Boundary formation in sea anemone oral-aboral patterning

During the development of any embryo, the organism has to be subdivided into distinct regions, which will form all the body parts and organs. To facilitate that, the embryo needs a system of molecular coordinates called body axes. Once the body axes are established, the genetic programs regulating the growth of each body part can be activated at correct positions in a process termed axial patterning. To study axial patterning, we use a morphologically simple experimental system the embryo of the sea anemone Nematostella vectensis. Sea anemones and corals belong to Cnidaria, an evolutionary sister to Bilateria (a large group encompassing all conventional animals i.e. vertebrates and a vast majority of invertebrates). Thus, the comparison of the axial patterning mechanisms in the Nematostella embryo with what is known in different Bilateria may inform us about how these mechanisms evolved. One of the features of axial patterning is the ability to create extremely sharp boundaries between the neighbouring spatial domains. At the level of gene expression, these boundaries are established much earlier than they become evident morphologically. Our goal is to understand the evolution of the molecular boundary formation mechanisms. In bilaterian embryos (fruit fly, mouse etc.), sharp boundaries usually are established when neighbouring cells start to express mutually repressive transcription factors. In this FWF-funded project, we will test the idea that mutual repression of two axial domains represents the ancestral axial patterning principle by investigating the mechanism of the formation of two very sharp molecular boundaries in the oral part of the Nematostella embryo: the aboral boundaries of FoxA and Brachyury gene expression. If the mutual repression hypothesis is correct, the genes encoding the transcriptional repressors of FoxA and Brachyury should be directly bound by FoxA and Brachyury transcription factors. We will identify candidate transcriptional repressors among the genes bound by Brachyury and FoxA and then systematically knock them down using RNAi. If our hypothesis is correct and we will be able to turn the sharp FoxA and Brachyury domain boundary into a fuzzy one. Another intriguing question we will be addressing is the mechanism of the formation of the aboral/anterior domain of the Nematostella embryo. In bilaterian animals and in Nematostella, anterior molecular identity is the default, maternally imposed identity, which then gets restricted to the anterior end of the embryo by signals emanating from the forming posterior end. However, the mechanism by which maternal anterior identity changes to a zygotic anterior identity in Nematostella differs drastically from the mechanism used in Bilateria, and we want to understand it. We will use 10x multiomics combined with knockdown experiments to identify the factors responsible for the formation of the zygotic anterior identity.