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FAIRE-Seq (Formaldehyde-Assisted Isolation of Regulatory Elements) is a method in molecular biology used for determining the sequences of those DNA regions in the genome associated with regulatory activity.[1] The technique was developed in the laboratory of Jason D. Lieb at the University of North Carolina, Chapel Hill. In contrast to DNase-Seq, the FAIRE-Seq protocol doesn't require the permeabilization of cells or isolation of nuclei, and can analyse any cell types. In a study of seven diverse human cell types, DNase-seq and FAIRE-seq produced strong cross-validation, with each cell type having 1-2% of the human genome as open chromatin.

The protocol is based on the fact that the formaldehyde cross-linking is more efficient in nucleosome-bound DNA than it is in nucleosome-depleted regions of the genome. This method then segregates the non cross-linked DNA that is usually found in open chromatin, which is then sequenced. The protocol consists of cross linking, phenol extraction and sequencing the DNA in aqueous phase.

FAIRE-seq data are mapped to the human genome assembly and displayed as part of the ENCODE project at the UCSC Genome Browser.


  1. ^ Giresi, PG; Kim, J; McDaniell, RM; Iyer, VR; Lieb, JD (Jun 2007). "FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.". Genome Research 17 (6): 877–85. doi:10.1101/gr.5533506. PMC 1891346. PMID 17179217.