Evidence map›Paper›PMID 41266351›Full record

ArticleNature communications2025

Engineered chromatin readers track damaged chromatin dynamics in live cells and animals.

Richard Cardoso da Silva, Kristeli Eleftheriou, Davide C Recchia, Vincent Portegijs, Douwe Ten Bulte, Niklas Kupfer, Nathalie P Vroegindeweij-de Wagenaar, Xabier Vergara, Ayoub Ouchene, Sander van den Heuvel and 1 more

Abstract read
In one paragraph

Article in Nature communications, 2025. 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. 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

11 authors.

Richard Cardoso da SilvaGenome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands. richicardoso.silva@gmail.com.ORCID http://orcid.org/0000-0003-2767-2053
Kristeli EleftheriouGenome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands.ORCID http://orcid.org/0000-0001-6529-7042
Davide C RecchiaGenome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands.ORCID http://orcid.org/0009-0004-5791-074X
Vincent PortegijsDevelopmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands.
Douwe Ten BulteGenome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands.
Niklas KupferGenome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands.ORCID http://orcid.org/0009-0000-7395-0638
Nathalie P Vroegindeweij-de WagenaarGenome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands.
Xabier VergaraDivision of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.
Ayoub OucheneDivision of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.
Sander van den HeuvelDevelopmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands.ORCID http://orcid.org/0000-0001-9015-7463
Tuncay BaubecGenome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands. t.baubec@uu.nl.ORCID http://orcid.org/0000-0001-8474-6587

Funding

EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council) 865094
6 · The paper itself

Abstract

DNA damage is a constant threat to genome integrity and function. Diminished capacity for DNA repair is linked to many human diseases, therefore, understanding the molecular pathways responding to DNA damage is key for developing novel therapies. Lack of unbiased probes to report DNA damage dynamics in living cells and animals limits our current efforts to completely understand DNA repair processes. In this study, we overcome these limitations by engineering protein probes containing the tandem-BRCT domain of MCPH1, which we show to have a specific affinity for the DNA-damage-associated histone mark γH2AX. We employ these probes to track DNA damage dynamics in living cells exposed to a panel of different genotoxic insults, to visualize DNA damage targeted to heterochromatinised satellite repeats, and to map DNA double strand breaks genome-wide. Finally, we highlight the versatility of our probe to visualize programmed double strand breaks during gametogenesis in C. elegans. Taken together, we present a novel protein probe with broad application potential for DNA damage research.

Indexed as

ChromatinDNA DamageAnimalsCaenorhabditis elegansDNA Breaks, Double-StrandedDNA RepairHeterochromatinHistonesHumansProtein EngineeringChromatinH2AX protein, humanHeterochromatinHistones

Identifiers

PMID41266351
PMCPMC12635110

What OpenQuestion holds

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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.