TY  - JOUR
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
Y1  - 2007/06/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 877 
EP  - 885 
DO  - 10.1101/gr.5533506 
VL  - 17 
IS  - 6 
UR  - http://genome.cshlp.org/content/17/6/877.abstract 
N2  - 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. 
ER  -