Abstract:

Genomic and computational approaches are identifying a large number of putative DNA cis -regulatory elements, but a central challenge in studying transcriptional networks is to map these short regulatory DNA sequences to the transcription factors that bind them. We have developed a rapid and systematic method based on yeast whole-genome phage display selection and microarray analysis in order to identify and characterize the transcription factor(s) associated with a given DNA regulatory element. This technique has been used to isolate phage expressing yeast DNA-binding domains from a background of genomic DNA, when selected against an oligonucleotide containing a predicted binding site motif. Fragments of representative transcription factors from the helix-turn-helix, MADS box, and zinc finger DNA-binding domain families have been enriched in this way. In addition, this method has identified the yeast protein Dot6 as a potential binding partner for the PAC cis -regulatory element. This approach has also been extended to other bimolecular interactions, such as those between transcription factors and phage-displayed fragments of other cellular proteins with which they interact to implement further layers of regulation.