title: Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.
abstract: Eviction or destabilization of nucleosomes from chromatin is a hallmark of functional regulatory elements in eukaryotic genomes. Historically identified by nuclease hypersensitivity, these regulatory elements are typically bound by transcription factors or other regulatory proteins. FAIRE (formaldehyde-assisted isolation of regulatory elements) is an alternative approach to identify these genomic regions and has proven successful in a multitude of eukaryotic cell and tissue types. Cells or dissociated tissues are cross-linked briefly with formaldehyde, lysed and sonicated. Sheared chromatin is subjected to phenol/chloroform extraction and the isolated DNA, typically encompassing 1-3% of the human genome, is purified. We provide guidelines for quantitative analysis by PCR, microarrays or next-generation sequencing. Regulatory elements enriched by FAIRE have high concordance with those identified by nuclease hypersensitivity or chromatin immunoprecipitation (ChIP), and the entire procedure can be completed in 3 d. FAIRE has low technical variability, which allows its usage in large-scale studies of chromatin from normal or diseased tissues.
authors.affiliation: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
authors.forename: Jeremy M
authors.initials: JM
authors.lastname: Simon
authors.forename: Paul G
authors.initials: PG
authors.lastname: Giresi
authors.forename: Ian J
authors.initials: IJ
authors.lastname: Davis
authors.forename: Jason D
authors.initials: JD
authors.lastname: Lieb
mesh_terms: D002843:Chromatin / Q000737:chemistry; D003432:Cross-Linking Reagents; D005557:Formaldehyde; D009707:Nucleosomes / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016133:Polymerase Chain Reaction / Q000379:methods; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013010:Sonication
chemical_list: D002843:Chromatin; D003432:Cross-Linking Reagents; D009707:Nucleosomes; D005557:Formaldehyde