Functional and evolutionary insights from the Ciona notochord transcriptome

Citations Over TimeTop 12% of 2017 papers

Abstract

The notochord of the ascidian Ciona consists of only 40 cells, and is a longstanding model for studying organogenesis in a small, simple embryo. Here, we perform RNAseq on flow-sorted notochord cells from multiple stages to define a comprehensive Ciona notochord transcriptome. We identify 1364 genes with enriched expression and extensively validate the results by in situ hybridization. These genes are highly enriched for Gene Ontology terms related to the extracellular matrix, cell adhesion and cytoskeleton. Orthologs of 112 of the Ciona notochord genes have known notochord expression in vertebrates, more than twice as many as predicted by chance alone. This set of putative effector genes with notochord expression conserved from tunicates to vertebrates will be invaluable for testing hypotheses about notochord evolution. The full set of Ciona notochord genes provides a foundation for systems-level studies of notochord gene regulation and morphogenesis. We find only modest overlap between this set of notochord-enriched transcripts and the genes upregulated by ectopic expression of the key notochord transcription factor Brachyury, indicating that Brachyury is not a notochord master regulator gene as strictly defined.

Related Papers

• → Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis(1997)476 cited
• → Functional Brachyury Binding Sites Establish a Temporal Read-out of Gene Expression in the Ciona Notochord(2013)50 cited
• → The identification of transcription factors expressed in the notochord of Ciona intestinalis adds new potential players to the brachyury gene regulatory network(2011)47 cited
• → The evolutionarily conserved leprecan gene: Its regulation by Brachyury and its role in the developing Ciona notochord(2009)34 cited
• → The Sea Squirt Ciona intestinalis: Figure 1.(2009)30 cited