Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila

Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9428-33. doi: 10.1073/pnas.1533393100. Epub 2003 Jul 22.


We demonstrate the use of a chromosomal walk (or "tiling path") printed as DNA microarrays for mapping protein-DNA interactions across large regions of contiguous genomic DNA in Drosophila melanogaster. Microarrays were constructed with genomic DNA fragments 430-920 bp in length, covering 2.9 million base pairs of the Adh-cactus region of chromosome 2 and 85,000 base pairs of the 82F region of chromosome 3. We performed DNA localization mapping for the heterochromatin protein HP1 and for the sequence-specific GAGA transcription factor, producing a comprehensive, high-resolution map of in vivo protein-DNA interactions throughout these regions of the Drosophila genome.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Animals
  • Chromatin / metabolism
  • DNA / metabolism*
  • DNA-Binding Proteins / chemistry*
  • Drosophila / genetics*
  • Oligonucleotide Array Sequence Analysis*
  • Precipitin Tests
  • Proteins / metabolism


  • Chromatin
  • DNA-Binding Proteins
  • Proteins
  • DNA