Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

Nat Biotechnol. 2006 Nov;24(11):1429-35. doi: 10.1038/nbt1246. Epub 2006 Sep 24.

Abstract

Transcription factors (TFs) interact with specific DNA regulatory sequences to control gene expression throughout myriad cellular processes. However, the DNA binding specificities of only a small fraction of TFs are sufficiently characterized to predict the sequences that they can and cannot bind. We present a maximally compact, synthetic DNA sequence design for protein binding microarray (PBM) experiments that represents all possible DNA sequence variants of a given length k (that is, all 'k-mers') on a single, universal microarray. We constructed such all k-mer microarrays covering all 10-base pair (bp) binding sites by converting high-density single-stranded oligonucleotide arrays to double-stranded (ds) DNA arrays. Using these microarrays we comprehensively determined the binding specificities over a full range of affinities for five TFs of different structural classes from yeast, worm, mouse and human. The unbiased coverage of all k-mers permits high-throughput interrogation of binding site preferences, including nucleotide interdependencies, at unprecedented resolution.

Publication types

  • 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

  • Animals
  • Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / chemistry
  • Binding Sites / physiology
  • Caenorhabditis elegans
  • Caenorhabditis elegans Proteins / chemistry
  • Early Growth Response Protein 1 / chemistry
  • Homeodomain Proteins / chemistry
  • Humans
  • Mice
  • Octamer Transcription Factor-1 / chemistry
  • Oligonucleotide Array Sequence Analysis / methods*
  • Protein Binding*
  • Saccharomyces cerevisiae
  • Saccharomyces cerevisiae Proteins / chemistry
  • Telomere-Binding Proteins / chemistry
  • Transcription Factors / chemistry
  • Transcription Factors / metabolism*

Substances

  • Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
  • CBF1 protein, S cerevisiae
  • CEH-22 protein, C elegans
  • Caenorhabditis elegans Proteins
  • Early Growth Response Protein 1
  • Egr1 protein, mouse
  • Homeodomain Proteins
  • Octamer Transcription Factor-1
  • RAP1 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Telomere-Binding Proteins
  • Transcription Factors