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.
Sun
Ling V
LV
Department of Genetics and Biostatistics Division, Yale University School of Medicine, New Haven, CT 06520, USA.
Chen
Liang
L
Greil
Frauke
F
Negre
Nicolas
N
Li
Tong-Ruei
TR
Cavalli
Giacomo
G
Zhao
Hongyu
H
Van Steensel
Bas
B
White
Kevin P
KP
D020816:Amino Acid Motifs; D000818:Animals; D002843:Chromatin / Q000378:metabolism; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D004330:Drosophila / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D011233:Precipitin Tests; D011506:Proteins / Q000378:metabolism
D002843:Chromatin; D004268:DNA-Binding Proteins; D011506:Proteins; D004247:DNA