Evolutionary co-option of a Drosophila enhancer of the yellow gene through shared chromatin accessibility input

The diversity of forms in multicellular organisms originates largely from the spatial redeployment of genes expressed during development. Several scenarios explain the emergence of cis-regulatory elements that govern novel aspects of a gene expression pattern. One scenario, enhancer co-option, holds that a DNA sequence producing an ancestral regulatory activity also becomes the template for a new regulatory activity and shares regulatory information. While enhancer co-option might fuel morphological diversification, it has rarely been documented and the regulatory mechanisms underlying this evolutionary process are elusive. Here we show how a novel enhancer of the Drosophila pigmentation gene yellow, the spot enhancer, has co-opted the ancestral wing blade enhancer. We mapped the sequences driving each regulatory activity, ancestral and derived, and identified a shared core element necessary for DNA accessibility in this regulatory region. Our results suggest a model where a new enhancer emerges by co-opting accessibility information intrinsic to an older enhancer, and gaining transcription factor binding sites that diversify its spatial activity. Using DNA accessibility profiling to assess the effect caused by a particular mutation on the cis-regulatory region