Identification of benzo(a)pyrene diol epoxide-binding DNA fragments using DNA immunoprecipitation technique

Benzo(a)pyrene diol epoxide (BPDE), an active metabolite of the tobacco carcinogen benzo(a)pyrene, can induce p53 gene mutation, down-regulate retinoic acid receptor beta, and increase cyclooxygenase-2 expression in human epithelial cells. However, it remains unknown whether these effects are direct or indirect. To investigate the direct effects of BPDE on gene expression, we used our newly developed DNA immunoprecipitation technique to identify and clone BPDE-binding DNA fragments. A total of 67 fragments were sequenced and grouped into four categories after their sequences were blasted in the GenBank database: (a). 15 fragments matched known gene sequences; (b). 24 matched expressed sequence tag clones; (c). 22 matched genomic DNA of unknown genes; and (d). 6 clones did not show any homology with GenBank sequences known to date. The 67 fragments include DNA repair and apoptosis-related genes, zinc finger protein, cellular enzymes, expressed sequence tag clones, and CpG islands. These data further demonstrate that BPDE-induced gene alterations are important events in carcinogenesis and that the identification of the resulting clones may help us to better understand the mechanisms of BPDE-induced carcinogenesis.