Decoding cnidarian cell type gene regulation

Animal cell types are defined by differential access to genomic information, yet the regulatory programs governing cell identity remain largely unexplored across the animal tree of life. We used scATAC-seq to map chromatin accessibility landscapes in ~60,000 cells from whole adult and gastrula stages of the sea anemone Nematostella vectensis. We quantified cell type-specific activity for ~112,000 cis-regulatory elements (CREs), revealing extensive combinatorial enhancer usage and distinct promoter architectures. To further decode regulatory motif grammars, we trained sequence-based models predicting CRE activity and studied ontogenetic relationships between cell types. Integrating sequence motifs with transcription factor expression and CRE accessibility, we reconstructed gene regulatory networks that define cnidarian cell identities. Our work uncovers the complexity and logic of cell type gene regulation in early-branching animals. Overall design: Nuclei suspensions were obtained from whole adult and gastrula-stage Nematostella vectensis wild-type animals, or Fluorescent-activated cell sorting (FACS) isolated elav+ neurons from NvElav1::mOrange transgenic polyps. Single cell ATACseq (scATACseq) libraries were prepared using 10x Genomics platform