Tissue-specific control of gene expression is crucial during development. In recent years, a number of genome-wide approaches have been used to identify potential regulatory elements that control gene expression, but determining which of these are functionally relevant has been a challenge. Here, Stephen Crews and colleagues describe an approach to identify active and biologically relevant enhancers (p. 3723). They focus on gene expression in Drosophila CNS midline neurons, which are well-characterized with regards to their gene regulatory mechanisms and hence serve as a useful model for studying transcriptional regulation. The researchers use formaldehyde-assisted isolation of regulatory elements sequencing (FAIRE-seq) analysis of purified midline cells and compare this with whole embryo FAIRE data. Using this approach, the authors identify known enhancers as well as novel enhancers that act specifically in midline cells. They also compare midline FAIRE-seq data with currently available midline expression and enhancer datasets, and reveal, for example, that many genomic fragments that have previously been shown to drive midline expression are unlikely to function in vivo. Overall, this approach emphasizes the importance of using highly purified cells in genome-wide analyses and highlights potential limitations to using standard reporter assays for identifying bona fide enhancers.
