ArticleLife science alliance2022
Expression regulation of genes is linked to their CpG density distributions around transcription start sites.
Article in Life science alliance, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 19 citations in OpenAlex.
- Dna methylation dynamics associated with visual system remodeling during flatfish metamorphosis.Epigenetics & chromatin · 2025Article
- Hierarchical Prediction and Perturbation of Chromatin Organization Reveal How Loop Domains Mediate Higher-Order Architectures.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- CHD6 eviction of promoter nucleosomes maintains housekeeping transcriptional program in prostate cancer.Molecular therapy. Nucleic acids · 2024Article
- Universal prediction of vertebrate species age at maturity.Communications biology · 2024Article
- Unraveling the key role of chromatin structure in cancer development through epigenetic landscape characterization of oral cancer.Molecular cancer · 2024Article
- CpG Island Definition and Methylation Mapping of the T2T-YAO Genome.Genomics, proteomics & bioinformatics · 2024Article
- Tet-mediated DNA methylation dynamics affect chromosome organization.Nucleic acids research · 2024Article
- Article
- DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle.Scientific reports · 2023Article
- Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The CpG dinucleotide and its methylation behaviors play vital roles in gene regulation. Previous studies have divided genes into several categories based on the CpG intensity around transcription starting sites and found that housekeeping genes tend to possess high CpG density, whereas tissue-specific genes are generally characterized by low CpG density. In this study, we investigated how the CpG density distribution of a gene affects its transcription and regulation pattern. Based on the CpG density distribution around transcription starting site, by means of a semi-supervised neural network we designed, which took data augmentation into account, we divided the human genes into three categories, and genes within each cluster shared similar CpG density distribution. Not only sequence properties, these different clusters exhibited distinctly different structural features, regulatory mechanisms, correlation patterns between the expression level and CpG/TpG density, and expression and epigenetic mark variations during tumorigenesis. For instance, the activation of cluster 3 genes relies more on 3D genome reorganization, compared with cluster 1 and 2 genes, whereas cluster 2 genes showed the strongest correlation between gene expression and H3K27me3. Genes exhibiting uncoupled correlation between gene regulation and histone modifications are mainly in cluster 3. These results emphasized that the usage of epigenetic marks in gene regulation is partially rooted in the sequence property of genes such as their CpG density distribution and explained to some extent why the relation between epigenetic marks and gene expression is controversial.
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