Unit

UNIT 21.26 A Detailed Protocol for Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE)

  1. Jeremy M. Simon1,2,3,
  2. Paul G. Giresi3,
  3. Ian J. Davis1,4,5,6,
  4. Jason D. Lieb1,2,3,6

Published Online: 1 APR 2013

DOI: 10.1002/0471142727.mb2126s102

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Simon, J. M., Giresi, P. G., Davis, I. J. and Lieb, J. D. 2013. A Detailed Protocol for Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE). Current Protocols in Molecular Biology. 102:21.26:21.26.1–21.26.15.

Author Information

  1. 1

    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina

  2. 2

    Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina

  3. 3

    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina

  4. 4

    Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina

  5. 5

    Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina

  6. 6

    Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina

Publication History

  1. Published Online: 1 APR 2013
  2. Published Print: APR 2013

Abstract

Nucleosome displacement is a key event in the regulation of gene expression in the eukaryotic genome. This unit details an approach called Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) for isolating nucleosome-depleted regions. FAIRE does not rely on the use of antibodies or enzymes, and has proven successful in most eukaryotic cells and tissues. The set of regulatory elements enriched by FAIRE is similar to those identified through DNase hypersensitivity. The enriched fragments can be detected by quantitative PCR, tiling DNA microarrays, or next-generation sequencing. Although the signal-to-noise ratio is typically lower than that observed for DNase assays, FAIRE has high sample-to-sample reproducibility, requires very low amounts of input material, is inexpensive, is amenable to high-throughput adaptations, and is a relatively simple procedure with a high rate of success, even for those without extensive experience in molecular biology protocols. Curr. Protoc. Mol. Biol. 102:21.26.1–21.26.15. © 2013 by John Wiley & Sons, Inc.

Keywords:

  • chromatin;
  • regulatory elements;
  • next-generation sequencing;
  • formaldehyde;
  • DNase;
  • ChIP