ArticleNature genetics2021
Three-dimensional folding dynamics of the Xenopus tropicalis genome.
Article in Nature genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 62 citations in OpenAlex.
- Non-coding DNA dynamics and its roles as a physical barrier in genome safeguarding across early development and evolution.Heredity · 2026Review
- Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- The roles of chromatin remodeling and 3D genome organization in cancers: from mechanistic insights to emerging treatment options.Molecular cancer · 2026Review
- Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation.Nature communications · 2026Article
- Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes.Nature ecology & evolution · 2026Article
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
- Nucleoskeletal Proteins in Early Embryogenesis.Advances in experimental medicine and biology · 2026Review
- CANTAC-seq analysis reveals E2f1 and Otx1 coordinate zygotic genome activation in Xenopus tropicalis.Nature communications · 2025Article
- The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity.Genome biology and evolution · 2025Review
- From Rabl-like Architecture to Chromosome Territories: A Conserved Developmental Transition in Animal Genomes.Molecular biology and evolution · 2025Article
- Article
- Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation.bioRxiv : the preprint server for biology · 2025Article
- The hierarchical folding dynamics of topologically associating domains during early embryo development.BMC biology · 2025Article
- Metabolic acclimation to warming links unexpected immune activation and sexual dimorphism attenuation in Xenopus tropicalis.Communications biology · 2025Article
- The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus.Nature reviews. Genetics · 2025Review
- HiCForecast: dynamic network optical flow estimation algorithm for spatiotemporal Hi-C data forecasting.Bioinformatics (Oxford, England) · 2025Article
- Hi-C Protocol for Studying Chromatin Spatial Organization in Early Zebrafish Development.Methods in molecular biology (Clifton, N.J.) · 2025Article
- HiChIP to Study 3D Genome Organization in Xenopus tropicalis Embryos.Methods in molecular biology (Clifton, N.J.) · 2025Article
- HTAD: a human-in-the-loop framework for supervised chromatin domain detection.Genome biology · 2024Article
- Evolution and function of chromatin domains across the tree of life.Nature structural & molecular biology · 2024Review
Corrections and comments
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Authors and funding
17 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Animal interphase chromosomes are organized into topologically associating domains (TADs). How TADs are formed is not fully understood. Here, we combined high-throughput chromosome conformation capture and gene silencing to obtain insights into TAD dynamics in Xenopus tropicalis embryos. First, TAD establishment in X. tropicalis is similar to that in mice and flies and does not depend on zygotic genome transcriptional activation. This process is followed by further refinements in active and repressive chromatin compartments and the appearance of loops and stripes. Second, within TADs, higher self-interaction frequencies at one end of the boundary are associated with higher DNA occupancy of the architectural proteins CTCF and Rad21. Third, the chromatin remodeling factor ISWI is required for de novo TAD formation. Finally, TAD structures are variable in different tissues. Our work shows that X. tropicalis is a powerful model for chromosome architecture analysis and suggests that chromatin remodeling plays an essential role in de novo TAD establishment.
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Registered trials
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.