ArticleOncogene2013
DNA methylation determines nucleosome occupancy in the 5'-CpG islands of tumor suppressor genes.
Article in Oncogene, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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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.
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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.
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Who cites it
22 citing papers in PubMed, 40 citations in OpenAlex.
- Epigenetic Age and the Risk of Incident Atrial Fibrillation.Circulation · 2021Trial
- The "Hit-and-Run" legacy: epigenetic locking and the survival switch in H. pylori-associated gastric cancer.Cell death discovery · 2026Review
- Nutrition-Based Paternal Influence on Gynecological Diseases in Female Offspring via Epigenetic Mechanisms.Nutrients · 2025Review
- Structural DNMT-nucleosome contacts are related to DNA methylation patterns.Epigenetics & chromatin · 2025Article
- Enhanced nucleosome assembly at CpG sites containing an extended 5-methylcytosine analogue.Nucleic acids research · 2022Article
- Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts.PLoS computational biology · 2022Article
- Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data.Bioinformatics (Oxford, England) · 2021Article
- Hypermethylation of theOncology letters · 2019Article
- Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize.Genome research · 2018Article
- CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing.Bioinformatics (Oxford, England) · 2017Article
- Whole genome DNA methylation: beyond genes silencing.Oncotarget · 2017Review
- Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems.Cell reports · 2016Article
- Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons.RNA (New York, N.Y.) · 2015Article
- Methylation of Integrin α4 and E-Cadherin Genes in Human Prostate Cancer.Pathology oncology research : POR · 2015Article
- The role of DNA methylation in directing the functional organization of the cancer epigenome.Genome research · 2015Article
- The ATP binding site of the chromatin remodeling homolog Lsh is required for nucleosome density and de novo DNA methylation at repeat sequences.Nucleic acids research · 2015Article
- Prediction of promoters and enhancers using multiple DNA methylation-associated features.BMC genomics · 2015Article
- Histone H2A.Z deregulation in prostate cancer. Cause or effect?Cancer metastasis reviews · 2014Review
- Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development.Genome research · 2014Article
- Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes.Epigenetics & chromatin · 2014Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Promoter CpG island hypermethylation of tumor suppressor genes is an epigenetic hallmark of human cancer commonly associated with nucleosome occupancy and the transcriptional silencing of the neighboring gene. Nucleosomes can determine the underlying DNA methylation status. Herein, we show that the opposite is also true: DNA methylation can determine nucleosome positioning. Using a cancer model and digital nucleosome positioning techniques, we demonstrate that the induction of DNA hypomethylation events by genetic (DNMT1/DNMT3B deficient cells) or drug (a DNA demethylating agent) approaches is associated with the eviction of nucleosomes from previously hypermethylated CpG islands of tumor suppressor genes. Most importantly, the establishment of a stable cell line that restores DNMT1/DNMT3B deficiency shows that nucleosomes reoccupy their positions in de novo methylated CpG islands. Finally, we extend these results to the genomic level, combining a DNA methylation microarray and the nucleosome positioning technique. Using this global approach, we observe the dependency of nucleosome occupancy upon the DNA methylation status. Thus, our results suggest that there is a close association between hypermethylated CpG islands and the presence of nucleosomes, such that each of these epigenetic mechanisms can determine the recruitment of the other.
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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.