ChIP–Quantitative Polymerase Chain Reaction (ChIP-qPCR)

It is critical to determine if the ChIP actually enriched the DNA sequences that are associated with the target protein. If there are known genomic binding sites, primers can be designed for quantitative PCR (qPCR) to determine if the known sites are specifically enriched by immunoprecipitation. If there are no known sites but candidate target genes are available, one can consider designing qPCR primers along the length of potential regulatory regions such as promoters and conserved noncoding sequences within intergenic and genic regions. If candidate target genes or potential sites are not available, ChIP-chip or ChIP-seq should be considered instead. Because real-time PCR can be performed in either a 96- or 384-well format in a minimal reaction volume and primers can be synthesized with minimal cost, ChIP-qPCR is an attractive strategy to interrogate target genes and potential regulatory regions across a large number of experimental conditions and different cell types.