Using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) to Identify Functional Regulatory DNA in Insect Genomes

  • Daniel J. McKayEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1858)


Differential regulation of gene expression determines cell-type-specific function, making identification of the cis-regulatory elements that control gene expression a central goal of developmental biology. In addition, changes in the sequence of cis-regulatory elements are thought to drive changes in gene expression patterns between species, making comparisons of cis-regulatory element usage important for evolutionary biology as well. Due to the number of extant species and the incredible morphological diversity that they exhibit, insects are favorite model organisms for both developmental and evolutionary biologists alike. However, identifying cis-regulatory elements in insect genomes is challenging. Here, I describe a method termed FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements, followed by high-throughput sequencing) that can be used to identify functional DNA regulatory elements from developing insect tissues, genome-wide.

Key words

Open chromatin Cis-regulatory element Enhancer FAIRE Drosophila development 


  1. 1.
    Giresi PG et al (2007) FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 17(6):877–885CrossRefGoogle Scholar
  2. 2.
    Giresi PG, Lieb JD (2009) Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods 48(3):233–239CrossRefGoogle Scholar
  3. 3.
    Gaulton KJ et al (2010) A map of open chromatin in human pancreatic islets. Nat Genet 42(3):255–259CrossRefGoogle Scholar
  4. 4.
    Song L et al (2011) Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 21(10):1757–1767CrossRefGoogle Scholar
  5. 5.
    Simon JM et al (2012) Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nat Protoc 7(2):256–267CrossRefGoogle Scholar
  6. 6.
    Simon JM et al (2013) A detailed protocol for formaldehyde-assisted isolation of regulatory elements (FAIRE). Curr Protoc Mol Biol Chapter 21:Unit21.26PubMedGoogle Scholar
  7. 7.
    Mueller B et al (2017) Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction. Genes Dev 31(5):451–462CrossRefGoogle Scholar
  8. 8.
    McKay DJ, Lieb JD (2013) A common set of DNA regulatory elements shapes Drosophila appendages. Dev Cell 27(3):306–318CrossRefGoogle Scholar
  9. 9.
    Uyehara CM et al (2017) Hormone-dependent control of developmental timing through regulation of chromatin accessibility. Genes Dev 31(9):862–875CrossRefGoogle Scholar
  10. 10.
    Pearson JC et al (2016) Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers. Development 143(20):3723–3732CrossRefGoogle Scholar
  11. 11.
    Davie K et al (2015) Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet 11(2):e1004994CrossRefGoogle Scholar
  12. 12.
    Behura SK et al (2016) High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti. BMC Genomics 17:341CrossRefGoogle Scholar
  13. 13.
    Richard G et al (2017) Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid. Epigenetics Chromatin 10:30CrossRefGoogle Scholar
  14. 14.
    Zhang Q et al (2017) Genome-wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori. Sci Rep 7(1):12919CrossRefGoogle Scholar
  15. 15.
    Lai YT, Deem KD, Borràs-Castells F, Sambrani N, Rudolf H, Suryamohan K, El-Sherif E, Halfon MS, McKay DJ, Tomoyasu Y (2018) Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum. Development 145(7). PMID: 29540499CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of BiologyThe University of North Carolina at Chapel HillChapel HillUSA
  2. 2.Department of Genetics, Integrative Program for Biological and Genome SciencesThe University of North Carolina at Chapel HillChapel HillUSA

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