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

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.