title: Unexpected complexity of the reef-building coral Acropora millepora transcription factor network.
abstract: BACKGROUND
  Coral reefs are disturbed on a global scale by environmental changes including rising sea surface temperatures and ocean acidification. Little is known about how corals respond or adapt to these environmental changes especially at the molecular level. This is mostly because of the paucity of genome-wide studies on corals and the application of systems approaches that incorporate the latter. Like in any other organism, the response of corals to stress is tightly controlled by the coordinated interplay of many transcription factors.
  
  
  RESULTS
  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".
  
  
  CONCLUSIONS
  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.
authors.affiliation: Division of Chemical & Life Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
authors.forename: Taewoo
authors.initials: T
authors.lastname: Ryu
authors.forename: Charalampos Harris
authors.initials: CH
authors.lastname: Mavromatis
authors.forename: Till
authors.initials: T
authors.lastname: Bayer
authors.forename: Christian R
authors.initials: CR
authors.lastname: Voolstra
authors.forename: Timothy
authors.initials: T
authors.lastname: Ravasi
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000235:genetics* / Q000254:growth & development; D005075:Biological Evolution; D018983:DNA Footprinting / Q000379:methods; D020869:Gene Expression Profiling; D023281:Genomics; D008954:Models, Biological; D009792:Oceans and Seas; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors