title: Defining in vivo targets of nuclear proteins by chromatin immunoprecipitation and microarray analysis.
abstract: 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.
authors.affiliation: Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Zarmik
authors.initials: Z
authors.lastname: Moqtaderi
authors.forename: Kevin
authors.initials: K
authors.lastname: Struhl
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004268:DNA-Binding Proteins / Q000032:analysis* / Q000378:metabolism; D016678:Genome; D009687:Nuclear Proteins / Q000032:analysis* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D009687:Nuclear Proteins