Evidence map›Paper›PMID 40738104›Full record

ArticleCell2025

DNA mutagenesis driven by transcription factor competition with mismatch repair.

Wei Zhu, Yuning Zhang, Harshit Sahay, Hana Wasserman, Ariel Afek, Jonathan Williams, Samantha Shaltz, Caitlin Johnson, Kyle Pinheiro, David M MacAlpine and 4 more

Abstract read
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 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

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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

14 authors.

Wei ZhuDepartment of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA.
Yuning ZhangCenter for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.
Harshit SahayCenter for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.
Hana WassermanCenter for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.
Ariel AfekCenter for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
Jonathan WilliamsDepartment of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
Samantha ShaltzDepartment of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
Caitlin JohnsonDepartment of Chemistry, University of North Carolina, Chapel Hill, NC 27514, USA.
Kyle PinheiroCenter for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Computer Science, Duke University, Durham, NC 27705, USA.
David M MacAlpineCenter for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.
Keith R WeningerDepartment of Physics, North Carolina State University, Raleigh, NC 27695, USA.
Dorothy A ErieDepartment of Chemistry, University of North Carolina, Chapel Hill, NC 27514, USA.
Sue Jinks-RobertsonDepartment of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA. Electronic address: sue.robertson@duke.edu.
Raluca GordânDepartment of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biostatistics & Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA; Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA. Electronic address: raluca.gordan@umassmed.edu.

Funding

Integrative single molecule studies: DNA repair and technology developmentR35GM127151 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI DOROTHY A ERIE · 2018 to 2026
$4.6M
Regulation of mitotic genome stability in yeast.R35GM118077 · NIGMS · DUKE UNIVERSITY · PI JINKS-ROBERTSON, SUE · 2016 to 2023
$4.5M
Chromatin-mediated mechanisms of genome integrityR35GM127062 · NIGMS · DUKE UNIVERSITY · PI David M MacAlpine · 2018 to 2026
$3.7M
The role of transcription factor proteins in mutagenesis at regulatory sitesR01GM135658 · NIGMS · DUKE UNIVERSITY · PI GORDAN, RALUCA · 2020 to 2023
$1.3M
Molecular Mechanisms of DNA Mismatch Repair InitiationR01GM132263 · NIGMS · NORTH CAROLINA STATE UNIVERSITY RALEIGH · PI WENINGER, KEITH R · 2019 to 2022
$1.2M
NIGMS NIH HHS R01 GM132263NIGMS NIH HHS R01 GM135658NIGMS NIH HHS R35 GM118077NIGMS NIH HHS R35 GM127062NIGMS NIH HHS R35 GM127151
6 · The paper itself

Abstract

Despite the remarkable fidelity of eukaryotic DNA replication, nucleotide misincorporation errors occur in every replication cycle, generating mutations that drive genetic diseases and genome evolution. Here, we show that transcription factor (TF) proteins, key players in gene regulation, can increase mutagenesis from replication errors by directly competing with the recognition of DNA mismatches by MutSα, the primary initiator of eukaryotic mismatch repair (MMR). We demonstrate this TF-induced mutagenesis mechanism using a yeast genetic assay that quantifies the accumulation of mutations in TF binding sites. Analyses of human cancer mutations recapitulate the trends observed in yeast, with mutations arising from MYC-bound mismatches being enriched in MMR-proficient cells. These findings implicate TF-MMR competition as a critical determinant of somatic hypermutation at TF binding sites in cancer. Furthermore, our results provide a molecular mechanism for the higher-than-expected rate of rare genetic variants at TF binding sites, with important implications for regulatory DNA evolution.

Indexed as

DNA Mismatch RepairMutagenesisTranscription FactorsBinding SitesDNA-Binding ProteinsDNA ReplicationHumansMutationNeoplasmsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsDNA-Binding ProteinsSaccharomyces cerevisiae ProteinsTranscription Factorscompetition with mismatch repairDNA mismatch repairDNA mutagenesisDNA replication errorshypermutationmutation patternsmutations in transcription factor binding sitesMutSαtranscription factors

Identifiers

PMID40738104
PMCPMC12327807

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.