ArticleGenome biology2012
Human genes with CpG island promoters have a distinct transcription-associated chromatin organization.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed, 134 citations in OpenAlex.
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- Curcumin and neuroplasticity: epigenetic mechanisms underlying cognitive enhancement in aging and neurodegenerative disorders.Frontiers in aging neuroscience · 2025Review
- Characterization and visualization of tandem repeats at genome scale.Nature biotechnology · 2024Article
- Regional-specific calibration enables application of computational evidence for clinical classification of 5' cis-regulatory variants in Mendelian disease.American journal of human genetics · 2024Article
- Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation.Nucleic acids research · 2024Article
- The Dynamics of Histone Modifications during Mammalian Zygotic Genome Activation.International journal of molecular sciences · 2024Review
- Polymorphisms in Glutathione S-Transferase (Genes · 2023Article
- DNA Methylation Signatures of Response to Conventional Synthetic and Biologic Disease-Modifying Antirheumatic Drugs (DMARDs) in Rheumatoid Arthritis.Biomedicines · 2023Review
- Promoter evolution of mammalian gene duplicates.BMC biology · 2023Article
- Molecular mechanisms of multi-omic regulation in breast cancer.Frontiers in oncology · 2023Review
- Expression of DNA Methyltransferase 3B Isoforms Is Associated with DNA Satellite 2 Hypomethylation and Clinical Prognosis in Advanced High-Grade Serous Ovarian Carcinoma.International journal of molecular sciences · 2022Article
- Expression regulation of genes is linked to their CpG density distributions around transcription start sites.Life science alliance · 2022Article
- Cap analysis of gene expression reveals alternative promoter usage in a rat model of hypertension.Life science alliance · 2022Article
- Histone modification and histone modification-targeted anti-cancer drugs in breast cancer: Fundamentals and beyond.Frontiers in pharmacology · 2022Review
- Transcriptional regulation ofFrontiers in cell and developmental biology · 2022Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMore than 50% of human genes initiate transcription from CpG dinucleotide-rich regions referred to as CpG islands. These genes show differences in their patterns of transcription initiation, and have been reported to have higher levels of some activation-associated chromatin modifications.
resultsHere we report that genes with CpG island promoters have a characteristic transcription-associated chromatin organization. This signature includes high levels of the transcription elongation-associated histone modifications H4K20me1, H2BK5me1 and H3K79me1/2/3 in the 5' end of the gene, depletion of the activation marks H2AK5ac, H3K14ac and H3K23ac immediately downstream of the transcription start site (TSS), and characteristic epigenetic asymmetries around the TSS. The chromosome organization factor CTCF may be bound upstream of RNA polymerase in most active CpG island promoters, and an unstable nucleosome at the TSS may be specifically marked by H4K20me3, the first example of such a modification. H3K36 monomethylation is only detected as enriched in the bodies of active genes that have CpG island promoters. Finally, as expression levels increase, peak modification levels of the histone methylations H3K9me1, H3K4me1, H3K4me2 and H3K27me1 shift further away from the TSS into the gene body.
conclusionsThese results suggest that active genes with CpG island promoters have a distinct step-like series of modified nucleosomes after the TSS. The identity, positioning, shape and relative ordering of transcription-associated histone modifications differ between genes with and without CpG island promoters. This supports a model where chromatin organization reflects not only transcription activity but also the type of promoter in which transcription initiates.
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