ArticleNucleic acids research2013
Functional DNA demethylation is accompanied by chromatin accessibility.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- The antileukemic activity of decitabine upon PML/RARA-negative AML blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation.Blood cancer journal · 2022Trial
- Activation-induced cytidine deaminase promotes DNA demethylation and expression of the Ninjurin-2 gene.Biology open · 2026Article
- A LINE-1 retrotransposon promotes SEMA3C expression as a cis-regulatory enhancer to sustain breast cancer stem cell survival.Science China. Life sciences · 2026Article
- Tracking single-cell evolution using clock-like chromatin accessibility loci.Nature biotechnology · 2025Article
- The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer.Nature structural & molecular biology · 2024Article
- A novel DNA methylation signature revealed GDF6 and RCC1 as potential prognostic biomarkers correlated with cell proliferation in clear cell renal cell carcinoma.Molecular biology reports · 2023Article
- Article
- DNMT and EZH2 inhibitors synergize to activate therapeutic targets in hepatocellular carcinoma.Cancer letters · 2022Article
- Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy.Nature communications · 2022Article
- Clonal hematopoiesis of indeterminate potential, DNA methylation, and risk for coronary artery disease.Nature communications · 2022Article
- Analysis of archaic human haplotypes suggests that 5hmC acts as an epigenetic guide for NCO recombination.BMC biology · 2022Article
- Review
- Article
- Characterizing DNA methylation signatures and their potential functional roles in Merkel cell carcinoma.Genome medicine · 2021Article
- Low-dose decitabine priming endows CAR T cells with enhanced and persistent antitumour potential via epigenetic reprogramming.Nature communications · 2021Article
- A Novel DNA Methylation Signature as an Independent Prognostic Factor in Muscle-Invasive Bladder Cancer.Frontiers in oncology · 2021Article
- Epigenetic plasticity potentiates a rapid cyclical shift to and from an aggressive cancer phenotype.International journal of cancer · 2020Article
- Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility.Genome biology · 2020Article
- Article
- Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes.Clinical epigenetics · 2019Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
DNA methylation inhibitors such as 5-aza-2'-deoxycytidine (5-Aza-CdR) are currently used for the treatment of myelodysplastic syndrome. Although global DNA demethylation has been observed after treatment, it is unclear to what extent demethylation induces changes in nucleosome occupancy, a key determinant of gene expression. We use the colorectal cancer cell line HCT116 as a model to address this question and determine that <2% of regions demethylated by 5-Aza-CdR treatment assume an open configuration. Consolidating our findings, we detect nucleosome retention at sites of global DNA methylation loss in DKO1, an HCT116-derived non-tumorigenic cell-line engineered for DNA methyltransferase disruption. Notably, regions that are open in both HCT116 cells after treatment and in DKO1 cells include promoters belonging to tumor suppressors and genes under-expressed in colorectal cancers. Our results indicate that only a minority of demethylated promoters are associated with nucleosome remodeling, and these could potentially be the epigenetic drivers causing the loss of tumorigenicity. Furthermore, we show that the chromatin opening induced by the histone deacetylase inhibitor suberoylanilide hydroxamic acid has strikingly distinct targets compared with those of 5-Aza-CdR, providing a mechanistic explanation for the importance of combinatorial therapy in eliciting maximal de-repression of the cancer epigenome.
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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.