Figure 1.

The DIP-ChIP method. A purified DNA-binding protein is incubated with purified, sheared yeast genomic DNA. Protein·DNA complexes are separated from unbound DNA using immunoprecipitation or affinity purification. Purified DNA fragments are amplified, labeled fluorescently, and identified by hybridization to a DNA microarray. Computational methods are then used to define a binding site based on enriched sequences (see text). A detailed description of the DIP-chip experimental methodology is available in the Methods.