ArticlePLoS biology2013
Functional Brachyury binding sites establish a temporal read-out of gene expression in the Ciona notochord.
Article in PLoS biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 50 citations in OpenAlex.
- Fine-Tuned Expression of Evolutionarily Conserved Signaling Molecules in theInternational journal of molecular sciences · 2024Article
- Single-cell Transcriptomic Studies Unveil Potential Nodes of the Notochord Gene Regulatory Network.Integrative and comparative biology · 2024Review
- Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona.Nature communications · 2024Article
- Loss of collagen gene expression in the notochord of the tailless tunicate Molgula occulta.Integrative and comparative biology · 2023Article
- Searching for marine embryos, finding my path.Genesis (New York, N.Y. : 2000) · 2023Article
- Tissue-specific expression of carbohydrate sulfotransferases drives keratan sulfate biosynthesis in the notochord and otic vesicles ofFrontiers in cell and developmental biology · 2023Article
- An ancestral Wnt-Brachyury feedback loop in axial patterning and recruitment of mesoderm-determining target genes.Nature ecology & evolution · 2022Article
- Article
- The Degenerate Tale of Ascidian Tails.Integrative and comparative biology · 2021Review
- Genome-Wide Identification, Comparison, and Expression Analysis of Transcription Factors in AscidianInternational journal of molecular sciences · 2021Article
- Brachyury controlsDevelopment (Cambridge, England) · 2021Article
- Dynamic patterning by morphogens illuminated by cis-regulatory studies.Development (Cambridge, England) · 2021Review
- The Roles of Embryonic Transcription Factor BRACHYURY in Tumorigenesis and Progression.Frontiers in oncology · 2020Review
- The notochord gene regulatory network in chordate evolution: Conservation and divergence from Ciona to vertebrates.Current topics in developmental biology · 2020Review
- Positioning a multifunctional basic helix-loop-helix transcription factor within the Ciona notochord gene regulatory network.Developmental biology · 2019Article
- Review
- Dynamic interplay of cell fate, polarity and force generation in ascidian embryos.Current opinion in genetics & development · 2018Review
- Functional and evolutionary insights from theDevelopment (Cambridge, England) · 2017Article
- Fibronectin contributes to notochord intercalation in the invertebrate chordate, Ciona intestinalis.EvoDevo · 2016Article
- Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.PLoS genetics · 2015Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
The appearance of the notochord represented a milestone in Deuterostome evolution. The notochord is necessary for the development of the chordate body plan and for the formation of the vertebral column and numerous organs. It is known that the transcription factor Brachyury is required for notochord formation in all chordates, and that it controls transcription of a large number of target genes. However, studies of the structure of the cis-regulatory modules (CRMs) through which this control is exerted are complicated in vertebrates by the genomic complexity and the pan-mesodermal expression territory of Brachyury. We used the ascidian Ciona, in which the single-copy Brachyury is notochord-specific and CRMs are easily identifiable, to carry out a systematic characterization of Brachyury-downstream notochord CRMs. We found that Ciona Brachyury (Ci-Bra) controls most of its targets directly, through non-palindromic binding sites that function either synergistically or individually to activate early- and middle-onset genes, respectively, while late-onset target CRMs are controlled indirectly, via transcriptional intermediaries. These results illustrate how a transcriptional regulator can efficiently shape a shallow gene regulatory network into a multi-tiered transcriptional output, and provide insights into the mechanisms that establish temporal read-outs of gene expression in a fast-developing chordate embryo.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.