Abstract. Cnidarians are important models for studying the evolution of animal development, regeneration, cell type differentiation, and allorecognition. T

Experiments in the cnidarian Nematostella vectensis show a role of gene body methylation in transposable element suppression and that epigenetic inheritance is constrained by chromatin context and tra...

A sea urchin is a head with a brain-like organization and a vertebrate-type retinal signature.

Genomic sequencing of the thermotolerant coral species Oculina patagonica, single-cell transcriptomic analyses of symbiotic and non-symbiotic specimens and comparisons with obligate symbiotic coral species reveal adaptations that provide resilience to coral bleaching.

Discovery of calcarins in calcareous sponges highlights gene duplication and neofunctionalization as drivers of parallel biomineralization, offering insight into the independent evolution of calcifica...

Recent work suggested that diploblast embryos (Cnidaria) may have germ layers that are similar to those seen in bilaterians, but how these are specified remained unclear. Here, they use scRNA-seq and ...

Species from diverse animal lineages have conserved groups of orthologous genes together on the same chromosome for over half a billion years since the last common ancestor of bilaterians. Although no...

Microbial holozoans are the closest unicellular relatives of animals. They share a substantial gene repertoire with animals and exhibit complex life cycles. Studying these organisms is crucial for und...

How did the chromatin folding mechanisms controlling gene regulation emerge during animal evolution? Kim et al. surveyed chromatin folding at high-resolution in unicellular relatives of animals as wel...

The authors evaluate heritable genetic variation in thermal tolerance in a common reef-building coral. They show widespread heritable genetic variation, which is strongly associated with marine heatwa...

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. However, the regulatory logic and specific gene networks that define cell identities remain poorly resolved across the animal tree of life. As early-branching metazoans, cnidarians can offer insights 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 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 ontogenetic relationships among cell types. By integrating sequence motifs, transcription factor expression, and CRE accessibility, we systematically reconstructed the gene regulatory networks that define cnidarian cell types. Our results reveal 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. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, ERC-StG 851647 Ministerio de Ciencia e Innovación, https://ror.org/05r0vyz12, PID2021-124757NB-I00, FPI Severo Ochoa PhD fellowship European Union, https://ror.org/019w4f821, Marie Skłodowska-Curie INTREPiD co-fund agreement 75442, Marie Skłodowska-Curie grant agreement 101031767

Woodgate et al. describe a new bilaterally symmetrical echinoderm, Atlascystis acantha, from the Cambrian of Morocco. Comparisons of plate growth with other echinoderms reveal that Atlascystis possess...

In Bilateria with centralized nervous systems (e.g. in vertebrates or arthropods), the minimum of the BMP signaling activity gradient defines the position of the central nervous system. BMP-dependent ...

Principle of ATAC-seq (left), overview of arthropod species with published ATAC-seq data (middle), summary of experimental design (right).