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

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.

Pubmed ID: 16998473


  • Berger MF
  • Philippakis AA
  • Qureshi AM
  • He FS
  • Estep PW
  • Bulyk ML


Nature biotechnology

Publication Data

November 9, 2006

Associated Grants

  • Agency: NHGRI NIH HHS, Id: R01 HG003420
  • Agency: NHGRI NIH HHS, Id: R01 HG003420
  • Agency: NHGRI NIH HHS, Id: R01 HG003985
  • Agency: NHGRI NIH HHS, Id: R01 HG003985

Mesh Terms

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