Cnidofest

Cnidofest is a biennial meeting of scientists interested in developing and using cnidarians as model systems to study molecular and cellular biology, developmental biology, neurobiology, and comparati...

cnidofest.org

biorxiv.org

Efficient genome editing using CRISPR–Cas9 in reef-building corals - Nature Protocols

In this protocol, the authors present straightforward and efficient methods to genetically modify corals and study gene function throughout various life-history stages using CRISPR–Cas9-based mutagene...

nature.com

Decoding cnidarian cell type gene regulation - Nature Ecology & Evolution

This study reconstructs the gene regulatory networks that define cell types in the sea anemone Nematostella vectensis, providing a valuable resource for comparative regulatory genomics and the evoluti...

nature.com

Whole body regeneration deploys a rewired embryonic gene regulatory network logic - Nature Communications

To what extent regeneration recapitulates embryonic development is a longstanding question. Here, they show that embryonic gene modules are re-used, rewired, and interconnected to specific injury-indu...

nature.com

Ectopic head regeneration after nervous system ablation in a sea anemone

Via genetic ablation of neurons, Mazloumi Gavgani et al. show that the nervous system is essential for defining axial polarity during whole-body regeneration in the sea anemone Nematostella vectensis.

cell.com

Staufen2 modulates the temporal dynamics of human neurogenesis in vitro

RNA-binding proteins (RBPs) play a central role in post-transcriptional regulation during brain development, yet their specific functions in coordinating human neural lineage decisions remain poorly u...

biorxiv.org

Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications

Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...

nature.com

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. 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

biorxiv.org