Defining in vivo targets of nuclear proteins by chromatin immunoprecipitation and microarray analysis

This unit describes the combination of chromatin immunoprecipitation (ChIP) with microarray hybridization to determine the genome-wide occupancy profile of a DNA-associated protein. After conventional ChIP, the immunoprecipitated material is amplified by a two-step process involving primer extension followed by PCR in the presence of a modified nucleotide. The amplified DNA is fluorescently labeled in a reaction that couples dye to the modified nucleotide, and the labeled sample is hybridized to a microarray representing a complete genome. This method allows the study of a protein's pattern of DNA association across an entire genome with no need for prior knowledge of potential DNA targets. Keywords: Chromatin immunoprecipitation; ChIP; microarray; amplification; PCR; dye coupling; protein-DNA interactions; ChIP-chip; ChIP-on-chip; genome-wide location; hybridization; whole-genome analysis