RT Journal
A1 Giresi, Paul G.
A1 Kim, Jonghwan
A1 McDaniell, Ryan M.
A1 Iyer, Vishwanath R.
A1 Lieb, Jason D.
T1 FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
JF Genome Research 
JO Genome Research 
YR 2007 
FD June 01 
VO 17 
IS 6 
SP 877 
OP 885 
DO 10.1101/gr.5533506 
UL http://genome.cshlp.org/content/17/6/877.abstract 
AB 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.