ArticleBMC genomics2019
CpG traffic lights are markers of regulatory regions in human genome.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it, 50 citations in OpenAlex.
- Development of a prognostic risk model for clear cell renal cell carcinoma by systematic evaluation of DNA methylation markers.Clinical epigenetics · 2021Pooled it
- Differential DNA methylation and gene expression in stem cell-derived cardiomyocytes from patients with and without a history of clozapine-induced myocarditis.Journal of psychiatry & neuroscience : JPN · 2025Article
- DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts.Genome biology · 2024Article
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- Influence of DNA Methylation on Vascular Smooth Muscle Cell Phenotypic Switching.International journal of molecular sciences · 2024Review
- HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.Nucleic acids research · 2024Article
- Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications.Clinical epigenetics · 2023Article
- RUNX1/CEBPA Mutation in Acute Myeloid Leukemia Promotes Hypermethylation and Indicates for Demethylation Therapy.International journal of molecular sciences · 2022Article
- MethReg: estimating the regulatory potential of DNA methylation in gene transcription.Nucleic acids research · 2022Article
- Strong Parallel Differential Gene Expression Induced by Hatchery Rearing Weakly Associated with Methylation Signals in Adult Coho Salmon (O. kisutch).Genome biology and evolution · 2022Article
- Childhood adversity correlates with stable changes in DNA methylation trajectories in children and converges with epigenetic signatures of prenatal stress.Neurobiology of stress · 2021Article
- Genetic Background Effects on the Expression of an Odorant Receptor Gene.Frontiers in cellular neuroscience · 2021Article
- Identification of cell type-specific methylation signals in bulk whole genome bisulfite sequencing data.Genome biology · 2020Article
- Epigenomics and the kidney.Current opinion in nephrology and hypertension · 2020Review
- Profiling haplotype specific CpG and CpH methylation within a schizophrenia GWAS locus on chromosome 14 in schizophrenia and healthy subjects.Scientific reports · 2020Article
- Molecular Pap Smear: Validation of HPV Genotype and Host Methylation Profiles ofFrontiers in microbiology · 2020Article
- Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing.Biostatistics (Oxford, England) · 2019Article
- Repression of TERRA Expression by Subtelomeric DNA Methylation Is Dependent on NRF1 Binding.International journal of molecular sciences · 2019Article
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundDNA methylation is involved in the regulation of gene expression. Although bisulfite-sequencing based methods profile DNA methylation at a single CpG resolution, methylation levels are usually averaged over genomic regions in the downstream bioinformatic analysis.
resultsWe demonstrate that on the genome level a single CpG methylation can serve as a more accurate predictor of gene expression than an average promoter / gene body methylation. We define CpG traffic lights (CpG TL) as CpG dinucleotides with a significant correlation between methylation and expression of a gene nearby. CpG TL are enriched in all regulatory regions. Among all promoters, CpG TL are especially enriched in poised ones, suggesting involvement of DNA methylation in their regulation. Yet, binding of only a handful of transcription factors, such as NRF1, ETS, STAT and IRF-family members, could be regulated by direct methylation of transcription factor binding sites (TFBS) or its close proximity. For the majority of TF, an alternative scenario is more likely: methylation and inactivation of the whole regulatory element indirectly represses functional TF binding with a CpG TL being a reliable marker of such inactivation.
conclusionsCpG TL provide a promising insight into mechanisms of enhancer activity and gene regulation linking methylation of single CpG to gene expression. CpG TL methylation can be used as reliable markers of enhancer activity and gene expression in applications, e.g. in clinic where measuring DNA methylation is easier compared to directly measuring gene expression due to more stable nature of DNA.
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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.