ArticleNature2013
The pluripotent genome in three dimensions is shaped around pluripotency factors.
Article in Nature, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 154 papers.
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Who cites it
154 citing papers in PubMed, 265 citations in OpenAlex.
- Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute toGenes & development · 2026Article
- Structure Variations and 3D Genome Disruption: Implications in Safety of hPSC-Based Cell Therapy.International journal of molecular sciences · 2026Review
- Retinol saturase in the mitochondria antagonizes IDH2 and GLUD1 acetylation to mediate heart repair.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Topologically associating domains define the 3D genome architecture of mouse totipotent-like stem cells.The Journal of biological chemistry · 2026Article
- Human pluripotent stem cell models of Friedreich's ataxia: innovations, considerations, and future perspectives.Stem cell research & therapy · 2026Review
- Many faces of mammalian NSD methyltransferases.Cellular & molecular biology letters · 2026Review
- The superpowers of imprinting control regions.Genome research · 2026Review
- Analysis of the three-dimensional genome of exhausted CD8Nature immunology · 2025Article
- Article
- Transformation of an Olfactory Placode-Derived Cell into One with Stem Cell Characteristics by Disrupting Epigenetic Barriers.Cellular reprogramming · 2025Article
- Master transcription-factor binding sites constitute the core of early replication control elements.The EMBO journal · 2025Article
- Endometrial tumorigenesis involves epigenetic plasticity demarcating non-coding somatic mutations and 3D-genome alterations.Genome biology · 2025Article
- Pioneer factor GATA6 promotes colorectal cancer through 3D genome regulation.Science advances · 2025Article
- Transcription-coupled changes in genomic region proximities during transcriptional bursting.Science advances · 2024Article
- Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories.Genome research · 2024Article
- Early inhibition of BRD4 facilitates iPSC reprogramming via accelerating rDNA dynamic expression.BMC biology · 2024Article
- RetSat stabilizes mitotic chromosome segregation in pluripotent stem cells.Cellular and molecular life sciences : CMLS · 2024Article
- The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition.Nucleic acids research · 2024Article
- Attraction and disruption: how loop extrusion and compartmentalisation shape the nuclear genome.Current opinion in genetics & development · 2024Review
- Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL.Nature communications · 2024Article
94 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is becoming increasingly clear that the shape of the genome importantly influences transcription regulation. Pluripotent stem cells such as embryonic stem cells were recently shown to organize their chromosomes into topological domains that are largely invariant between cell types. Here we combine chromatin conformation capture technologies with chromatin factor binding data to demonstrate that inactive chromatin is unusually disorganized in pluripotent stem-cell nuclei. We show that gene promoters engage in contacts between topological domains in a largely tissue-independent manner, whereas enhancers have a more tissue-restricted interaction profile. Notably, genomic clusters of pluripotency factor binding sites find each other very efficiently, in a manner that is strictly pluripotent-stem-cell-specific, dependent on the presence of Oct4 and Nanog protein and inducible after artificial recruitment of Nanog to a selected chromosomal site. We conclude that pluripotent stem cells have a unique higher-order genome structure shaped by pluripotency factors. We speculate that this interactome enhances the robustness of the pluripotent state.
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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.