Microarray approaches to finding protein–DNA binding

Mapping protein localization to DNA using chromatin immunoprecipitation and DNA microarrays^32, 33. In this technique, proteins are crosslinked to genomic DNA in a cellular context. The DNA is sheared or digested, leaving DNA–protein complexes that can be precipitated using protein-specific antibodies. Two pools of DNA fragment — those released from the protein and those from control DNA — are amplified and labelled using different fluorescent dyes. Both sets of probes are simultaneously hybridized to a DNA microarray that contains intragenic DNA sequences. The greater the difference in the fluorescent intensity at any fragment on the array, the stronger the binding of the protein to that fragment. b | Mapping protein localization to DNA using DNA adenine methyltransferase identification³⁴. In this method, the DNA adenine methyltransferase enzyme is fused to a chromatin-associated protein and is expressed in cells; the chimeric protein binds to chromatin and methylates adenine residues in the vicinity of the protein-binding site. The methylation-specific restriction enzyme Dpn1 recognizes and cleaves the DNA at methylated GATC sites. The resulting fragments are fractionated by size, then labelled and probed to the array.