ArticleDevelopmental biology2009
A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo.
Article in Developmental biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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52 citing papers in PubMed, 113 citations in OpenAlex.
- PFAS compounds PFOA and Gen X are teratogenic to sea urchin embryos.Developmental biology · 2025Article
- An RNA interference approach for functional studies in the sea urchin and its use in analysis of nodal signaling gradients.Developmental biology · 2024Article
- Contrasting the development of larval and adult body plans during the evolution of biphasic lifecycles in sea urchins.Development (Cambridge, England) · 2024Article
- An RNA interference approach for functional studies in the sea urchin and its use in analysis of Nodal signaling gradients.bioRxiv : the preprint server for biology · 2024Article
- Hybrid Epigenomes Reveal Extensive Local Genetic Changes to Chromatin Accessibility Contribute to Divergence in Embryonic Gene Expression Between Species.Molecular biology and evolution · 2023Article
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- Homologous gene regulatory networks control development of apical organs and brains in Bilateria.Science advances · 2022Article
- Limb Mesoderm and Head Ectomesenchyme Both Express a Core Transcriptional Program During Chondrocyte Differentiation.Frontiers in cell and developmental biology · 2022Article
- Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea UrchinBiomedicines · 2021Article
- Developmental gene regulatory network connections predicted by machine learning from gene expression data alone.PloS one · 2021Article
- Genetic basis for divergence in developmental gene expression in two closely related sea urchins.Nature ecology & evolution · 2020Article
- Gastrulation in the sea urchin.Current topics in developmental biology · 2020Review
- An Effective Microinjection Method and TALEN-Mediated Genome Editing in Pacific Abalone.Marine biotechnology (New York, N.Y.) · 2019Article
- Reference assembly and gene expression analysis of Apostichopus japonicus larval development.Scientific reports · 2019Article
- Divergence of ectodermal and mesodermal gene regulatory network linkages in early development of sea urchins.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Article
- Developmental gene regulatory networks in sea urchins and what we can learn from them.F1000Research · 2016Review
- Ca²⁺ influx-linked protein kinase C activity regulates the β-catenin localization, micromere induction signalling and the oral-aboral axis formation in early sea urchin embryos.Zygote (Cambridge, England) · 2015Article
- Nodal signaling is required for mesodermal and ventral but not for dorsal fates in the indirect developing hemichordate, Ptychodera flava.Biology open · 2015Article
- Response to Nodal morphogen gradient is determined by the kinetics of target gene induction.eLife · 2015Article
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Authors and funding
6 authors at 3 institutions in 1 country.
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Abstract
The current gene regulatory network (GRN) for the sea urchin embryo pertains to pregastrular specification functions in the endomesodermal territories. Here we extend gene regulatory network analysis to the adjacent oral and aboral ectoderm territories over the same period. A large fraction of the regulatory genes predicted by the sea urchin genome project and shown in ancillary studies to be expressed in either oral or aboral ectoderm by 24 h are included, though universally expressed and pan-ectodermal regulatory genes are in general not. The loci of expression of these genes have been determined by whole mount in situ hybridization. We have carried out a global perturbation analysis in which expression of each gene was interrupted by introduction of morpholino antisense oligonucleotide, and the effects on all other genes were measured quantitatively, both by QPCR and by a new instrumental technology (NanoString Technologies nCounter Analysis System). At its current stage the network model, built in BioTapestry, includes 22 genes encoding transcription factors, 4 genes encoding known signaling ligands, and 3 genes that are yet unknown but are predicted to perform specific roles. Evidence emerged from the analysis pointing to distinctive subcircuit features observed earlier in other parts of the GRN, including a double negative transcriptional regulatory gate, and dynamic state lockdowns by feedback interactions. While much of the regulatory apparatus is downstream of Nodal signaling, as expected from previous observations, there are also cohorts of independently activated oral and aboral ectoderm regulatory genes, and we predict yet unidentified signaling interactions between oral and aboral territories.
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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.