Evidence map›Paper›PMID 40531993›Full record

ArticleScience advances2025

ZC3H4 safeguards genome integrity by preventing transcription-replication conflicts at noncoding RNA loci.

Yann Frey, Liana Goehring, Majd Haj, Gergely Rona, Carel Fijen, Michele Pagano, Tony T Huang, Eli Rothenberg, Yael Ziv, Yosef Shiloh

Abstract read
In one paragraph

Article in Science advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Review
  2. Review
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  4. Review
  5. 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

10 authors.

Yann FreyThe David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.ORCID 0009-0002-5953-0674
Liana GoehringDepartment of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.
Majd HajThe David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.ORCID 0000-0002-9251-5612
Gergely RonaDepartment of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.ORCID 0000-0003-3222-7261
Carel FijenDepartment of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.ORCID 0000-0003-4160-2086
Michele PaganoDepartment of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.ORCID 0000-0003-3210-2442
Tony T HuangDepartment of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.ORCID 0000-0001-9291-5002
Eli RothenbergDepartment of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.ORCID 0000-0002-1382-1380
Yael ZivThe David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.ORCID 0000-0002-2131-5648
Yosef ShilohThe David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.ORCID 0000-0002-1538-6060

Funding

Structural determinants of Pol theta functionP01CA247773 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI DALE A RAMSDEN · 2020 to 2026
$15.2M
Mechanisms of Human DNA Double-Strand Break Repair via Quantitative Single-Molecule Imaging - Equipment SupplementR35GM134947 · NIGMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Eli Rothenberg · 2020 to 2026
$3.4M
Regulation of the cell proliferation by CRL ubiquitin ligases-diversity supplementR35GM136250 · NIGMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI MICHELE PAGANO · 2020 to 2026
$2.7M
NCI NIH HHS P01 CA247773NIGMS NIH HHS R35 GM134947NIGMS NIH HHS R35 GM136250
6 · The paper itself

Abstract

The cellular networks that maintain genome stability encompass numerous pathways involved in all aspects of nucleic acid metabolism. Through bioinformatic analysis, we identified the Zinc Finger CCCH-Type Containing 4 protein (ZC3H4), a suppressor of noncoding RNA (ncRNA) production, as a pivotal player in this system. Experimentally, ZC3H4 deficiency led to increased DNA damage, abnormal mitosis, and cellular senescence. Biochemical analysis and super-resolution microscopy revealed that the loss of ZC3H4 increased replication stress (RS)-a major driver of genome instability-by inducing a hypertranscription state that promoted R loop formation and transcription-replication conflicts (TRCs), both of which drive RS. Further bioinformatic analysis demonstrated that ZC3H4 preferentially binds to genomic regions prone to TRCs and R loops, where it suppresses ncRNA bursts, functioning as part of the Restrictor complex. Our findings identify ZC3H4 as a crucial factor in maintaining genome integrity, strategically positioned at the critical intersection of DNA and RNA synthesis.

Indexed as

DNA ReplicationGenetic LociGenomic InstabilityRNA-Binding ProteinsRNA, UntranslatedTranscription, GeneticDNA DamageHumansR-Loop StructuresRNA-Binding ProteinsRNA, Untranslated

Identifiers

PMID40531993
PMCPMC12175896

What OpenQuestion holds

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LicenceCC BY-NC
Read underepoch 390

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.