Early origin and deep conservation of enhancers in animals

Transcription factors (TFs) bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs, the evolution of enhancers has been difficult to trace because of their rapid evolution. Here, we show enhancers from the sponge Amphimedon queenslandica can drive cell type-specific reporter gene expression in zebrafish and mouse, despite sponge and vertebrate lineages diverging over 700 million years ago. Although sponge enhancers, which are present in both highly conserved syntenic gene regions (Islet:Scaper, Ccne1:Uri and Tdrd3:Diaph3) and sponge-specific intergenic regions, have no significant sequence identity with vertebrate genomic sequences, the type and frequency of TF binding motifs in the sponge enhancer allow for the identification of homologous enhancers in bilaterians. Islet enhancers identified in human and mouse Scaper genes drive zebrafish reporter expression patterns that are almost identical to the sponge Islet enhancer. The existence of homologous enhancers in these disparate metazoans suggests animal development is controlled by TF-enhancer DNA interactions that were present in the first multicellular animals.