Ectopic expression of the Brachyury transcription factor upregulates only a subset of notochord expressed genes

The key notochord transcription factor Brachyury was ectopically expressed in Ciona embryos under the control of the FoxAa cis-regulatory region (which drives expression in neural, endodermal and mesenchymal lineages in addition to notochord). Misexpression of Brachyury induced 925 genes compared to a control reporter plasmid (Bra>GFP). There was only modest overlap with a set of notochord-enriched genes previously identified by RNAseq of flow-sorted notochord cells, indicating that Brachyury is not a notochord master regulator gene as strictly defined. Fertilized dechorionated eggs were electroporated with either FoxAa>Venus-Bra plasmid or control plasmid (Bra