Mapping the genomic binding sites of the activated retinoid X receptor in murine bone marrow-derived macrophages using chromatin immunoprecipitation sequencing

Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) is a powerful technique to map the genomic location of a given chromatin bound factor (i.e., transcription factors, cofactors) or epigenetic marks, such as histone modifi cation. The procedure is based on cross-linking of proteins to DNA followed by the capture of the protein-DNA complexes by “ChIP-grade” antibodies. In this chapter we describe in detail the experimental method developed in our laboratory to investigate in vivo the DNA- binding characteristics of a key heterodimeric nuclear receptor, the retinoid X receptor (RXR) in murine bone marrow-derived macrophages.