{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.demethylation","code":"thing-q900386","url":"https://ver.cy/models/thing/q900386/","name":"demethylation","alternateNames":["oxidative demethylation","protein demethylation","DNA demethylation","oxidative DNA demethylation","hydrolytic DNA demethylation"],"kind":"thing","status":"published","version":"0.2.0-wave.4","language":"en","classifiers":{"family":"Thing Registry","category":"Activities and processes","entryKind":"thing","plane":"ACT","domain":["ACT.PRC"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"The chemical removal of a methyl group from a molecule, occurring in metabolism, such as the demethylation of drugs by cytochrome P450 enzymes, in epigenetics as DNA demethylation, either passive through dilution during replication or active through TET enzymes oxidising 5-methylcytosine followed by base excision repair, described as oxidative DNA demethylation, or hydrolytic routes proposed in some organisms, and as protein demethylation of histones by enzymes such as LSD1 and Jumonji-domain demethylases, including oxidative demethylation mechanisms; it also appears in industrial chemistry. Demethylation of DNA and histones regulates gene expression and is a target of some cancer drugs.","purpose":"Let an agent explain demethylation, relay chemical and biological mechanisms, epigenetic roles and medical relevance from biochemistry sources, describe the named forms, and distinguish demethylation from methylation, deacetylation, dealkylation in general and demethylating drugs as a treatment class.","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["Methyl group removal","Enzymatic in biology","Epigenetic regulation","Drug target"],"structure":{"bundles":[{"id":"understand","name":"Understand","description":"What demethylation is.","layers":[{"id":"definition","name":"Definition","description":"Definition.","findings":[{"id":"definition-finding","name":"Definition","description":"Definition.","questions":[{"text":"What is demethylation, and how does it differ from methylation, deacetylation, dealkylation and demethylating drugs?","kind":"definition"},{"text":"Is the question about chemistry, epigenetics or a treatment, which a clinician can advise on?","kind":"boundary"}]}]},{"id":"forms","name":"Forms","description":"Named forms.","findings":[{"id":"forms-finding","name":"Forms","description":"Forms.","questions":[{"text":"What are oxidative, protein, DNA, oxidative DNA and hydrolytic DNA demethylation?","kind":"definition"},{"text":"Which entry fits the specific form?","kind":"action"}]}]}]},{"id":"epigenetics","name":"Epigenetics","description":"Epigenetics.","layers":[{"id":"dna","name":"DNA","description":"DNA demethylation.","findings":[{"id":"dna-finding","name":"DNA","description":"DNA.","questions":[{"text":"How do passive and TET-mediated active DNA demethylation work?","kind":"provenance"},{"text":"Which references are standard?","kind":"provenance"}]}]},{"id":"histones","name":"Histones","description":"Histone demethylases.","findings":[{"id":"histones-finding","name":"Histones","description":"Histones.","questions":[{"text":"How do LSD1 and Jumonji demethylases regulate chromatin?","kind":"provenance"},{"text":"Which sources are cited?","kind":"provenance"}]}]}]},{"id":"medicine","name":"Medicine","description":"Medicine.","layers":[{"id":"cancer","name":"Cancer","description":"Cancer epigenetics.","findings":[{"id":"cancer-finding","name":"Cancer","description":"Cancer.","questions":[{"text":"How are hypomethylating agents used in blood cancers, in general terms?","kind":"provenance"},{"text":"Which entry fits azacitidine?","kind":"action"}]}]},{"id":"drugs","name":"Drug metabolism","description":"Drug metabolism.","findings":[{"id":"drugs-finding","name":"Drug metabolism","description":"Drug metabolism.","questions":[{"text":"How do liver enzymes demethylate drugs such as codeine?","kind":"provenance"},{"text":"Which entry fits cytochrome P450?","kind":"action"}]}]}]},{"id":"context","name":"Context","description":"Development.","layers":[{"id":"reprogramming","name":"Reprogramming","description":"Epigenetic reprogramming.","findings":[{"id":"reprogramming-finding","name":"Reprogramming","description":"Reprogramming.","questions":[{"text":"Why is DNA demethylated in early embryos and germ cells?","kind":"provenance"},{"text":"Which entry fits epigenetic reprogramming?","kind":"action"}]}]},{"id":"hype","name":"Claims","description":"Epigenetic claims.","findings":[{"id":"hype-finding","name":"Claims","description":"Claims.","questions":[{"text":"How should popular claims about changing epigenetics be evaluated, with evidence attributed?","kind":"provenance"},{"text":"Is the presentation neutral and attributed?","kind":"boundary"}]}]}]}]},"agentConduct":{"may":["Explain demethylation in metabolism and epigenetics from scientific sources.","Distinguish DNA demethylation from histone demethylation."],"mustNot":["Overstate what epigenetic research shows about health or inheritance.","Confuse DNA demethylation with histone demethylation.","Promote unproven epigenetic tests, diets or products.","Present proposed mechanisms as established."],"requiresHuman":["Using epigenetic findings in clinical decisions for a patient."]},"ethics":{"considerations":["Hype around epigenetics can sell false hope and blame people for their biology."],"affectedParties":["Patients and consumers","Researchers"]},"owners":{"steward":"Nobody owns the process; it belongs to chemistry and biology.","roles":[],"masterSystems":[]},"relations":[{"target":"Q1057","type":"parent","note":"registry parent class"},{"target":"metabolism","type":"related","note":"in registry terms"},{"target":"methylation","type":"related"},{"target":"TET enzymes","type":"related"},{"target":"deacetylation","type":"related"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.demethylation","Wikidata: Q900386 (https://www.wikidata.org/wiki/Q900386)"]},"properties":{"applicability":"not-applicable","items":["LSD1 discovery: 2004 year - first histone demethylase","TET enzyme role described: 2009 year - 5-hydroxymethylcytosine","azacitidine US approval: 2004 year - hypomethylating agent"]},"recognition":{"applicability":"optional","items":["Removal of a methyl group","Oxidative demethylation, protein demethylation, DNA demethylation, oxidative DNA demethylation, hydrolytic DNA demethylation","Methylation adds methyl groups; deacetylation removes acetyl groups; dealkylation removes alkyl groups generally; demethylating drugs are medicines","Not visible; studied by sequencing and chemical assays."]},"capabilities":{"applicability":"required","items":["explain mechanisms","relay epigenetic roles","describe named forms","relay medical relevance in general terms"]},"hazards":{"applicability":"required","items":["Oversimplifying epigenetics claims","Confusing DNA and histone demethylation","Promoting unproven epigenetic products"]},"interfaces":{"applicability":"required","items":["No direct regulation; drug approval rules for hypomethylating agents"]},"context":{"applicability":"required","items":["Removing methyl groups in chemistry and biology.","DNA demethylation","histone and protein demethylation","RNA demethylation","drug metabolism N- and O-demethylation","chemical demethylation"]}},"sources":[{"title":"Wikidata item Q900386: demethylation","url":"https://www.wikidata.org/wiki/Q900386","note":"identity and sense of the item"},{"title":"Wikipedia: Demethylation","url":"https://en.wikipedia.org/wiki/Demethylation","note":"general description of the item"}],"openQuestions":["Should DNA demethylation be a separate entry?","How should the evidence for hydrolytic demethylation be presented?","How should biochemistry references be linked?"],"resources":{"spec":"/models/things/publications/thing-q900386/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q900386/spec.json"],"providers":["Claude"],"researchStatus":"unreviewed","generatedAt":"2026-09-13T22:52:39Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"not-applicable","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-06T19:52:02+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass","interaction.properties":"Plane ACT: no invented physical properties."},"score":1.0}}