DOI: 10.1101/gr.5533506. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

10.1101/gr.5533506

Crossref journal-article

Cold Spring Harbor Laboratory

Genome Research (246)

Abstract

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-AssistedIsolation ofRegulatoryElements). 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.

Bibliography

Giresi, P. G., Kim, J., McDaniell, R. M., Iyer, V. R., & Lieb, J. D. (2006). FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research, 17(6), 877â885.

Authors 5

Paul G. Giresi (first)
Jonghwan Kim (additional)
Ryan M. McDaniell (additional)
Vishwanath R. Iyer (additional)
Jason D. Lieb (additional)

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Dates

Type	When
Created	18 years, 8 months ago (Dec. 19, 2006, 10:09 p.m.)
Deposited	7 months, 3 weeks ago (Jan. 12, 2025, 12:28 p.m.)
Indexed	12 minutes ago (Sept. 3, 2025, 6:45 a.m.)
Issued	18 years, 8 months ago (Dec. 19, 2006)
Published	18 years, 8 months ago (Dec. 19, 2006)
Published Online	18 years, 8 months ago (Dec. 19, 2006)
Published Print	18 years, 3 months ago (June 1, 2007)

Funders 0

None

BibTeX

@article{Giresi_2006, title={FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin}, volume={17}, ISSN={1088-9051}, url={http://dx.doi.org/10.1101/gr.5533506}, DOI={10.1101/gr.5533506}, number={6}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Giresi, Paul G. and Kim, Jonghwan and McDaniell, Ryan M. and Iyer, Vishwanath R. and Lieb, Jason D.}, year={2006}, month=dec, pages={877–885} }

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  "abstract": "<jats:p>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 (<jats:underline>F</jats:underline>ormaldehyde-<jats:underline>A</jats:underline>ssisted<jats:underline>I</jats:underline>solation of<jats:underline>R</jats:underline>egulatory<jats:underline>E</jats:underline>lements). 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\u2013specific 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.</jats:p>",
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