Gene Body Methylation Can Alter Gene Expression and Is a Therapeutic Target in Cancer
Open accessAbstract
DNA methylation in promoters is well known to silence genes and is the presumed therapeutic target of methylation inhibitors. Gene body methylation is positively correlated with expression, yet its function is unknown. We show that 5-aza-2'-deoxycytidine treatment not only reactivates genes but decreases the overexpression of genes, many of which are involved in metabolic processes regulated by c-MYC. Downregulation is caused by DNA demethylation of the gene bodies and restoration of high levels of expression requires remethylation by DNMT3B. Gene body methylation may, therefore, be an unexpected therapeutic target for DNA methylation inhibitors, resulting in the normalization of gene overexpression induced during carcinogenesis. Our results provide direct evidence for a causal relationship between gene body methylation and transcription.
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Increased CGI gene body methylation positively correlates with transcriptional activation.
“Increased CGI gene body methylation positively correlates with transcriptional activation [6, 25, 55]”
From Comprehensive in silico CpG methylation analysis in hepatocellular carcinoma identifies tissue- and tumor-type specific marks disconnected from gene expression (2024) · cites this paper as [55]
The Results section reports a positive correlation between gene-body methylation and expression for a subset of probes, supporting the general relationship. But most of those positively correlated sites were outside CpG islands, while 62% of a negatively correlated gene-body subset were within CpG islands. The paper therefore does not establish the claim specifically for CGI gene-body methylation; page numbers were not available in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredPromoter CGI hypermethylation represses transcription, whereas hypermethylation at gene body CGIs activates gene expression.
“It is well-known that promoter CGI hypermethylation represses transcription [43, 45], whereas hypermethylation at gene body CGIs activates gene expression [6, 55].”
From Comprehensive in silico CpG methylation analysis in hepatocellular carcinoma identifies tissue- and tumor-type specific marks disconnected from gene expression (2024) · cites this paper as [55]
The Discussion says the authors’ experiments show that gene-body DNA methylation increases gene expression. But the Results section on rapid remethylation says most positively correlated gene-body CpGs were outside CpG islands; another Results section reports that many gene-body probes within CpG islands were negatively correlated with expression. The paper therefore supports the gene-body methylation point, but not the claim that hypermethylation at gene-body CGIs generally activates expression. (LLM, conf=0.87)
Experimental — accuracy not yet measuredThe location of CGIs determines the direction of this regulation.
“and that the location of these CGIs determines the direction of this regulation [6, 43, 45, 55]”
From Comprehensive in silico CpG methylation analysis in hepatocellular carcinoma identifies tissue- and tumor-type specific marks disconnected from gene expression (2024) · cites this paper as [55]
The Results sections report that promoter methylation can be negatively correlated with gene expression, while some gene-body methylation is positively correlated. But the paper also reports gene-body probes with a negative correlation, including probes within CpG islands. Location is therefore relevant, but the source does not support the unqualified claim that CGI location determines the direction of regulation. Page numbers were not provided in our copy. (LLM, conf=0.85)
Experimental — accuracy not yet measuredThere is a positive correlation between gene expression and gene body methylation.
“Another study demonstrated a positive correlation between gene expression and gene body methylation.55”
From Epigenetic regulation in major depression and other stress-related disorders: molecular mechanisms, clinical relevance and therapeutic potential (2023) · cites this paper as [55]
The level of methylation in CGIs regulates gene expression.
“it is widely accepted that the level of methylation in the regions known as CGI regulates gene expression”
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- Authors
- Yang, X., Han, H., De Carvalho, D. D., Lay, F. D., Jones, P. A., & Liang, G.
- Affiliations
- University of Southern California (US)
- Corresponding author
- Jones, Peter A.
- Liang, Gangning
- Venue
- Cancer Cell
- Publisher
- Elsevier BV
- Published
- 2014-10
- Volume
- 26
- Issue
- 4
- Pages
- 577-590
- ISSN
- 1535-6108 (ISSN-L)
- PMC
- PMC4224113
- OpenAlex
- W2055986128
- Cited by
- 1,199
- References
- 62
- Citations by year
- 2026: 61 · 2025: 77 · 2024: 104 · 2023: 109 · 2022: 105 · 2021: 120 · 2020: 120 · 2019: 134 · 2018: 128 · 2017: 97 · 2016: 79 · 2015: 55 · 2014: 8
- FWCI
- 32.82
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cancer Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Princess Margaret Cancer Foundation
- National Institutes of Health
- National Cancer Institute (R01CA170550, R01CA124518, R01CA082422, P30CA014089, R37CA082422)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cancer-related gene regulation
- Keywords
- gene body methylation, DNA methylation, decitabine, DNA demethylation, DNMT3B, c-Myc, gene overexpression, transcriptional regulation, DNA methylation inhibitors, cancer therapy, carcinogenesis, metabolic genes
- MeSH terms
- Cell Division, Colonic Neoplasms, Humans, Promoter Regions, Genetic, Gene Expression, DNA Methylation
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