FIGURE 1. Strategy for analysing genome-wide protein–DNA interactions.
From the following article:
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
Vishwanath R. Iyer, Christine E. Horak, Charles S. Scafe, David Botstein, Michael Snyder and Patrick O. Brown
Nature 409, 533-538(25 January 2001)
doi:10.1038/35054095
The reference probe can either consist of DNA generated in parallel from a strain bearing a deletion of the gene encoding the protein of interest (as depicted), or of unfractionated genomic DNA amplified and labelled in the same manner. Alternatively, an epitope-tagged version of the protein of interest can be immunoprecipitated with an antibody directed against the epitope. The DNA microarray includes all of the intergenic regions or promoters from the genome. The Cy5/Cy3 fluorescence ratio for each locus reflects its enrichment by immunoprecipitation (IP) and therefore, in general, its relative occupancy by the cognate protein.