Cells were grown in BPYE medium with 25% bactopeptone, 20% yeast extract and 5% heat inactivated fetal calf serum. Expression plasmids for Dam-fusion and Dam-only proteins were transfected in parallel by electroporation, and cells were isolated 24 hr later. The Dam enzyme deposits stable adenine-methylation footprings at genomic sites bound by the Dam-fusion.

Genomic DNA was isolated and adenine-methylated fragments were amplified by methylation-specific PCR using Cy-dye labeled random nonamers. To correct for nonspecific binding of Dam and local differences in DNA accessibility, methylated fragments of Kc cells transfected with a Dam-only construct were labeled with a different fluorescent dye.

Isolated DNA was hybridized to NimbleGen Drosophila 385k array rel4 300bp genomic tiling array.