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Description
Ascidians, especially Ciona robusta, have been a great model for neurodevelopmental biology. Their unique phylogenetic position as the closest invertebrate chordate to vertebrate gives advantages as a model organism. Their embryonic nervous system is remarkably simple but has structures very similar to neural crest and cranial placodes of vertebrate. Understanding the development of their nervous system can be a hint to unravel the mysteries of our nervous system development. In the early stages of this developmental process, one gene is known to be expressed universally in preneural cells: Pou4. Previous studies suggest that Pou4 plays a key role in the development of sensory cells in multiple species by providing the “ground state” sensory neurons. However, very few features are known about Pou4. This research project was conducted to predict the putative direct target genes of Pou4 within the C. robusta genome utilizing accessible data and computational tools. Binding and Expression Target Analysis (BETA) was used for the target identification, which requires TFBS data and gene expression profile. ChIP-seq-like TFBS data were computationally generated by Hypergeometric Optimization of Motif EnRichment (HOMER), and the expression profile was obtained by an RNA-seq experiment when Pou4 is misexpressed. GO term analysis was conducted after BETA, which refined the results and selected only the genes that are involved in nervous system development. Finally, in situ hybridization expression data on Ghost Database helped select only the genes expressed when and where Pou4 is available. A total number of 2370 genes were predicted to be target genes of Pou4 according to BETA results, which includes some of the genes that are presumed to be direct targets of Pou4 in our lab such as Atonal, Pou4, and Gelsolin. After the GO terms and in situ expression analysis, 32 putative target genes of Pou4 that are involved in nervous system development were found. Despite the limitations of this project, our finding can lead further research into those newly found targets, which can help us better understand the features of Pou4 and nervous system development.
