TFs that caused a growth phenotype when overexpressed showed that the majority caused increased transcript levels of genes in specific physiological categories, suggesting a mechanism for growth inhibition. Induced genes typically included established targets and genes with consensus promoter motifs, if known, indicating that these data are useful for identifying potential new target genes and binding sites. We identified the sequence 5'-TCACGCAA as a binding sequence for Hms1p, a TF that positively regulates pseudohyphal growth and previously had no known motif. The general strategy outlined here presents a straightforward approach to discovery of TF activities and mapping targets that could be adapted to any organism with transgenic technology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Binding Sites
  • Gene Expression Regulation, Fungal*
  • Genetic Techniques
  • Genetics*
  • Models, Genetic
  • Oligonucleotide Array Sequence Analysis / methods*
  • Phenotype
  • Promoter Regions, Genetic
  • Protein Binding
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Transcription Factors / genetics*
  • Transgenes


  • Saccharomyces cerevisiae Proteins
  • Transcription Factors