PUBLICATION
Functional and evolutionary insights from the Ciona notochord transcriptome.
- Authors
- Reeves, W.M., Wu, Y., Harder, M.J., Veeman, M.T.
- ID
- ZDB-PUB-171012-6
- Date
- 2017
- Source
- Development (Cambridge, England) 144: 3375-3387 (Journal)
- Registered Authors
- Keywords
- Ciona, Notochord, Transcriptome
- MeSH Terms
-
- Animals
- Biological Evolution*
- Ciona intestinalis/embryology*
- Ciona intestinalis/genetics*
- Cytoskeleton/genetics
- Embryo, Nonmammalian/metabolism
- Extracellular Matrix/metabolism
- Fetal Proteins/genetics
- Fetal Proteins/metabolism
- Gene Expression Regulation, Developmental
- Gene Ontology
- In Situ Hybridization
- Mice
- Notochord/embryology*
- Notochord/metabolism*
- Reproducibility of Results
- Sequence Analysis, RNA
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
- Transcriptome/genetics*
- Zebrafish/embryology
- Zebrafish/genetics
- PubMed
- 28928284 Full text @ Development
Citation
Reeves, W.M., Wu, Y., Harder, M.J., Veeman, M.T. (2017) Functional and evolutionary insights from the Ciona notochord transcriptome.. Development (Cambridge, England). 144:3375-3387.
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping