Chromatin Immunoprecipitation Assays: Molecular Analysis of Chromatin Modification and Gene Regulation

Gene expression pattern in cancer cells differ significantly from their normal counter parts, owing to mutations in oncogenes and tumor suppressor genes, their downstream targets, or owing to increased proliferation, and altered apoptotic potential. Various microarray based techniques have been widely utilized to study the differential expression of genes in cancer in recent years. Along with this, attempts have been made to study the transcriptional regulatory mechanisms and chromatin modifications facilitating such differential gene expression. One of the widely used assays for this purpose is the chromatin immunoprecipitation (ChIP) assay, which enables the analysis of the association of regulatory molecules with specific promoters or changes in histone modifications in vivo, without overexpressing any component. This has been of immense value, because ChIP assays can provide a snapshot of the regulatory mechanisms involved in the expression of a single gene, or a variety of genes at the same time. This review article outlines the general strategies and protocols used to carry out ChIP assays to study the differential recruitment of transcription factors, based on the experience in studying E2F1 and histone modifications as well as other published protocols. In addition, the use of ChIP assays to carry out global analysis of transcription factor recruitment is also addressed.