title: FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.
abstract: DNA segments that actively regulate transcription in vivo are typically characterized by eviction of nucleosomes from chromatin and are experimentally identified by their hypersensitivity to nucleases. Here we demonstrate a simple procedure for the isolation of nucleosome-depleted DNA from human chromatin, termed FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements). To perform FAIRE, chromatin is crosslinked with formaldehyde in vivo, sheared by sonication, and phenol-chloroform extracted. The DNA recovered in the aqueous phase is fluorescently labeled and hybridized to a DNA microarray. FAIRE performed in human cells strongly enriches DNA coincident with the location of DNaseI hypersensitive sites, transcriptional start sites, and active promoters. Evidence for cell-type-specific patterns of FAIRE enrichment is also presented. FAIRE has utility as a positive selection for genomic regions associated with regulatory activity, including regions traditionally detected by nuclease hypersensitivity assays.
authors.affiliation: Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA.
authors.forename: Paul G
authors.initials: PG
authors.lastname: Giresi
authors.forename: Jonghwan
authors.initials: J
authors.lastname: Kim
authors.forename: Ryan M
authors.initials: RM
authors.lastname: McDaniell
authors.forename: Vishwanath R
authors.initials: VR
authors.lastname: Iyer
authors.forename: Jason D
authors.initials: JD
authors.lastname: Lieb
mesh_terms: D002478:Cells, Cultured; D003850:Deoxyribonuclease I / Q000737:chemistry; D005347:Fibroblasts / Q000737:chemistry* / Q000166:cytology / Q000378:metabolism; D005404:Fixatives / Q000737:chemistry*; D005557:Formaldehyde / Q000737:chemistry*; D006801:Humans; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D050436:Regulatory Elements, Transcriptional; D014158:Transcription, Genetic
chemical_list: D005404:Fixatives; D009707:Nucleosomes; D005557:Formaldehyde; D003850:Deoxyribonuclease I