Epigenomic and transcriptomic profiling of cnidocyte subtypes in the sea anemone Nematostella vectensis [RNA-Seq]

Cnidarians, including corals, sea anemones, and jellyfish, possess specialized stinging cells called cnidocytes that function in prey capture and defense. These cells represent a striking evolutionary innovation and include distinct types such as venom injecting nematocytes and mechanically acting spirocytes. While their biomechanics and transcriptional regulation have been studied extensively, little is known about their epigenetic regulation. Here, we combined epigenetic profiling with RNA sequencing in the sea anemone Nematostella vectensis to explore regulatory programs underlying cnidocyte diversity. We identified cell type specific regulatory elements in promoter and enhancer regions and linked them to distinct gene expression programs. This analysis revealed fundamental differences between nematocytes and spirocytes and uncovered a previously unrecognized nematocyte population that expresses the nep3 toxin but lacks most other toxins. These findings highlight the complexity of cnidocyte regulation and suggest greater cellular diversity within this defining cnidarian cell type than previously appreciated. This study investigates the chromatin and transcriptional programs underlying cnidocyte specialization in the sea anemone Nematostella vectensis. Cnidocyte types (Ncol3⁺ and Nep3⁺) and their negative counterparts were isolated from adult polyps by fluorescence activated cell sorting (FACS). CUT&Tag (H3K27ac) and RNA-seq were performed in four biological replicates per condition to identify cell type-specific regulatory regions and gene expression programs. The design allows direct comparisons between positive and negative populations for each reporter line.