Nat Protocol

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http://www.nature.com/nprot/jour ... nprot.2011.444.html; k; X$ q  t6 |: y
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Nat Protoc. 2012 Jan 19;7(2):256-67. doi: 10.1038/nprot.2011.444.
0 {; r3 E, i% u8 e; M" |! u- A) F) WUsing formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.
7 [7 ^6 C9 [7 q0 ?( t# CSimon JM, Giresi PG, Davis IJ, Lieb JD.  [8 u/ Y# |  A% n$ N- g# l! K
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Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.) U0 q5 \# W" _/ i) M9 ]. @

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7 P/ N+ i: r' ]" dEviction 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.

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