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

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

Abstract

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 

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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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