Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq
Open accessAbstract
The emergence and diversification of cell types is a leading factor in animal evolution. So far, systematic characterization of the gene regulatory programs associated with cell type specificity was limited to few cell types and few species. Here, we perform whole-organism single-cell transcriptomics to map adult and larval cell types in the cnidarian Nematostella vectensis, a non-bilaterian animal with complex tissue-level body-plan organization. We uncover eight broad cell classes in Nematostella, including neurons, cnidocytes, and digestive cells. Each class comprises different subtypes defined by the expression of multiple specific markers. In particular, we characterize a surprisingly diverse repertoire of neurons, which comparative analysis suggests are the result of lineage-specific diversification. By integrating transcription factor expression, chromatin profiling, and sequence motif analysis, we identify the regulatory codes that underlie Nematostella cell-specific expression. Our study reveals cnidarian cell type complexity and provides insights into the evolution of animal cell-specific genomic regulation.
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In both Nematostella and Aurelia, the combination of exocrine and insulinergic cells is confined to tissues expressing the foxA transcription factor.
“In both Nematostella and Aurelia (see above), the combination of exocrine and insulinergic cells is confined to tissues expressing the foxA transcription factor, which is a conserved marker of bilaterian endoderm, midgut or vertebrate foregut (Sebé-Pedrós et al. 2018b; Steinmetz et al. 2017).”
From A non-bilaterian perspective on the development and evolution of animal digestive systems (2019) · cites this paper as Sebé-Pedrós et al. 2018b
In Nematostella, the expression of genes encoding secreted digestive enzymes is strictly restricted to the pharynx and cnidoglandular tract.
“In Nematostella, the expression of genes encoding for secreted digestive enzymes, and thus reflecting the location of potential zymogen cells, is strictly restricted to the pharynx and cnidoglandular tract.”
From A non-bilaterian perspective on the development and evolution of animal digestive systems (2019) · cites this paper as Sebé-Pedrós et al. 2018b
The juvenile trophic tract co-expresses Nematostella orthologs of foxC, six4/5 and nkx3/bagpipe transcription factors, whose bilaterian counterparts are consistently co-localised to bilaterian visceral mesoderm.
“Instead, this phagocytic tissue co-expresses Nematostella orthologs of foxC, six4/5 and nkx3/bagpipe transcription factors, whose bilaterian counter-parts are consistently co-localised to bilaterian visceral mesoderm (Sebé-Pedrós et al. 2018b; Steinmetz et al. 2017).”
From A non-bilaterian perspective on the development and evolution of animal digestive systems (2019) · cites this paper as Sebé-Pedrós et al. 2018b
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- Authors
- Sebé-Pedrós, A., Saudemont, B., Chomsky, E., Plessier, F., Mailhé, M.-P., Renno, J., Loe-Mie, Y., Lifshitz, A., Mukamel, Z., Schmutz, S., Novault, S., Steinmetz, P. R. H., Spitz, F., Tanay, A., & Marlow, H.
- Affiliations
- Weizmann Institute of Science (IL)
- Centre National de la Recherche Scientifique (FR)
- École Normale Supérieure de Lyon (FR)
- Institut Pasteur (FR)
- University of Bergen (NO)
- Corresponding author
- Tanay, Amos
- Marlow, Heather
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2018-05
- Volume
- 173
- Issue
- 6
- Pages
- 1520-1534.e20
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2807587036
- Cited by
- 330
- References
- 13
- Citations by year
- 2026: 30 · 2025: 41 · 2024: 36 · 2023: 38 · 2022: 55 · 2021: 48 · 2020: 31 · 2019: 41 · 2018: 10
- FWCI
- 22.95
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Funders
- EMBO (ALTF 841-2014)
- Region Ile de France (SESAME 2016)
- Pasteur Citech
- European Research Council (724824)
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- Nematostella vectensis, cell type diversity, cell type-specific gene regulation, neurons, cnidocytes, digestive cells, larval development, transcription factors, chromatin profiling, sequence motifs
- MeSH terms
- Actins, Animals, Chromatin, Neurons, Phylogeny, RNA, Sea Anemones, Tubulin, Cluster Analysis, Genome, Sequence Analysis, RNA, Gene Expression Regulation, Developmental, Amino Acid Motifs, Gene Expression Profiling, Genomics, Transcriptome
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