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

  1. Paul G. Giresi1,
  2. Jonghwan Kim2,
  3. Ryan M. McDaniell2,
  4. Vishwanath R. Iyer2, and
  5. Jason D. Lieb1,3
  1. 1 Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA;
  2. 2 Institute for Cellular and Molecular Biology and Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712-0159, USA

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-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.

Footnotes

  • 3 Corresponding author.

    3 E-mail jlieb{at}bio.unc.edu; fax (919) 962-1625.

  • [Supplemental material is available online at www.genome.org.]

  • Article is online at http://www.genome.org/cgi/doi/10.1101/gr.5533506

    • Received May 21, 2006.
    • Accepted August 15, 2006.
  • Freely available online through the Genome Research Open Access option.

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