Identifying transcription factor functions and targets by phenotypic activation.
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.
Chua
Gordon
G
Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 1A8.
Morris
Quaid D
QD
Sopko
Richelle
R
Robinson
Mark D
MD
Ryan
Owen
O
Chan
Esther T
ET
Frey
Brendan J
BJ
Andrews
Brenda J
BJ
Boone
Charles
C
Hughes
Timothy R
TR
D020816:Amino Acid Motifs; D001665:Binding Sites; D015966:Gene Expression Regulation, Fungal; D005821:Genetic Techniques; D005823:Genetics; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010641:Phenotype; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics*; D019076:Transgenes
D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors