The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA inDrosophila

Abstract

AbstractThe density and distribution of regulatory information in non-coding DNA of eukaryotic genomes is largely unknown. Evolutionary analyses have estimated that ∼60% of nucleotides in intergenic regions of theD. melanogastergenome is functionally relevant. This estimate is difficult to reconcile with the commonly accepted idea that enhancers are compact regulatory elements that generally encompass less than 1 kilobase of DNA. Here, we approached this issue through a functional dissection of the regulatory region of the geneshavenbaby(svb). Most of the ∼90 kilobases of this large regulatory region is highly conserved in the genusDrosophila, though characterized enhancers occupy a small fraction of this region. By analyzing the regulation ofsvbin different contexts ofDrosophiladevelopment, we found that the regulatory architecture that drivessvbexpression in the abdominal pupal epidermis is organized in a dramatically different way than the information that drivessvbexpression in the embryonic epidermis. While in the embryonic epidermissvbis activated by compact and dispersed enhancers,svbexpression in the pupal epidermis is driven by large regions with enhancer activity, which occupy a great portion of thesvb cis-regulatory DNA. We observed that other developmental genes also display a dense distribution of putative regulatory elements in their regulatory regions. Furthermore, we found that a large percentage of conserved non-coding DNA of theDrosophilagenome is contained within putative regulatory DNA. These results suggest that part of the evolutionary constraint on non-coding DNA ofDrosophilais explained by the density of regulatory information.