ArticleEpigenetics & chromatin2017
A screening system to identify transcription factors that induce binding site-directed DNA demethylation.
Article in Epigenetics & chromatin, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it, 49 citations in OpenAlex.
- Adipose Tissue Epigenetic Profile in Obesity-Related Dysglycemia - A Systematic Review.Frontiers in endocrinology · 2021Pooled it
- Cross-Scale Convergence in Epigenetic Gene Regulation: A Perspective on Functional Enrichment Analytics for Cancer.Current issues in molecular biology · 2026Article
- How Oncovirus Affects Drug Resistance in Cancer Cells.Recent patents on anti-cancer drug discovery · 2026Review
- Physicochemical features of intrinsically disordered regions predict DNA-demethylation-promoting activity of transcription factors.Epigenetics & chromatin · 2025Article
- Article
- FLI1 is associated with regulation of DNA methylation and megakaryocytic differentiation in FPDMM caused by a RUNX1 transactivation domain mutation.Scientific reports · 2024Article
- Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models.Nucleic acids research · 2023Article
- TET2 lesions enhance the aggressiveness of CEBPA-mutant acute myeloid leukemia by rebalancing GATA2 expression.Nature communications · 2023Article
- RUNX1/CEBPA Mutation in Acute Myeloid Leukemia Promotes Hypermethylation and Indicates for Demethylation Therapy.International journal of molecular sciences · 2022Article
- Enhancer methylation dynamics drive core transcriptional regulatory circuitry in pan-cancer.Oncogene · 2022Article
- GATA6 is predicted to regulate DNA methylation in an in vitro model of human hepatocyte differentiation.Communications biology · 2022Article
- Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers.Epigenetics & chromatin · 2022Article
- Prediction of transcription factors associated with DNA demethylation during human cellular development.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2022Article
- Modification Patterns of DNA Methylation-Related lncRNAs Regulating Genomic Instability for Improving the Clinical Outcomes and Tumour Microenvironment Characterisation of Lower-Grade Gliomas.Frontiers in molecular biosciences · 2022Article
- Gene-Targeted DNA Methylation: Towards Long-Lasting Reprogramming of Gene Expression?Advances in experimental medicine and biology · 2022Review
- A Modular Mathematical Model of Exercise-Induced Changes in Metabolism, Signaling, and Gene Expression in Human Skeletal Muscle.International journal of molecular sciences · 2021Article
- Deciphering the genetic code of DNA methylation.Briefings in bioinformatics · 2021Review
- Ascorbic Acid PromotesJournal of immunology (Baltimore, Md. : 1950) · 2020Article
- Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types.Nucleic acids research · 2020Article
- A method for identifying allele-specific hydroxymethylation.Epigenetics · 2020Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA methylation is a fundamental epigenetic modification that is involved in many biological systems such as differentiation and disease. We and others recently showed that some transcription factors (TFs) are involved in the site-specific determination of DNA demethylation in a binding site-directed manner, although the reports of such TFs are limited.
resultsHere, we develop a screening system to identify TFs that induce binding site-directed DNA methylation changes. The system involves the ectopic expression of target TFs in model cells followed by DNA methylome analysis and overrepresentation analysis of the corresponding TF binding motif at differentially methylated regions. It successfully identified binding site-directed demethylation of SPI1, which is known to promote DNA demethylation in a binding site-directed manner. We extended our screening system to 15 master TFs involved in cellular differentiation and identified eight novel binding site-directed DNA demethylation-inducing TFs (RUNX3, GATA2, CEBPB, MAFB, NR4A2, MYOD1, CEBPA, and TBX5). Gene ontology and tissue enrichment analysis revealed that these TFs demethylate genomic regions associated with corresponding biological roles. We also describe the characteristics of binding site-directed DNA demethylation induced by these TFs, including the targeting of highly methylated CpGs, local DNA demethylation, and the overlap of demethylated regions between TFs of the same family.
conclusionsOur results show the usefulness of the developed screening system for the identification of TFs that induce DNA demethylation in a site-directed manner.
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