Short verdict: Keep, but avoid implying DNA methylation is uniformly repressive. Promoter CpG island methylation is strongly associated with silencing; gene-body and enhancer methylation have context-specific meanings.
What the current graph claims
Node definition: DNA methylation, especially CpG 5mC written by DNMTs, maintained across replication, and oxidized by TET enzymes.
SILENCER -> ZONES: 5mC / → comp. B [context/dashed]
Literature-grounded assessment
What is strongly supported: DNMT1/3A/3B and TET enzymes form a well-established methylation/demethylation system; promoter CpG methylation recruits methyl-CpG readers and repressive complexes.
What is context-dependent: Gene-body methylation can correlate with active transcription and splicing; enhancer methylation can be dynamic; non-CpG methylation is important in neurons and pluripotent cells.
What is weak, controversial, or assay-biased: Causality is locus-dependent: methylation can be consequence, maintenance mark, or driver depending on promoter class and chromatin state.
What may be duplicate biology under another name: Overlaps with WRITER-R and ZONES for heterochromatin.
Missing or excessive graph structure
Missing edges: Add SILENCER -> KEYS inhibitory edge for methylated motif/promoter exclusion; add TET/active demethylation in notes.
Excess edges: SILENCER -> ZONES should be reciprocal and context-dependent rather than simply 5mC -> B compartment.
Candidate splits: No split for map scale, though 5mC maintenance vs de novo vs TET oxidation are distinct.
Candidate merges: No merge.
Candidate renames: DNA-METHYLATION would be clearer.
Recommendation
Concrete graph change, if any: Keep; wording should distinguish promoter repression from gene-body/enhancer context.
Concrete technical-notes/blog wording change, if any: Mirror the graph recommendation in the glossary and relation catalogue, and explicitly mark the confidence/caveat where the claim is context-dependent or assay-sensitive.
Key sources
PMID 22353506 — classic review on DNA methylation and regulation.
PMID 31673078 — modern review on mammalian DNA methylation dynamics.
PMID 24705243 — TET-mediated oxidation and active demethylation review.
PMID 27716473 — DNA methylation in gene bodies/regulatory regions cautions against simple silencing model.