Methylation is the addition of a methyl group (-CH₃) to DNA, histones, proteins, or small molecules.
DNA methylation (at CpG sites) is the primary epigenetic mechanism silencing gene expression, and it requires the methyl donor S-adenosylmethionine (SAMe), which depends on the methionine cycle—itself dependent on B12, folate, and Homocysteine metabolism.
The Gut Microbiome produces B12 and folate, making it a direct regulator of the host's methylation capacity.
Evidence map4 cited passagesInspect provenance +
Arsenic: Arsenite is methylated by arsenite methyltransferase (AS3MT) using SAMe as methyl donor. Chronic arsenic exposure depletes SAMe pools, causing genome-wide hypomethylation → aberrant gene activation → carcinogenesis.
Nickel: Induces DNA hypermethylation at tumor suppressor gene promoters, silencing their expression → carcinogenesis.
Hashimoto's: Altered methylation profiles linked to microbiome-metabolome interactions.
CRC: Aberrant methylation of tumor suppressors driven by microbiome-metabolome crosstalk.
Metal-Methylation Interface#
Arsenic: Arsenite is methylated by arsenite methyltransferase (AS3MT) using SAMe as methyl donor. Chronic arsenic exposure depletes SAMe pools, causing genome-wide hypomethylation → aberrant gene activation → carcinogenesis.[1]Genetic and Epigenetic Mechanisms in Metal Carcinogenesis and Cocarcinogenesis: Nickel, Arsenic, and ChromiumKonstantin Salnikov, Anatoly Zhitkovich · 2008Open reference 1 ↓
Nickel: Induces DNA hypermethylation at tumor suppressor gene promoters, silencing their expression → carcinogenesis.[2]Genchi 2020 — Nickel: Human Health and Environmental ToxicologyGenchi G, Carocci A, Lauria G et al. · 2020Open reference 2 ↓ Cadmium: Disrupts DNA methyltransferase activity, causing both hypo- and hypermethylation.
Microbiome Connection#
Gut bacteria produce B12 and folate—essential cofactors for methionine synthase (converts homocysteine → methionine → SAMe). Dysbiosis-driven loss of B-vitamin producers reduces methylation capacity.
Hashimoto's: Altered methylation profiles linked to microbiome-metabolome interactions.[3]Identifying the metabolic profile of Hashimoto's thyroiditis from the METHAP clinical studySarandi E, Tsoukalas D, Rudofsky G et al. · 2025Open reference 3 ↓ CRC: Aberrant methylation of tumor suppressors driven by microbiome-metabolome crosstalk.[4]Metabolomics and 16S rRNA Sequencing of Human Colorectal Cancers and Adjacent MucosaLoke MF, Chua EG, Gan HM et al. · 2018Open reference 4 ↓
Cross-References#
- Vitamin B12—essential cofactor for methionine synthase
- Homocysteine—methylation cycle intermediate
- Arsenic—SAMe-depleting methylation
- Nickel—epigenetic gene silencing via hypermethylation
- Epigenetic Modifications—broader epigenetic context
References 4
Numbered by first appearance in the article, then reconciled with its declared source list.
- 1
Konstantin Salnikov, Anatoly Zhitkovich (2008). Genetic and Epigenetic Mechanisms in Metal Carcinogenesis and Cocarcinogenesis: Nickel, Arsenic, and Chromium. Chemical Research in Toxicology.
- 2
Genchi G, Carocci A, Lauria G et al. (2020). Genchi 2020 — Nickel: Human Health and Environmental Toxicology. International Journal of Environmental Research and Public Health.
- 3
Sarandi E, Tsoukalas D, Rudofsky G et al. (2025). Identifying the metabolic profile of Hashimoto's thyroiditis from the METHAP clinical study. Scientific Reports.
- 4
Loke MF, Chua EG, Gan HM et al. (2018). Metabolomics and 16S rRNA Sequencing of Human Colorectal Cancers and Adjacent Mucosa. PLOS ONE.
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Revised “Microbiome Connection”: now reads “(converts homocysteine → methionine → SAMe). dysbiosis-driven loss of B-vitamin producers reduces methylation”.
Revised “Microbiome Connection”: changed “(converts homocysteine → methionine → SAMe). Dysbiosis-driven loss of B-vitamin producers reduces methylation” to “(converts homocysteine → methionine → SAMe). dysbiosis-driven loss of B-vitamin producers reduces methylation”. · Karen Pendergrass · +1 −1
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Created “Methylation”: Methylation is the addition of a methyl group (-CH₃) to DNA, histones, proteins, or small molecules. DNA methylation (at CpG sites) is the primary epigenetic mechanism silencing gene expression, and…
Created “Methylation”: Methylation is the addition of a methyl group (-CH₃) to DNA, histones, proteins, or small molecules. DNA methylation (at CpG sites) is the primary epigenetic mechanism silencing gene expression, and… Published sections: Overview; Metal-Methylation Interface; Microbiome Connection; Cross-References. · WikiBiome Deploy Bot · +43 −0
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