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Published online on July 22, 2003, 10.1073/pnas.1533393100
PNAS | August 5, 2003 | vol. 100 | no. 16 | 9428-9433


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

Ling V. Sun *, Liang Chen * {dagger}, Frauke Greil {ddagger}, Nicolas Negre §, Tong-Ruei Li *, Giacomo Cavalli §, Hongyu Zhao * {dagger}, Bas van Steensel {ddagger} ¶, and Kevin P. White * ¶

*Department of Genetics and {dagger}Biostatistics Division, Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520; {ddagger}Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; and §Chromatin and Cell Biology Laboratory, Institute of Human Genetics, Centre National de la Recherche Scientifique, 34396 Montpellier, Cedex 5, France

Communicated by Walter J. Gehring, University of Basel, Basel, Switzerland, June 4, 2003 (received for review November 11, 2002)

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.

Abbreviations: ChIP, chromatin immunoprecipitation; Dam, DNA adenine methyltransferase.

To whom correspondence may be addressed. E-mail: b.v.steensel{at}nki.nl or kevin.white{at}yale.edu.


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