Preprint maps how shadow enhancers arise from duplication, transposable elements, and splitting in fly and mouse

A preprint posted to bioRxiv reports a genome-wide investigation into the evolutionary origins of shadow enhancers in Drosophila and mouse. Shadow enhancers are pairs or groups of DNA regulatory elements that independently drive overlapping expression patterns for the same target gene; large-scale surveys have established that they regulate the majority of developmental genes in animal genomes, but how they originate has been less thoroughly studied.

The authors searched for sequence signatures of three proposed birth mechanisms: duplication of pre-existing enhancers, co-option of transposable elements (TEs), and TE-mediated splitting of a single ancestral enhancer into two. They find that genome architecture — including the three-dimensional organisation of regulatory domains — shapes which mechanism predominates for a given locus.

The work is relevant to researchers in gene regulation, developmental genetics, and evolutionary genomics, and to those studying the contribution of transposable elements to regulatory innovation. It adds to a growing body of work demonstrating that TEs are not merely selfish genetic elements but contributors to the regulatory repertoire of animal genomes. The preprint has not yet been peer-reviewed.