Microarray profiling of phage-display selections for rapid mapping of transcription factor-DNA interactions

PLoS Genet. 2009 Apr;5(4):e1000449. doi: 10.1371/journal.pgen.1000449. Epub 2009 Apr 10.

Abstract

Modern computational methods are revealing putative transcription-factor (TF) binding sites at an extraordinary rate. However, the major challenge in studying transcriptional networks is to map these regulatory element predictions to the protein transcription factors that bind them. We have developed a microarray-based profiling of phage-display selection (MaPS) strategy that allows rapid and global survey of an organism's proteome for sequence-specific interactions with such putative DNA regulatory elements. Application to a variety of known yeast TF binding sites successfully identified the cognate TF from the background of a complex whole-proteome library. These factors contain DNA-binding domains from diverse families, including Myb, TEA, MADS box, and C2H2 zinc-finger. Using MaPS, we identified Dot6 as a trans-active partner of the long-predicted orphan yeast element Polymerase A & C (PAC). MaPS technology should enable rapid and proteome-scale study of bi-molecular interactions within transcriptional networks.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacteriophages / genetics*
  • Binding Sites
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism*
  • Fungal Proteins / chemistry
  • Fungal Proteins / genetics
  • Fungal Proteins / metabolism*
  • Gene Library
  • Oligonucleotide Array Sequence Analysis / methods*
  • Protein Binding
  • Protein Structure, Tertiary
  • Transcription Factors / chemistry
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism
  • Yeasts / chemistry
  • Yeasts / genetics
  • Yeasts / metabolism*

Substances

  • Fungal Proteins
  • Transcription Factors
  • DNA