Nanopore direct RNA sequencing (DRS) holds promise for advancing our understanding of the epitranscriptome by detecting RNA modifications in native RNA molecules. Recently, Oxford Nanopore Technologie...

The authors uncover a mechano-metabolic adaptation where confinement induces rapid mitochondrial relocalization to the nuclear periphery, generating localized nuclear ATP surges that support chromatin...

Transcriptome-scale maps of RNA secondary structure ensembles in living cells detect candidate RNA structural switches.

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

Millions of ribosomes are packed within mammalian cells, yet we lack tools to visualize them in toto and characterize their subcellular composition. In this study, we present ribosome expansion micros...

In a recent article in Nature, Nobori et al. unveil spatiotemporal dynamics of immune states of plant cells during pathogen infection. Cells in contact with the pathogen act as primary immune responders (PRIMER) and propagate immune responses to mount…