An active enhancer resides in open chromatin and is marked by histones with specific post-translational modifications (H3K4me1 or H3K27ac). Genome-wide screens for both of these features exist, but they cannot quantify enhancer activity. To do so, Arnold et al. developed self-transcribing active regulatory region sequencing (STARR-seq), which takes advantage of the fact that enhancers function independently of their positions relative to a promoter. The researchers cloned randomly sheared genomic DNA from Drosophila melanogaster behind a minimal promoter, expecting the enhancers to regulate their own transcription. They transfected S2 cells with these fragments and then sequenced their RNA. The level of enrichment of every fragment correlated with its strength as an enhancer. Interestingly, 30% of strong enhancers were in closed chromatin, indicating that they were not active in the particular cells tested.
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Genome-wide enhancer maps. Nat Methods 10, 193 (2013). https://doi.org/10.1038/nmeth.2383