Functional regulatory evolution outside of the minimal even-skipped stripe 2 enhancer

Transcriptional enhancers are regions of DNA that drive precise patterns of gene expression. Although many studies have elucidated how individual enhancers can evolve, most of this work has focused on what are called 'minimal' enhancers, the smallest DNA regions that drive expression that approximates an aspect of native gene expression. Here, we explore how the Drosophila erecta even-skipped (eve) locus has evolved by testing its activity in the divergent D. melanogaster genome. We found, as has been reported previously, that the D. erecta eve stripe 2 enhancer (eveS2) fails to drive appreciable expression in D. melanogaster However, we found that a large transgene carrying the entire D. erecta eve locus drives normal eve expression, including in stripe 2. We performed a functional dissection of the region upstream of the D. erecta eveS2 region and found multiple Zelda motifs that are required for normal expression. Our results illustrate how sequences outside of minimal enhancer regions can evolve functionally through mechanisms other than changes in transcription factor-binding sites that drive patterning.