ArticleThe EMBO journal2017
A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture.
Article in The EMBO journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 251 papers.
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Who cites it
251 citing papers in PubMed, 399 citations in OpenAlex.
- Article
- Nested TAD hierarchy defines cohesion zones on replicated chromosomes.The EMBO journal · 2026Article
- Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Genome folding and nuclear speckles converge to orchestrate fibroblast activation.Science advances · 2026Article
- High-resolution chromatin mapping reveals that CTCF anchors meiotic loops to the chromosome axis.Nature communications · 2026Article
- Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions.Nature communications · 2026Article
- Contribution of cohesins STAG1 and STAG2 to preimplantation development in mice.Communications biology · 2026Article
- Mechanisms coordinating exit from the stem cell state in mammals.Genes & development · 2026Review
- Context-dependent regulation of IgH V(D)J recombination by cohesin-STAG1 and cohesin-STAG2.Nature communications · 2026Article
- Cohesin activity accelerates the homology search.bioRxiv : the preprint server for biology · 2026Article
- RNAPII and DNA supercoiling regulate cohesin engagement in neurons.Nucleic acids research · 2026Article
- RAD21 regulation of the enhancer-promoter chromatin loop of RAD51 promotes PARPi resistance in ovarian cancer.Journal of translational medicine · 2026Article
- Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.Molecular cell · 2026Article
- Cohesin bridging as a physical principle of enhancer-promoter communication.bioRxiv : the preprint server for biology · 2026Article
- Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption.Molecular cell · 2026Article
- A universal polymer signature in Hi-C resolves cohesin loop density and supports monomeric extrusion.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Unique territorial and compartmental organization of chromosomes in the holocentric silkworm.The EMBO journal · 2026Article
- Clinical,medRxiv : the preprint server for health sciences · 2026Article
- Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation.Nature communications · 2026Article
- NSD3 stabilizes nuclear compartmentalization and promotes megabase-scale chromatin interactions.bioRxiv : the preprint server for biology · 2026Article
191 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 5 institutions in 3 countries.
Funding
Abstract
Fertilization triggers assembly of higher-order chromatin structure from a condensed maternal and a naïve paternal genome to generate a totipotent embryo. Chromatin loops and domains have been detected in mouse zygotes by single-nucleus Hi-C (snHi-C), but not bulk Hi-C. It is therefore unclear when and how embryonic chromatin conformations are assembled. Here, we investigated whether a mechanism of cohesin-dependent loop extrusion generates higher-order chromatin structures within the one-cell embryo. Using snHi-C of mouse knockout embryos, we demonstrate that the zygotic genome folds into loops and domains that critically depend on Scc1-cohesin and that are regulated in size and linear density by Wapl. Remarkably, we discovered distinct effects on maternal and paternal chromatin loop sizes, likely reflecting differences in loop extrusion dynamics and epigenetic reprogramming. Dynamic polymer models of chromosomes reproduce changes in snHi-C, suggesting a mechanism where cohesin locally compacts chromatin by active loop extrusion, whose processivity is controlled by Wapl. Our simulations and experimental data provide evidence that cohesin-dependent loop extrusion organizes mammalian genomes over multiple scales from the one-cell embryo onward.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.