Caught in the evolutionary act: Precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins

Abstract

The regulatory control of otxbeta1/2 in the sea urchin Strongylocentrotus purpuratus and the sea star Asterina miniata provides an exceptional opportunity to determine the genomic basis of evolutionary change in gene regulatory network (GRN) architectures. Network perturbation analyses in both taxa show that Otx regulates the transcription factors gatae and krox/blimp1 and both of these transcription factors also feed back and regulate otx. The otx gene also autoregulates. This three way interaction is an example of a GRN kernel. It has been conserved for 500 million years since these two taxa last shared a common ancestor. Amid this high level of conservation we show here one significant regulatory change. Tbrain is required for correct otxbeta1/2 expression in the sea star but not in the sea urchin. In sea urchin, tbrain is not co-expressed with otxbeta1/2 and instead has an essential role in specification of the embryonic skeleton. Tbrain in these echinoderms is thus a perfect example of an orthologous gene co-opted for entirely different developmental processes. We isolate and test the sea star otxbeta1/2 cis-regulatory module and demonstrate functional binding sites for each of the predicted inputs, including Tbrain. We compare it to the logic processing operating in the sea urchin otxbeta1/2 cis-regulatory module and present an evolutionary scenario of the change in Tbrain dependence. Finally, inter-specific gene transfer experiments confirm this scenario and demonstrate evolution occurring at the level of sequence changes to the cis-regulatory module.

A gene regulatory network for apical organ neurogenesis and its spatial control in sea star embryos

“…Sequencing confirmed successful integration (Yu et al, 2000). Constructs were prepared and injected as described previously (Hinman et al, 2007).…”

Transphyletic conservation of developmental regulatory state in animal evolution

“…However, highly conserved cis-regulatory sequences account for only a minor fraction of the large number of genomic cis-regulatory modules likely to exist in animal genomes (8), and cis-regulatory comparisons at significant evolutionary distance often reveal conserved control functions even when sequence conservation is not detectable across the cis-regulatory module. In such examples, where functional assays carried out by insertion of known cis-regulatory modules into the genomes of different species reveal conserved function, it is found that only the specific transcription factor (TF) target sites are retained, spaced in nonconserved DNA sequence, often in diverse site order and number (9)(10)(11). Whether the DNA sequence of the cis-regulatory module is largely conserved or not, if the function remains the same, the implication is that the set of TFs to which its target sites respond are largely the same.…”

Evolutionary crossroads in developmental biology: sea urchins

“…A comparative analysis of the endomesoderm GRN between sea urchins and sea stars showed that much of the early circuitry responsible for activation of endoderm is conserved, despite an evolutionary separation from a common ancestor more than 500 million years ago (Hinman et al, 2003;Hinman et al, 2007). More distant comparisons show that many of the genes that operate early in the sea urchin GRN are also likely to govern the activation of GRNs in hemichordates (Lowe et al, 2006;Lemons et al, 2010), and components of the early network may also be conserved in other deuterostomes.…”