Evidence map›Paper›PMID 41145704›Full record

ArticleMolecular systems biology2026

FACT depletion demonstrates a role for nucleosome organization in TAD formation.

Clemens Mauksch, Yi Zhu, Taras Velychko, Spyridoula Sagropoulou, Abrar Aljahani, Shyam Ramasamy, Kristina Žumer, A Marieke Oudelaar

Abstract read
In one paragraph

Article in Molecular systems biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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

8 authors.

Clemens MaukschMax Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany.ORCID http://orcid.org/0009-0006-1403-2136
Yi ZhuMax Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany.ORCID http://orcid.org/0009-0008-3909-1321
Taras VelychkoMax Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany.ORCID http://orcid.org/0000-0003-4087-3730
Spyridoula SagropoulouMax Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany.ORCID http://orcid.org/0009-0005-4438-3618
Abrar AljahaniMax Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany.
Shyam RamasamyMax Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany.ORCID http://orcid.org/0000-0003-0617-694X
Kristina ŽumerMax Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany.ORCID http://orcid.org/0000-0003-3986-6509
A Marieke OudelaarMax Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany. marieke.oudelaar@mpinat.mpg.de.ORCID http://orcid.org/0000-0002-4016-6158

Funding

Deutsche Forschungsgemeinschaft (DFG) 469281184EC | European Research Council (ERC) 101115401
6 · The paper itself

Abstract

Mammalian genomes are organized into distinct chromatin structures, which include small-scale nucleosome arrays and large-scale topologically associating domains (TADs). The mechanistic interplay between chromatin structures across scales is poorly understood. Here, we investigate how changes in nucleosome organization impact TAD structure by studying the role of the histone chaperone facilitates chromatin transcription (FACT) in 3D genome organization. We show that FACT depletion perturbs TADs, causing decreased insulation and weaker CTCF loops. These changes in TAD structure cannot be attributed to changes in chromatin occupancy of CTCF or cohesin and occur specifically in transcribed regions of the genome, where we observe perturbed nucleosome organization in the absence of FACT. FACT depletion therefore allows us to separate the role of nucleosome organization and CTCF binding and to demonstrate that the organization of nucleosomes at TAD boundaries contributes to TAD formation.

Indexed as

DNA-Binding ProteinsHigh Mobility Group ProteinsNucleosomesTranscriptional Elongation FactorsAnimalsCCCTC-Binding FactorCell Cycle ProteinsChromatinChromatin Assembly and DisassemblyChromosomal Proteins, Non-HistoneCohesinsHistonesHumansProtein BindingTranscription, GeneticCCCTC-Binding FactorCell Cycle ProteinsChromatinChromosomal Proteins, Non-HistoneCohesinsDNA-Binding ProteinsHigh Mobility Group ProteinsHistonesNucleosomesSSRP1 protein, humanTranscriptional Elongation Factors3D Genome OrganizationCTCFFACTNucleosomeTopologically Associating Domain (TAD)

Identifiers

PMID41145704
PMCPMC12759068

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Registered trials

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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.