ArticlePLoS genetics2007
RETRACTED: DNA damage, homology-directed repair, and DNA methylation.
Article in PLoS genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It has been retracted, and should not be counted. Cited by 108 papers, 2 of them syntheses that pooled 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.
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.
Who cites it
108 citing papers in PubMed, 2 syntheses or guidelines pooled it, 192 citations in OpenAlex.
- Polymorphisms in DNA Repair Gene and Susceptibility to Glioma: A Systematic Review and Meta-Analysis Based on 33 Studies with 15 SNPs in 9 Genes.Cellular and molecular neurobiology · 2017Pooled it
- 15q12 variants, sputum gene promoter hypermethylation, and lung cancer risk: a GWAS in smokers.Journal of the National Cancer Institute · 2015Pooled it
- Feasibility Outcomes of a Pilot Randomized Clinical Trial to Increase Cruciferous and Green Leafy Vegetable Intake in Posttreatment Head and Neck Cancer Survivors.Journal of the Academy of Nutrition and Dietetics · 2019Trial
- DNA methylation heterogeneity in complex tumor microenvironment: Quantitative methods, influencing factors, and clinical implications.Genes & diseases · 2026Review
- CRISPR-Cas9-induced double-strand breaks disrupt maintenance of epigenetic information.Genome biology · 2025Article
- Epigenetic networks coordinate DNA methylation across the genome.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Retraction: DNA Damage, Homology-Directed Repair, and DNA Methylation.PLoS genetics · 2025Article
- The OGG1 Ser326Cys polymorphism: molecular mechanisms of disease susceptibility and precision medicine applications.Clinical epigenetics · 2025Review
- Effects of Ionizing Radiation on DNA Methylation Patterns and Their Potential as Biomarkers.International journal of molecular sciences · 2025Review
- Article
- The DNA methylome of pediatric brain tumors appears shaped by structural variation and predicts survival.Nature communications · 2024Article
- Somatic mutation as an explanation for epigenetic aging.bioRxiv : the preprint server for biology · 2023Article
- Identification of a robust DNA methylation signature for Fanconi anemia.American journal of human genetics · 2023Article
- Article
- Inflammation and DNA damage: cause, effect or both.Nature reviews. Rheumatology · 2023Review
- Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic substitutions.Nucleic acids research · 2023Article
- DNA Methylation of the Dopamine TransporterInternational journal of molecular sciences · 2023Article
- Role of primary aging hallmarks in Alzheimer´s disease.Theranostics · 2023Review
- FOXO3a Mediates Homologous Recombination Repair (HRR) via Transcriptional Activation of MRE11, BRCA1, BRIP1, and RAD50.Molecules (Basel, Switzerland) · 2022Article
- Methylation in the Promoter Region of the Dopamine TransporterInternational journal of environmental research and public health · 2022Article
48 more citing papers are in PubMed but not listed here.
Corrections and comments
- Retraction · 2017-02-10Duplication of/in Image · Euphemisms for Duplication · Investigation by Journal/Publisher · Investigation by Third Party · Objections by Author(s) · Original Data and/or Images not Provided and/or not Available · Upgrade/Update of Prior Notice(s) · · See also: https://pubpeer.com/publications/4CCE5DC380B7A83C39CAA4FAFD01B1
- Retraction · 2025-10-27Duplication of/in Image · Error in Image · Investigation by Journal/Publisher · Investigation by Third Party · Objections by Author(s) · Original Data and/or Images not Provided and/or not Available · Unreliable Data · Upgrade/Update of Prior Notice(s) · · See also: https://pubpeer.com/publications/4CCE5DC380B7A83C39CAA4FAFD01B1
- Erratum issued
- Retracted
Authors and funding
14 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To explore the link between DNA damage and gene silencing, we induced a DNA double-strand break in the genome of Hela or mouse embryonic stem (ES) cells using I-SceI restriction endonuclease. The I-SceI site lies within one copy of two inactivated tandem repeated green fluorescent protein (GFP) genes (DR-GFP). A total of 2%-4% of the cells generated a functional GFP by homology-directed repair (HR) and gene conversion. However, approximately 50% of these recombinants expressed GFP poorly. Silencing was rapid and associated with HR and DNA methylation of the recombinant gene, since it was prevented in Hela cells by 5-aza-2'-deoxycytidine. ES cells deficient in DNA methyl transferase 1 yielded as many recombinants as wild-type cells, but most of these recombinants expressed GFP robustly. Half of the HR DNA molecules were de novo methylated, principally downstream to the double-strand break, and half were undermethylated relative to the uncut DNA. Methylation of the repaired gene was independent of the methylation status of the converting template. The methylation pattern of recombinant molecules derived from pools of cells carrying DR-GFP at different loci, or from an individual clone carrying DR-GFP at a single locus, was comparable. ClustalW analysis of the sequenced GFP molecules in Hela and ES cells distinguished recombinant and nonrecombinant DNA solely on the basis of their methylation profile and indicated that HR superimposed novel methylation profiles on top of the old patterns. Chromatin immunoprecipitation and RNA analysis revealed that DNA methyl transferase 1 was bound specifically to HR GFP DNA and that methylation of the repaired segment contributed to the silencing of GFP expression. Taken together, our data support a mechanistic link between HR and DNA methylation and suggest that DNA methylation in eukaryotes marks homologous recombined segments.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.