Chromatin Immunoprecipitation (ChIP) Protocols for the Cancer and Developmental Biology Laboratory

Chromatin immunoprecipitation assays permit the isolation and subsequent identification of genomic DNA (gDNA) fragments bound directly or indirectly to proteins of interest, including transcription factors, co-factors, or chromatin remodeling proteins. These isolated DNA fragments may include gene regulatory regions from enhancers, super-enhancers, promoters, and/or insulators. Cells of interest can be obtained from embryonic tissues at various developmental time points or cancer cells from patients or derived from model systems, including patient-derived xenotransplants and primary cancer stem cells and cell lines. ChIP variants include ChIP-reChIP to identify targets bound to different transcription factors or members of protein complexes or, alternatively, to characterize the histone modifications accompanying occupation of specific regulatory regions by the protein of interest, such as a transcription factor. Subsequent analysis of ChIP experiments includes standard PCR, quantitative PCR (qPCR), and ChIPseq.