Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo
Open accessAbstract
We dissect the transcriptional regulatory relationships coordinating the dynamic expression patterns of two signaling genes, wnt8 and delta, which are central to specification of the sea urchin embryo endomesoderm. cis-Regulatory analysis shows that transcription of the gene encoding the Notch ligand Delta is activated by the widely expressed Runx transcription factor, but spatially restricted by HesC-mediated repression through a site in the delta 5'UTR. Spatial transcription of the hesC gene, however, is controlled by Blimp1 repression. Blimp1 thus represses the repressor of delta, thereby permitting its transcription. The blimp1 gene is itself linked into a feedback circuit that includes the wnt8 signaling ligand gene, and we showed earlier that this circuit generates an expanding torus of blimp1 and wnt8 expression. The finding that delta expression is also controlled at the cis-regulatory level by the blimp1-wnt8 torus-generating subcircuit now explains the progression of Notch signaling from the mesoderm to the endoderm of the developing embryo. Thus the specific cis-regulatory linkages of the gene regulatory network encode the coordinated spatial expression of Wnt and Notch signaling as they sweep outward across the vegetal plate of the embryo.
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Genes of antagonistic repressor pairs and/or their immediate targets provide direct positive or negative inputs into terminal differentiation genes of the alternate lineages.
“An important point is that the genes of the antagonistic repressor pairs, and/or the regulatory genes that are their immediate targets, also provide direct positive or negative inputs into terminal differentiation genes of the alternate lineages37,39.”
From Emerging properties of animal gene regulatory networks (2010) · cites this paper as [39]
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- Authors
- Smith, J., & Davidson, E. H.
- Affiliations
- California Institute of Technology (US)
- ORCID
- Smith, Joel
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2008-12-23
- Volume
- 105
- Issue
- 51
- Pages
- 20089-20094
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC2629318
- OpenAlex
- W2095234579
- Cited by
- 69
- References
- 40
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- FWCI
- 4.12
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Funders
- California Institute for Regenerative Medicine
- National Institutes of Health (5p01hd037105-20)
- National Institute of General Medical Sciences (R24GM075089, GM075089, GM 061005, R01GM061005)
- National Institute of Child Health and Human Development (037105)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD 037105, P01-HD037105)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- gene regulatory networks, sea urchin embryo, Wnt signaling, Notch signaling, Delta, Wnt8, Blimp-1, RUNX, cis-regulatory elements, 5' untranslated region, endomesoderm specification, mesoderm, feedback circuits, spatial gene expression, transcriptional repression
- MeSH terms
- Animals, Embryo, Nonmammalian, Endoderm, Enhancer Elements, Genetic, Membrane Proteins, Mesoderm, Sea Urchins, Transcription, Genetic, Signal Transduction, Gene Expression Regulation, Developmental, Intracellular Signaling Peptides and Proteins, Wnt Proteins, Gene Regulatory Networks
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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