ArticleNature communications2026
Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation.
Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells.bioRxiv : the preprint server for biology · 2026Article
- Sequence design for three-dimensional genome folding using Akita Semifreddo.bioRxiv : the preprint server for biology · 2026Article
- Unique territorial and compartmental organization of chromosomes in the holocentric silkworm.The EMBO journal · 2026Article
- The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control.bioRxiv : the preprint server for biology · 2026Article
- Cohesin-mediated chromatin organization controls the differentiation and function of dendritic cells.Science immunology · 2026Article
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
- Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm.Nature cell biology · 2026Article
- Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes.Genome biology · 2025Article
- Cohesin forms fountains at active enhancers in C. elegans.Nature communications · 2025Article
- Pan-cancer 3D genomic analysis revealed extremely long Polycomb loops as the biomarker for sensitivity to Polycomb inhibition.bioRxiv : the preprint server for biology · 2025Article
- Characterization of induced cohesin loop extrusion trajectories in living cells.Nature genetics · 2025Article
- MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets.bioRxiv : the preprint server for biology · 2025Article
- Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers.Nucleic acids research · 2025Article
- Super RNA Pol II domains enhance minor ZGA through 3D interaction to ensure the integrity of major transcriptional waves in late-ZGA mammals.Cell genomics · 2025Article
- Article
- Cohesin organizes 3D DNA contacts surrounding active enhancers inGenome research · 2025Article
- Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis.Nature communications · 2025Article
- Liquid condensates: a new barrier to loop extrusion?Cellular and molecular life sciences : CMLS · 2025Review
- Transcriptional machinery as an architect of genome structure.Current opinion in structural biology · 2024Review
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11 authors.
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Abstract
The initiation of gene expression during development, known as zygotic genome activation (ZGA), is accompanied by massive changes in chromosome organization. However, the earliest events of chromosome folding and their functional roles remain unclear. Using Hi-C on zebrafish embryos, we discovered that chromosome folding begins early in development with the formation of fountains, distinct elements of chromosome organization. Emerging preferentially at enhancers, fountains show an initial accumulation of cohesin, which later redistributes to CTCF sites at TAD borders. Knockouts of pioneer transcription factors driving ZGA enhancers cause a specific loss of fountains, establishing a causal link between enhancer activation and fountain formation. Polymer simulations demonstrate that fountains may arise as sites of facilitated cohesin loading, requiring two-sided but desynchronized loop extrusion, potentially caused by cohesin collisions with obstacles or internal switching. Moreover, we detected cohesin-dependent fountain patterns at enhancers in mouse cells and found them reemerging with cohesin loading after mitosis. Altogether, fountains represent enhancer-specific elements of chromosome organization and suggest that chromosome folding during development and after cell division starts with facilitated cohesin loading. Observations in multiple systems further support facilitated loading at enhancers as a widespread phenomenon.
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