Chromatin Immunoprecipitation on Fixed Tissues and Cell Lines

Abstract

Chromatin immunoprecipitation (ChIP) has been used over three decades to characterize protein-DNA interactions in cells and tissues. The samples are initially cross-linked with formaldehyde and subjected to lysis with detergents followed by sonication to generate smaller fragments of DNA covalently bound to nuclear proteins. Antibodies against the protein of interest are then used to immunoprecipitate the protein-DNA complex, allowing for the purification of the genomic locations bound to the protein of interest. The DNA can then be analyzed by several techniques such as PCR, quantitative PCR, DNA microarrays, and next-generation sequencing (NGS). ChIP can be used in cell culture systems and animal tissues to provide insights into how the identity of cells and tissues is established, and how transcriptional programs can be disrupted or reactivated in disease states.

Keywords: ChIP; ChIP on cell lines; ChIP on tissues; Double-cross-linking ChIP; Protein–DNA interactions; X-ChIP.