SCRIBE audit

Verdict

Status: keep
Confidence: high
Short verdict: Keep. This is a central coupling node; retain emphasis on pausing and CTD-mediated RNA-processing coordination.

Node definition: RNA polymerase II initiation, promoter-proximal pausing, pause release, elongation, and CTD phosphorylation code.
Incoming edges:
- WRITER-A -> SCRIBE: H3K4me3 / → Pol II recruit
- HUBS -> SCRIBE: P-TEFb release / pause→elongation
- KEYS -> SCRIBE: TF→Mediator/PIC / → Pol II recruitment
- SWITCH -> SCRIBE: P-TEFb/CDK9 / Ser2-CTD
Outgoing edges:
- SCRIBE -> ZONES: active txn / → comp. A [context/dashed]
- SCRIBE -> SHIELD: Ser5-P CTD / → capping co-tx
- SCRIBE -> SPLICER: Pol II rate / → exon inclusion / (kinetic coupling C) [emphasized]
- SCRIBE -> TRIMMER: CTD → CstF / cleavage/polyA
- SCRIBE -> STAMP: CTD recruits METTL3/14 / (co-tx m6A, B)
- SCRIBE -> WRITER-A: SETD2 coupled / Ser2-P → H3K36me3 (C) [emphasized]

What is strongly supported: Promoter-proximal pausing by NELF/DSIF and release by P-TEFb/CDK9 are well established; CTD phosphorylation coordinates capping, elongation, splicing, 3 end processing, and chromatin marks.
What is context-dependent: Pausing is gene- and stimulus-specific; CTD marks are combinatorial and not a simple linear code.
What is weak, controversial, or assay-biased: “CTD code” can be too deterministic; reader recruitment is dynamic and redundant.
What may be duplicate biology under another name: Overlaps with SHIELD/SPLICER/TRIMMER/STAMP/WRITER-A via co-transcriptional coupling.

Missing edges: Add SCRIBE -> RECODER only indirectly? ADAR editing is often nuclear/co-transcriptional but more substrate/dsRNA-driven.
Excess edges: SCRIBE -> STAMP as CTD recruits METTL3/14 is supported but should be caveated as not all m6A is strictly co-transcriptionally determined by CTD.
Candidate splits: No split.
Candidate merges: No merge.
Candidate renames: POL-II would be clearer but SCRIBE is fine.

Concrete graph change, if any: Keep; caveat CTD-code determinism and pausing generality.
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.