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Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

Nature Protocols volume 7, pages 256–267 (2012)Cite this article

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An Addendum to this article was published on 01 February 2014

This article has been updated

Abstract

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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Figure 1: Example timeline for FAIRE protocol.
Figure 2: Representative gel image showing varying degrees of sonication.
Figure 3: Expected results from FAIRE-seq experiments.

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Change history

  • 13 January 2014

     The authors have added some new information regarding the types of species and cell types in which formaldehyde-assisted isolation of regulatory elements (FAIRE) has been successfully performed, according to recently published reports. This information has been appended to the PDF version of the article.

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Acknowledgements

We acknowledge members of the Lieb and Davis labs for their constructive feedback. Support for this work was provided by ENCODE grant U54HG004563 from the National Human Genome Research Institute.

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Authors and Affiliations

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

    Jeremy M Simon, Ian J Davis & Jason D Lieb

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

    Jeremy M Simon & Jason D Lieb

  3. Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA

    Jeremy M Simon, Paul G Giresi & Jason D Lieb

  4. Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA

    Ian J Davis

  5. Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA

    Ian J Davis

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

    Ian J Davis & Jason D Lieb

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  1. Jeremy M Simon
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Contributions

The work presented here was carried out in collaboration between all authors. P.G.G. and J.M.S. designed and improved the method. J.M.S., P.G.G., I.J.D. and J.D.L. wrote the manuscript. All authors have contributed to, reviewed and approved of the manuscript.

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Correspondence to Jason D Lieb.

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Simon, J., Giresi, P., Davis, I. et al. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nat Protoc 7, 256–267 (2012). https://doi.org/10.1038/nprot.2011.444

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