ArticlePLoS genetics2015
Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
25 citing papers in PubMed, 44 citations in OpenAlex.
- Reversion of passaged nucleus pulposus cells to notochordal-type cells by FoxA2 upregulation.NPJ Regenerative medicine · 2025Article
- 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
- CRISPR/Cas9 Protocols for Disrupting Gene Function in the Non-vertebrate Chordate Ciona.Integrative and comparative biology · 2024Review
- Dedifferentiation-like reprogramming of degenerative nucleus pulposus cells into notochordal-like cells by defined factors.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Article
- Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona.Nature communications · 2024Article
- Searching for marine embryos, finding my path.Genesis (New York, N.Y. : 2000) · 2023Article
- Spatially multicellular variability of intervertebral disc degeneration by comparative single-cell analysis.Cell proliferation · 2023Article
- In Vitro Embryogenesis and Gastrulation Using Stem Cells in Mice and Humans.International journal of molecular sciences · 2023Review
- DNA Sequence and Structure under the Prism of Group Theory and Algebraic Surfaces.International journal of molecular sciences · 2022Article
- Spatial transcriptomic profiling to identify mesoderm progenitors with precision genomic screening and functional confirmation.Cell proliferation · 2022Article
- Article
- Article
- Spatially defined single-cell transcriptional profiling characterizes diverse chondrocyte subtypes and nucleus pulposus progenitors in human intervertebral discs.Bone research · 2021Article
- Brachyury controlsDevelopment (Cambridge, England) · 2021Article
- The AscidiaFrontiers in cell and developmental biology · 2021Article
- Evolution of Developmental Programs for the Midline Structures in Chordates: Insights From Gene Regulation in the Floor Plate and Hypochord Homologues ofFrontiers in cell and developmental biology · 2021Article
- Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos.eLife · 2020Article
- Review
- The lateral plate mesoderm.Development (Cambridge, England) · 2020Review
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues. This study focuses on elucidating how gene expression is initiated in the notochord, an axial structure that provides support and patterning signals to embryos of humans and all other chordates. Although numerous notochord genes have been identified, the regulatory DNAs that orchestrate development and propel evolution of this structure by eliciting notochord gene expression remain mostly uncharted, and the information on their configuration and recurrence is still quite fragmentary. Here we used the simple chordate Ciona for a systematic analysis of notochord cis-regulatory modules (CRMs), and investigated their composition, architectural constraints, predictive ability and evolutionary conservation. We found that most Ciona notochord CRMs relied upon variable combinations of binding sites for the transcription factors Brachyury and/or Foxa2, which can act either synergistically or independently from one another. Notably, one of these CRMs contains a Brachyury binding site juxtaposed to an (AC) microsatellite, an unusual arrangement also found in Brachyury-bound regulatory regions in mouse. In contrast, different subsets of CRMs relied upon binding sites for transcription factors of widely diverse families. Surprisingly, we found that neither intra-genomic nor interspecific conservation of binding sites were reliably predictive hallmarks of notochord CRMs. We propose that rather than obeying a rigid sequence-based cis-regulatory code, most notochord CRMs are rather unique. Yet, this study uncovered essential elements recurrently used by divergent chordates as basic building blocks for notochord CRMs.
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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.