Ancestral and derived transcriptional enhancers share regulatory sequence and a pleiotropic site affecting chromatin accessibility

Abstract

The diversity of forms in multicellular organisms originates largely from the spatial redeployment of developmental genes [S. B. Carroll,Cell134, 25–36 (2008)]. Several scenarios can explain the emergence ofcis-regulatory elements that govern novel aspects of a gene expression pattern [M. Rebeiz, M. Tsiantis,Curr. Opin. Genet. Dev.45, 115–123 (2017)]. One scenario, enhancer co-option, holds that a DNA sequence producing an ancestral regulatory activity also becomes the template for a new regulatory activity, sharing regulatory information. While enhancer co-option might fuel morphological diversification, it has rarely been documented [W. J. Glassford et al.,Dev. Cell34, 520–531 (2015)]. Moreover, if two regulatory activities are borne from the same sequence, their modularity, considered a defining feature of enhancers [J. Banerji, L. Olson, W. Schaffner,Cell33, 729–740 (1983)], might be affected by pleiotropy. Sequence overlap may thereby play a determinant role in enhancer function and evolution. Here, we investigated this problem with two regulatory activities of theDrosophilageneyellow, the novelspotenhancer and the ancestralwing bladeenhancer. We used precise and comprehensive quantification of each activity inDrosophilawings to systematically map their sequences along the locus. We show that thespotenhancer has co-opted the sequences of thewing bladeenhancer. We also identified a pleiotropic site necessary for DNA accessibility of a shared regulatory region. While the evolutionary steps leading to the derived activity are still unknown, such pleiotropy suggests that enhancer accessibility could be one of the molecular mechanisms seeding evolutionary co-option.