title: Chromatin tandem affinity purification sequencing.
abstract: Chromatin immunoprecipitation coupled with ultra-high-throughput sequencing (ChIP-seq) is a widely used method for mapping the interactions of proteins with DNA. However, the requirements for ChIP-grade antibodies impede wider application of this method, and variations in results can be high owing to differences in affinity and cross-reactivity of antibodies. Therefore, we developed chromatin tandem affinity purification (ChTAP) as an effective alternative to ChIP. Through the use of affinity tags and reagents that are identical for all proteins investigated, ChTAP enables one to directly compare the binding between different transcription factors and to directly assess the background in control experiments. Thus, ChTAP-seq can be used to rapidly map the genome-wide binding of multiple DNA-binding proteins in a wide range of cell types. ChTAP can be completed in 3-4 d, starting from cross-linking of chromatin to purification of ChIP DNA.
authors.affiliation: Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.
authors.forename: Vahab D
authors.initials: VD
authors.lastname: Soleimani
authors.forename: Gareth A
authors.initials: GA
authors.lastname: Palidwor
authors.forename: Parameswaran
authors.initials: P
authors.lastname: Ramachandran
authors.forename: Theodore J
authors.initials: TJ
authors.lastname: Perkins
authors.forename: Michael A
authors.initials: MA
authors.lastname: Rudnicki
mesh_terms: D001665:Binding Sites; D002843:Chromatin / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D002846:Chromatography, Affinity / Q000379:methods*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D057809:HEK293 Cells; D006801:Humans; D013010:Sonication
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins