What is strongly supported: TFs recruit coactivators, corepressors, remodelers, Mediator, and Pol II; pioneer factors can engage nucleosomal or compact chromatin and seed regulatory programs.
What is context-dependent: Motif occupancy depends on chromatin, cofactors, concentration, post-translational state, and 3D enhancer-promoter context.
What is weak, controversial, or assay-biased: ChIP-seq peaks and motifs overpredict function; many binding events are low-effect, opportunistic, or indirect.
What may be duplicate biology under another name: Overlaps with OPENER/SHUFFLER/HUBS because TFs recruit those mechanisms.
Missing or excessive graph structure
Missing edges: Add KEYS -> BRIDGES to indicate enhancer-bound TFs help establish promoter communication.
Excess edges: KEYS -> GUIDES/SPONGE should be phrased as transcriptional control of ncRNA genes, not mechanism-specific targeting.
Candidate splits: No split in main map; optional activators/repressors/pioneer factors in notes.
Candidate merges: No merge.
Candidate renames: TFs would be clearer.
Recommendation
Concrete graph change, if any: Keep; add binding-vs-function caveat and KEYS -> BRIDGES.
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 31827280 — TF binding, regulatory grammar, and gene-control review.
PMID 24270712 — pioneer factor concept and chromatin opening.
PMID 29126285 — enhancer logic and TF/cofactor recruitment review.
PMID 31285669 — functional interpretation caveats for TF ChIP and enhancer assays.