title: Isolation of intracellular protein--DNA complexes using HaloCHIP, an antibody-free alternative to chromatin immunoprecipitation.
abstract: 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.
authors: Promega Corporation, Madison, WI, USA.
authors: Danette L
authors: DL
authors: Daniels
authors: Marjeta
authors: M
authors: Urh
mesh_terms: D000818:Animals; D018929:Cell Culture Techniques; D002478:Cells, Cultured; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D003432:Cross-Linking Reagents / Q000737:chemistry; D004247:DNA / Q000302:isolation & purification*; D053837:DNA Cleavage; D004268:DNA-Binding Proteins / Q000302:isolation & purification*; D005557:Formaldehyde / Q000737:chemistry; D006801:Humans; D011485:Protein Binding; D013010:Sonication; D016707:Tissue Fixation
chemical_list: D003432:Cross-Linking Reagents; D004268:DNA-Binding Proteins; D005557:Formaldehyde; D004247:DNA