Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network

Here, we develop and apply a new system-wide approach in order to infer combinatorial transcription factor networks of the reef-building coral Acropora millepora. By integrating sequencing-derived transcriptome measurements, a network of physically interacting transcription factors, and phylogenetic network footprinting we were able to infer such a network. Analysis of the network across a phylogenetically broad sample of five species, including human, reveals that despite the apparent simplicity of corals, their transcription factors repertoire and interaction networks seem to be largely conserved. In addition, we were able to identify interactions among transcription factors that appear to be species-specific lending strength to the novel concept of "Taxonomically Restricted Interactions".This study provides the first look at transcription factor networks in corals. We identified a transcription factor repertoire encoded by the coral genome and found consistencies of the domain architectures of transcription factors and conserved regulatory subnetworks across eumetazoan species, providing insight into how regulatory networks have evolved.Deciphering and predicting transcriptional regulatory networks is of considerable importance in understanding how organisms function, adapt, and respond to changes in their environment. Much effort has been addressed to elucidate these regulatory networks in several model organisms. For instance, global transcription factors (TFs) combinatorial interaction maps were built in human and mouse [1] and developmental gene regulatory circuits were elucidated in the sea urchin embryo [2,3]. However, little effort has been made so far in understanding the structure, function, and conversation of transcriptional networks in non-model organisms, e.g. corals, despite their ecological importance.Corals are members of the phylum Cnidaria that includes such diverse forms as jellyfish, hydra, and sea anemones. Reef-building corals (Cnidaria: Hex