TRIMMER audit

Verdict

Status: keep
Confidence: high
Short verdict: Keep. The 3UTR-length logic is valid but should also include coding-region and promoter-proximal APA/termination effects.

Node definition: Alternative cleavage and polyadenylation choosing different 3 prime ends and often changing 3UTR regulatory site content.
Incoming edges:
- SCRIBE -> TRIMMER: CTD → CstF / cleavage/polyA
Outgoing edges:
- TRIMMER -> READERS: 3’UTR length / → RBP sites
- TRIMMER -> DARTS: 3’UTR length / → miRNA sites

What is strongly supported: Widespread APA changes transcript isoform abundance, 3UTR length, miRNA/RBP site exposure, localization, and sometimes protein C-termini.
What is context-dependent: APA shifts vary with proliferation, differentiation, immune activation, and cancer; distal versus proximal site use does not always map simply to higher protein output.
What is weak, controversial, or assay-biased: Shorter 3UTR does not automatically escape regulation if alternative sites add other elements or change localization/translation.
What may be duplicate biology under another name: Overlaps with TIMER, READERS, DARTS, SCRIBE.

Missing edges: Add TRIMMER -> TIMER edge for polyA tail/3UTR-dependent stability; add SPLICER <-> TRIMMER coupling.
Excess edges: TRIMMER -> DARTS/READERS is correct but should be “changes potential sites,” not guaranteed targeting.
Candidate splits: No split.
Candidate merges: No merge.
Candidate renames: APA would be clearer.

Concrete graph change, if any: Keep; expand from 3UTR shortening to broader 3 end processing/APA.
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.