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

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.

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