ArticleNucleic acids research2019
Identification of DNA motifs that regulate DNA methylation.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 62 citations in OpenAlex.
- Molecular Genetics and Epigenetics Regulatory Role of miRNAs on Adipogenesis and Intramuscular Fat Development in Beef Cattle: In the Context of Meat Quality.Molecular biotechnology · 2026Review
- DNA methylation of theiScience · 2026Article
- How to Unmask an Unknown: The Restriction-Modification SystemInternational journal of molecular sciences · 2026Article
- A novel gene therapy platform for the treatment of type 2 diabetes and obesity.Molecular therapy. Nucleic acids · 2025Article
- AI-directed gene fusing prolongs the evolutionary half-life of synthetic gene circuits.Science advances · 2025Article
- Epigenetic networks coordinate DNA methylation across the genome.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Identifying DNA methylation types and methylated base positions from bacteria using nanopore sequencing with multi-scale neural network.Bioinformatics (Oxford, England) · 2025Article
- Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties.BMC biology · 2025Article
- Interplay of somatic mutations and epigenetic aging clocks.Nature aging · 2025Article
- Somatic mutation as an explanation for epigenetic aging.Nature aging · 2025Article
- Unraveling the intricate molecular landscape and potential biomarkers in lung adenocarcinoma through integrative epigenomic and transcriptomic profiling.Scientific reports · 2025Article
- Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly.Frontiers in genetics · 2025Article
- The Research Progress of DNA Methylation in the Development and Function of the Porcine Placenta.International journal of molecular sciences · 2024Review
- Development and characterization of a first-in-class adjustable-dose gene therapy system.Gene · 2024Article
- LXRα Promotes Abdominal Aortic Aneurysm Formation Through UHRF1 Epigenetic Modification of miR-26b-3p.Circulation · 2024Article
- Interpretable prediction of mRNA abundance from promoter sequence using contextual regression models.NAR genomics and bioinformatics · 2024Article
- DNA methylation haplotype block signatures responding to Staphylococcus aureus subclinical mastitis and association with production and health traits.BMC biology · 2024Article
- The Causes for Genomic Instability and How to Try and Reduce Them Through Rational Design of Synthetic DNA.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Somatic mutation as an explanation for epigenetic aging.bioRxiv : the preprint server for biology · 2023Article
- Predicting regional somatic mutation rates using DNA motifs.PLoS computational biology · 2023Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is an important epigenetic mark but how its locus-specificity is decided in relation to DNA sequence is not fully understood. Here, we have analyzed 34 diverse whole-genome bisulfite sequencing datasets in human and identified 313 motifs, including 92 and 221 associated with methylation (methylation motifs, MMs) and unmethylation (unmethylation motifs, UMs), respectively. The functionality of these motifs is supported by multiple lines of evidence. First, the methylation levels at the MM and UM motifs are respectively higher and lower than the genomic background. Second, these motifs are enriched at the binding sites of methylation modifying enzymes including DNMT3A and TET1, indicating their possible roles of recruiting these enzymes. Third, these motifs significantly overlap with "somatic QTLs" (quantitative trait loci) of methylation and expression. Fourth, disruption of these motifs by mutation is associated with significantly altered methylation level of the CpGs in the neighbor regions. Furthermore, these motifs together with somatic mutations are predictive of cancer subtypes and patient survival. We revealed some of these motifs were also associated with histone modifications, suggesting a possible interplay between the two types of epigenetic modifications. We also found some motifs form feed forward loops to contribute to DNA methylation dynamics.
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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.