To extend our previous ChIP studies (see Renthal and Nestler, 2008), which identified that cocaine or amphetamine administration alters histone acetylation and methylation at specific genes in the NAc, we mapped the genome-wide promoter binding of these histone modifications in the NAc from mice treated chronically with cocaine (20 mg/kg/day for 7 days, i.p.) or saline. To do this, we performed ChIP with antibodies directed against polyacetylated H3 (K9 and K14), polyacetylated H4 (K5, K8, K12, and K16), or dimethylated H3 (K9 and K27) on independent pools of NAc lysates, with each pooled sample representing bilateral NAc dissections from 8 mice. These histone modifications have been widely shown to reflect the state of gene activation or repression (Kouzarides, 2007). The immunoprecipitated DNA, as well as input (total) DNA, was sheared and then repaired, amplified, and labeled with a fluorescent dye with the use of ligation-mediated PCR (Sikder et al., 2006). Cy5-labeled immunoprecipitated DNA and Cy3-labeled total DNA were mixed and hybridized to MM8 NimbleGen promoter microarrays (Madison, WI), which span the promoters of ~20,000 genes. After pre-processing, normalization, and identification
