title: Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP.
abstract: This protocol describes the batch isolation of tissue-specific chromatin for immunoprecipitation (BiTS-ChIP) for analysis of histone modifications, transcription factor binding, or polymerase occupancy within the context of a multicellular organism or tissue. Embryos expressing a cell type-specific nuclear marker are formaldehyde cross-linked and then subjected to dissociation. Fixed nuclei are isolated and sorted using FACS on the basis of the cell type-specific nuclear marker. Tissue-specific chromatin is extracted, sheared by sonication and used for ChIP-seq or other analyses. The key advantages of this method are the covalent cross-linking before embryo dissociation, which preserves the transcriptional context, and the use of FACS of nuclei, yielding very high purity. The protocol has been optimized for Drosophila, but with minor modifications should be applicable to any model system. The full protocol, including sorting, immunoprecipitation and generation of sequencing libraries, can be completed within 5 d.
authors.affiliation: Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Bonn
authors.forename: Robert P
authors.initials: RP
authors.lastname: Zinzen
authors.forename: Alexis
authors.initials: A
authors.lastname: Perez-Gonzalez
authors.forename: Andrew
authors.initials: A
authors.lastname: Riddell
authors.forename: Anne-Claude
authors.initials: AC
authors.lastname: Gavin
authors.forename: Eileen E M
authors.initials: EE
authors.lastname: Furlong
mesh_terms: D000818:Animals; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry / Q000378:metabolism; D004330:Drosophila / Q000235:genetics*; D004742:Enhancer Elements, Genetic; D005434:Flow Cytometry; D005786:Gene Expression Regulation; D015723:Gene Library; D017930:Genes, Reporter; D006657:Histones / Q000737:chemistry / Q000378:metabolism*; D013010:Sonication; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism
chemical_list: D006657:Histones; D014157:Transcription Factors; D004259:DNA-Directed DNA Polymerase