Figure 4.

An updated Hydra single-cell RNA-seq atlas reveals novel regulators of gene coexpression in Hydra. (A) Uniform manifold approximation and projection (UMAP) dimensional reduction of the Hydra single-cell RNA-seq atlas mapped to the AEP reference genome captures virtually all known cell states in adult polyps. Inset shows UMAP colored by the three stem cell lineages in adult Hydra. (NCs) Nematocytes; (NBs) nematoblasts; (SCs) stem cells; (Ecto) ectodermal epithelial cells; (Endo) endodermal epithelial cells; (GCs) gland cells; (Ec) neuron subtypes found in the ectoderm; (En) neuron subtypes found in the endoderm. (B) The gene G008733 is a specific marker for isorhiza nematocytes. (C–E) In situ hybridization targeting G008733 labels isorhiza nematocytes (black arrowheads) in upper body column tissue. (F) scleraxis is a specific marker for ectodermal somatic gonad cells. (G) In situ hybridization targeting scleraxis in male polyps labels ectodermal testes cells. (H) In situ hybridization reveals scleraxis is expressed in egg patches in female polyps. (I–M) Motif enrichment and gene expression patterns reveal candidate regulators of cell state. (I) TCF motif enrichment and wnt3 expression data corroborate the role of TCF/Wnt signaling in epithelial head tissue. (J) GATA motif enrichment and expression data corroborate the role of gata1-3 in aboral epithelial tissue and suggest an additional function in Ec3 neurons. (K) Pou4 motif enrichment and expression data suggest pou4 regulates transcription in differentiating and mature neurons and nematocytes. (L) Ebf motif enrichment and expression data suggest ebf regulates transcription during oogenesis. (M) NR2F motif enrichment and expression data suggest nr2f-like regulates transcription during nematogenesis. Corresponding JASPAR motif IDs are provided in the parenthetical text under the motif names (Fornes et al. 2020). (ES) Enrichment score; (NC) normalized counts.