ArticleeLife2013
DNA methylation presents distinct binding sites for human transcription factors.
Article in eLife, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 210 papers, 1 of them a synthesis that pooled it.
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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
210 citing papers in PubMed, 1 synthesis or guideline pooled it, 361 citations in OpenAlex.
- Aryl hydrocarbon receptor gene transitions (c.-742C>T; c.1661G>A) and idiopathic male infertility: a case-control study with in silico and meta-analysis.Environmental science and pollution research international · 2017Pooled it
- DNA methylation loci in placenta associated with birthweight and expression of genes relevant for early development and adult diseases.Clinical epigenetics · 2020Trial
- Integrative Methylome and Transcriptome Analysis of DNA Methylation and Sex-Biased Gene Expression in Northern Pike (Animals : an open access journal from MDPI · 2026Article
- Gene regulatory mechanisms downstream of DNA methylation.Nature reviews. Genetics · 2026Review
- Identification of methylation-sensitive human transcription factors using meSMiLE-seq.Nature communications · 2026Article
- Cooperative care influences genome-wide levels of DNA methylation in nestling chestnut-crowned babblers.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2026Article
- DNA hypomethylation enables the transcriptional repressor SlSPL-CNR to control fruit flavor ester biosynthesis.Nature communications · 2026Article
- Kaiso reads methylated CpGs at nucleosome entry/exit and displaces the H3 tail.bioRxiv : the preprint server for biology · 2026Article
- MeDReaders 2.0: an updated database for modified DNA readers.BMC genomics · 2026Article
- Epigenetic Modulation of the ACE System Underlies the Slow Aerobic Muscle Phenotype and Metabolic Exercise Response.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Article
- The pioneering work of Howard Cedar and his team in unraveling the roles DNA methylation plays in regulating genome function.Frontiers in epigenetics and epigenomics · 2026Article
- Quantifying transcription factor specificity with advanced DNA universal microarrays featuring long and modified binding sites.Nucleic acids research · 2025Article
- Adverse gestational environment configures a subpopulation of ventral dentate granule cells for recruitment to drive innate anxiety.Cell reports · 2025Article
- Bisphenol A diglycidyl ether-induced DNA methylation abnormalities may disrupt testis development in adult male zebrafish.Environmental analysis, health and toxicology · 2025Article
- Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes.Genome research · 2025Article
- Active DNA demethylation upstream of rod-photoreceptor fate determination is required for retinal development.PLoS biology · 2025Article
- Unveiling Epigenetic Regulatory Elements Associated with Breast Cancer Development.International journal of molecular sciences · 2025Article
- The Role of Methylation Modification in Neural Injury and Repair.International journal of molecular sciences · 2025Review
- Association of placental weight and placental-fetal weight ratio with DNA methylation in placenta.Epigenomics · 2025Article
150 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors at 4 institutions in 2 countries.
Funding
Abstract
DNA methylation, especially CpG methylation at promoter regions, has been generally considered as a potent epigenetic modification that prohibits transcription factor (TF) recruitment, resulting in transcription suppression. Here, we used a protein microarray-based approach to systematically survey the entire human TF family and found numerous purified TFs with methylated CpG (mCpG)-dependent DNA-binding activities. Interestingly, some TFs exhibit specific binding activity to methylated and unmethylated DNA motifs of distinct sequences. To elucidate the underlying mechanism, we focused on Kruppel-like factor 4 (KLF4), and decoupled its mCpG- and CpG-binding activities via site-directed mutagenesis. Furthermore, KLF4 binds specific methylated or unmethylated motifs in human embryonic stem cells in vivo. Our study suggests that mCpG-dependent TF binding activity is a widespread phenomenon and provides a new framework to understand the role and mechanism of TFs in epigenetic regulation of gene transcription. DOI:http://dx.doi.org/10.7554/eLife.00726.001.
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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.