DNA with histones and other DNA-binding proteins and then immunoprecipitated for a protein of interest (e.g., acetylated H3), can be used to assess the extent to which a given gene is associated with these markers of activation or repression. For example, we recently demonstrated by use of ChIP that chronic administration of cocaine or related psychostimulants increases or decreases histone acetylation in the NAc at the promoters of several genes whose mRNA levels are known to be increased or decreased, respectively, by the drug. Moreover, we directly implicated ΔFosB in mediating some of these effects by carrying out ChIP for this transcription factor under these conditions (Kumar et al., 2005; Renthal et al., 2008).
