ChIP-re-ChIP: Co-occupancy Analysis by Sequential Chromatin Immunoprecipitation

Abstract

Chromatin immunoprecipitation (ChIP) exploits the specific interactions between DNA and DNA-associated proteins. It can be used to examine a wide range of experimental parameters. A number of proteins bound at the same genomic location can identify a multi-protein chromatin complex where several proteins work together to regulate gene transcription or chromatin configuration. In many instances, this can be achieved using sequential ChIP; or simply, ChIP-re-ChIP. Whether it is for the examination of specific transcriptional or epigenetic regulators, or for the identification of cistromes, the ability to perform a sequential ChIP adds a higher level of power and definition to these analyses. In this chapter, we describe a simple and reliable method for the sequential ChIP assay.

Keywords: ChIP-re-ChIP; Chemical cross-linking; Chromatin immunoprecipitation (ChIP); Co-occupancy; Polymerase chain reaction (PCR); Promoter/regulatory region occupancy; Protein–protein interactions.