Evidence map›Paper›PMID 39815045›Full record

ArticleNature structural & molecular biology2025

Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates.

Michael Uckelmann, Vita Levina, Cyntia Taveneau, Xiao Han Ng, Varun Pandey, Jasmine Martinez, Shweta Mendiratta, Justin Houx, Marion Boudes, Hari Venugopal and 11 more

Abstract read
In one paragraph

Article in Nature structural & molecular biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Review
  6. Review
  7. Article
  8. Review
  9. Gout Risk Allele RegulatingInternational journal of molecular sciences · 2025
    Article
  10. Article
  11. Article
  12. In-cell chromatin structure by Cryo-FIB and Cryo-ET.Current opinion in structural biology · 2025
    Review
  13. Article
  14. Article
  15. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

21 authors.

Michael UckelmannDepartment of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.
Vita LevinaDepartment of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.
Cyntia TaveneauDepartment of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.ORCID http://orcid.org/0000-0002-3395-4957
Xiao Han NgDepartment of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.ORCID http://orcid.org/0009-0001-3634-0352
Varun PandeyDepartment of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Jasmine MartinezDepartments of Biochemistry and Molecular Medicine, and Stem Cell and Regenerative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
Shweta MendirattaDepartments of Biochemistry and Molecular Medicine, and Stem Cell and Regenerative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
Justin HouxEMBL Australia Node for Single Molecule Science and School of Biomedical Sciences, Faculty of Medicine, The University of New South Wales, Sydney, New South Wales, Australia.
Marion BoudesDepartment of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.ORCID http://orcid.org/0000-0003-2577-710X
Hari VenugopalRamaciotti Centre for Cryo-Electron Microscopy, Monash University, Monash, Victoria, Australia.ORCID http://orcid.org/0000-0001-5230-2973
Sylvain TrépoutRamaciotti Centre for Cryo-Electron Microscopy, Monash University, Monash, Victoria, Australia.
Alex J FulcherMonash Micro Imaging, Monash University, Clayton, Victoria, Australia.ORCID http://orcid.org/0000-0002-6278-7211
Qi ZhangDepartment of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.ORCID http://orcid.org/0000-0003-1121-8817
Sarena FlaniganDepartment of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.
Minrui LiDepartment of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.
Emma SiereckiEMBL Australia Node for Single Molecule Science and School of Biomedical Sciences, Faculty of Medicine, The University of New South Wales, Sydney, New South Wales, Australia.ORCID http://orcid.org/0000-0001-9970-868X
Yann GambinEMBL Australia Node for Single Molecule Science and School of Biomedical Sciences, Faculty of Medicine, The University of New South Wales, Sydney, New South Wales, Australia.ORCID http://orcid.org/0000-0001-7378-8976
Partha Pratim DasDepartment of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.ORCID http://orcid.org/0000-0003-3544-2629
Oliver BellDepartments of Biochemistry and Molecular Medicine, and Stem Cell and Regenerative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0002-7639-5948
Alex de MarcoDepartment of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.
Chen DavidovichDepartment of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia. Chen.Davidovich@monash.edu.ORCID http://orcid.org/0000-0002-1085-6094

Funding

Training in Developmental Biology, Stem Cells and RegenerationT32HD060549 · NICHD · UNIVERSITY OF SOUTHERN CALIFORNIA · PI Gage D Crump · 2011 to 2026
$2.5M
Epigenetic Maintenance of Neural Cell IdentityR01MH122565 · NIMH · UNIVERSITY OF SOUTHERN CALIFORNIA · PI BELL, OLIVER · 2021 to 2025
$2.1M
NICHD NIH HHS T32 HD060549NIMH NIH HHS R01 MH122565
6 · The paper itself

Abstract

The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organization and dynamics of chromatin compacted by gene-repressing factors are unknown. Here, using cryo-electron tomography, we solved the three-dimensional structure of chromatin condensed by the polycomb repressive complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilized through multivalent dynamic interactions of PRC1 with chromatin. Mechanistically, positively charged residues on the internally disordered regions of CBX8 mask negative charges on the DNA to stabilize the condensed state of chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provide a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.

Indexed as

ChromatinPolycomb Repressive Complex 1AnimalsCryoelectron MicroscopyHumansMiceModels, MolecularMouse Embryonic Stem CellsChromatinPolycomb Repressive Complex 1

Identifiers

PMID39815045
PMCPMC11919719

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

None linked

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.