In the post-genomic era, identifying and characterzing various DNA-protein interactions are a major challenge in the research of gene transcriptional regulation. Now, chromatin immunoprecipitation assay (ChIP) is ideally suited for investigating DNA-protein interactions in vivo. The conditions of chromatin immunoprecipitation assay was optimized and utilized to screen unknown target genes of transcription factor AP-2 alpha. The results yielded a more complete understanding of AP-2α-regulated signaling pathways and further elucidated the complex transcriptional networks.