Divergence of gene regulatory network linkages during specification of ectoderm and mesoderm in early development of sea urchins

Abstract

Developmental gene regulatory networks (dGRNs) are assemblages of interacting regulatory factors that direct ontogeny of animal body plans. The hierarchical topology of these networks predicts that their nodes will evolve at different rates and consequently will bias the trajectories of embryonic evolution. To test this, detailed, comparative analyses of dGRNs that specify early, global embryonic domains are required. The most extensively detailed dGRNs have been documented for one of the two subclasses of extant sea urchins, the euechinoids. Remarkably, euechinoid dGRNs operating in early development show little appreciable change even though they diverged approximately 90 million years ago (mya). Therefore, to better understand the evolutionary dynamics of dGRNs, comparative microdissection must be undertaken for sea urchins that diverged deeper in geological time. Recent studies of cidaroids, the sister clade of euechinoid sea urchins, suggest that comparative analyses of their embryonic domain specification may prove insightful for understanding the evolutionary dynamics of dGRNs. Here, I report the spatiotemporal dynamics of 19 regulatory factors involved in dorsal-ventral patterning of non-skeletogenic mesodermal and ectodermal domains in the early development of Eucidaris tribuloides, a cidaroid sea urchin. Multiple lines of evidence indicate that deployment of ectodermal regulatory factors is more impervious to change than mesodermal regulatory factors in the sea urchin lineage and are supported by multiple lines of experimental evidence. Additionally, endogenous spatiotemporal expression data, intra-class reporter microinjections, and perturbation analyses of Nodal and Notch signaling allow the enumeration of numerous alterations to regulatory factor deployment since the divergence of echinoids. These results provide a global view of early embryonic developmental processes in two clades that diverged at least 268.8 mya and show that the dGRNs controlling embryonic specification exhibit differential lability, supporting the hypothesis that the topologies of dGRNs bias rates of evolutionary change and alter the developmental evolutionary trajectories of embryogenesis.\n\nAuthor SummaryEarly in the development of an embryo, networks of genes are initiated to differentiate the rapidly dividing cells into distinct territories that will later serve specific functions. Sea urchins have revealed much about how this process unfolds. Recent studies have focused on one of the two modern lineages of sea urchins and have shown that these processes have not appreciably changed over the past 90 million years. I sought to determine if this trend extends over even larger evolutionary distances by investigating similar processes in a sea urchin from the second modern lineage, which is removed by 268 million years of evolution. By revealing where and when these genes are expressed and interfering with common mechanisms of development in a distantly related sea urchin, I show that changes to these networks of genes have occurred at all levels of the network. Additionally, I present data that suggests that changes to these networks of genes occur disproportionately in certain embryonic territories, which may be true for early development for other groups of organisms as well.