Nat Protocol

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http://www.nature.com/nprot/jour ... nprot.2011.444.html! ^9 [/ R8 F" l. l& [+ I# m" V
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Nat Protoc. 2012 Jan 19;7(2):256-67. doi: 10.1038/nprot.2011.444.
: l9 K* M' B) pUsing formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.
/ n$ y" u3 o! }+ O; k* VSimon JM, Giresi PG, Davis IJ, Lieb JD.
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/ s4 w4 ], q  V" \) x/ V+ C# i7 oLineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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Abstract3 U# j% N4 b, u, w! {; C8 t" G
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.

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