Chromatin Immunoprecipitation to Study the Binding of Proteins to the Adenovirus Genome In Vivo

The encapsidation of adenovirus DNA into virus particles depends on cis -acting sequences located at the left end of the viral genome. Repeated DNA sequences in the packaging domain contribute to viral DNA encapsidation, and several viral proteins bind to these repeats when analyzed using in vitro DNAprotein-binding assays. This chapter describes a chromatin immunoprecipitation approach to study the binding of viral proteins to packaging sequences in vivo. The technique is easily adaptable to study the interaction of any viral or cellular protein to Ad DNA or to cellular genomic DNA sequences. The assay permits accurate quantification over a wide range of DNA concentrations. The use of formaldehyde cross-linking to stabilize DNAprotein and proteinprotein complexes formed in vivo allows the identification of macromolecular complexes found in living cells.