Evidence map›Paper›PMID 41197626›Full record

ArticleCell2025

Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions.

Hangpeng Li, James L T Dalgleish, George Lister, Maria Julia Maristany, Jan Huertas, Ana M Dopico-Fernandez, Joseph C Hamley, Nicholas Denny, Gianna Bloye, Weijiao Zhang and 15 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing 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

14 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026
    Review
  5. Review
  6. Article
  7. Review
  8. Review
  9. Article
  10. Article
  11. Article
  12. Resolving Sub-Nuclear Architecture from Compartments to Functional Domains.International journal of molecular sciences · 2026
    Review
  13. Review
  14. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

25 authors.

Hangpeng LiMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
James L T DalgleishMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
George ListerMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
Maria Julia MaristanyMaxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK; Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
Jan HuertasYusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
Ana M Dopico-FernandezMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
Joseph C HamleyMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
Nicholas DennyMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
Gianna BloyeMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
Weijiao ZhangMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
Lance HentgesMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
Roman DollMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
Ye WeiMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
Michela MarescaDivision of Gene Regulation, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
Emilia DimitrovaDepartment of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
Lior PytowskiSir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Pixel Biology Ltd., Oxford, UK.
Edward A J TunnacliffeMRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
Mira KassoufMRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
Doug HiggsMRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, UK.
Elzo de WitDivision of Gene Regulation, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
Robert J KloseDepartment of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
Lothar SchermellehDepartment of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
Rosana Collepardo-GuevaraMaxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK; Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
Thomas A MilneMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
James O J DaviesMRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK; MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; National Institute of Health Research Blood and Transplant Research Unit in Precision Cellular Therapeutics, University of Oxford, Oxford OX3 9DU, UK; Oxford National Institute of Health Research Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK. Electronic address: james.davies@imm.ox.ac.uk.

Funding

Wellcome Trust 209400Wellcome Trust 225220
6 · The paper itself

Abstract

Chromatin structure is a key determinant of gene expression in eukaryotes, but it has not been possible to define the structure of cis-regulatory elements at the scale of the proteins that bind them. Here, we generate multidimensional chromosome conformation capture (3C) maps at base-pair resolution using Micro Capture-C ultra (MCCu). This can resolve contacts between individual transcription factor motifs within cis-regulatory elements. Using degron systems, we show that removal of Mediator complex components alters fine-scale promoter structure and that nucleosome depletion plays a key role in transcription factor-driven enhancer-promoter contacts. We observe that chromatin is partitioned into nanoscale domains by nucleosome-depleted regions. This structural conformation is reproduced by chemically specific coarse-grained molecular dynamics simulations of the physicochemical properties of chromatin. Combining MCCu with molecular dynamics simulations and super-resolution microscopy allows us to propose a unified model in which the biophysical properties of chromatin orchestrate contacts between cis-regulatory elements.

Indexed as

ChromatinHumansMolecular Dynamics SimulationNucleosomesPromoter Regions, GeneticRegulatory Sequences, Nucleic AcidTranscription FactorsChromatinNucleosomesTranscription Factorschromatin structurechromosome conformation capturecis-regulatory elementsenhancer-promoter interactionsgene regulationmediator complexmolecular dynamics simulationsnuclear organizationtranscription factors

Identifiers

PMID41197626
PMCPMC7618578

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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.