Decoding cnidarian cell type gene regulation.

Animal cell types are defined by differential access to genomic information-a process orchestrated by the combinatorial activity of transcription factors that bind to cis-regulatory elements (CREs) to control gene expression. Changes in these gene regulatory networks (GRNs) underlie the origin and diversification of cell types, yet the regulatory logic and specific GRNs that define cell identities remain poorly resolved across the animal tree of life. Cnidarians, as early-branching metazoans, provide a critical window into the early evolution of cell type-specific genome regulation. Here we profiled chromatin accessibility in 60,000 cells from whole adults and gastrula-stage embryos of the sea anemone Nematostella vectensis. We identified 112,728 putative CREs and quantified their activity across cell types, revealing pervasive combinatorial enhancer usage and distinct promoter architectures. To decode the underlying regulatory grammar, we trained sequence-based models predicting CRE accessibility and used these models to infer cell type similarities that reflect known ontogenetic relationships. By integrating sequence motifs, transcription factor expression and CRE accessibility, we reconstructed the GRNs that define cnidarian cell types. Our results show the regulatory complexity underlying cell differentiation in a morphologically simple animal and highlight conserved principles in animal gene regulation. This work provides a foundation for comparative regulatory genomics to understand the evolutionary emergence of animal cell type diversity.