Isolation of Intracellular Protein DNA Complexes Using HaloCHIP, an Antibody-Free Alternative to Chromatin Immunoprecipitation

Mapping of protein binding sites within the genome has been significantly advanced by microarray and sequencing technologies, yet the method traditionally used to isolate protein–DNA complexes, chromatin immunoprecipitation, has remained dependent of the use of antibodies. Furthermore, cross-linking is commonly used to trap protein–DNA complexes and the challenge of using antibodies has come in recognition of the cross-linked epitopes, sometimes limiting the success of the approach. Here we present a method, HaloCHIP, which utilizes a HaloTag protein fusion and corresponding interaction resin, HaloLink, for capture of cross-linked protein–DNA complexes directly from a cellular lysate. This process alleviates the need for using an antibody, yields the DNA fragments bound to a particular protein of interest, and allows for a variety of downstream analyses such as PCR, qPCR, microarrays, and sequencing.