ArticleNature communications2021
Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 52 citations in OpenAlex.
- Delicate inhibition of NFκB/RELA circuitry facilitates efficient transition towards ground-state pluripotency in human.Nature communications · 2026Article
- Quantitative Control of Transposable Elements: From Genome Plasticity to Immune Regulatory Circuits.Cell biochemistry and function · 2026Review
- Transcriptional Bursting in Pluripotent Stem Cells.Biology · 2026Review
- H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs.Nature genetics · 2026Article
- Peripheral Nerve Surgery and Chemotherapy: A Review, Index, and Decision Tree for Nerve Surgeons Considering Neurotization After Oncological Nerve Injuries.Neurosurgery practice · 2026Review
- Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs.Nature structural & molecular biology · 2026Article
- Analysis of Chromatin Structure Using Network Approaches: A Step-by-Step Guide.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The nuclear matrix stabilizes primed-specific genes in human pluripotent stem cells.Nature cell biology · 2025Article
- Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR.Genome biology · 2024Article
- MICA: a multi-omics method to predict gene regulatory networks in early human embryos.Life science alliance · 2024Article
- Through the lens of phase separation: intrinsically unstructured protein and chromatin looping.Nucleus (Austin, Tex.) · 2023Review
- Epigenetic dynamics during capacitation of naïve human pluripotent stem cells.Science advances · 2023Article
- Evidence for low nanocompaction of heterochromatin in living embryonic stem cells.The EMBO journal · 2023Article
- Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components.Nucleic acids research · 2023Article
- NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naïve pluripotent stem cells.Development (Cambridge, England) · 2023Article
- 3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells.Nucleic acids research · 2022Article
- Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction.Nature cell biology · 2022Article
- HNRNPM Regulates HCC Tumorigenesis and Cancer Stemness: Identification of a Novel Therapeutic Target?Cellular and molecular gastroenterology and hepatology · 2022Article
- Enhancer-Promoter Communication: It's Not Just About Contact.Frontiers in molecular biosciences · 2022Article
- Modulation of the high-order chromatin structure by Polycomb complexes.Frontiers in cell and developmental biology · 2022Review
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
The transition from naive to primed pluripotency is accompanied by an extensive reorganisation of transcriptional and epigenetic programmes. However, the role of transcriptional enhancers and three-dimensional chromatin organisation in coordinating these developmental programmes remains incompletely understood. Here, we generate a high-resolution atlas of gene regulatory interactions, chromatin profiles and transcription factor occupancy in naive and primed human pluripotent stem cells, and develop a network-graph approach to examine the atlas at multiple spatial scales. We uncover highly connected promoter hubs that change substantially in interaction frequency and in transcriptional co-regulation between pluripotent states. Small hubs frequently merge to form larger networks in primed cells, often linked by newly-formed Polycomb-associated interactions. We identify widespread state-specific differences in enhancer activity and interactivity that correspond with an extensive reconfiguration of OCT4, SOX2 and NANOG binding and target gene expression. These findings provide multilayered insights into the chromatin-based gene regulatory control of human pluripotent states.
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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.