identifier: traitmech:000713 label: enhanced transcriptional reactivation memory definition: A physiological phenotype in which a microbial cell or lineage retains a non-genetic state from prior inducing conditions that enhances the rate or magnitude of later transcriptional activation after intervening repression. definition_source: DOI:10.7554/eLife.77646 trait_category: PHYSIOLOGY term_kind: CLASS mapping_status: PROPOSED parent_traits: - METPO:1000059 evidence: - reference: DOI:10.7554/eLife.77646 snippet: Upon Anchor Away of Opi1, reactivation was faster than activation notes: Sump et al. 2022, PMID:35579426, PMC9129879; Results s2-1, paragraph 2, contiguous in primary XML and publisher Version of Record HTML. Figure 1D uses synthetic Opi1 Anchor Away to bypass upstream induction control; enhancement is lost in mrs and nup100 mutants. Ordinary-starvation INO1 reactivation in Figure 1B is not clearly faster than activation. Figure 1 supplement 1C separately measures CHO1/ACT1 after three-hour repression; its generic statistical-comparator caption is ambiguous. Figure 1 supplement 2E measures 18-hour peripheral localization, not that duration of enhanced transcription; the main Results mispoints to supplement 1. Figure 1G competitive fitness is a different endpoint, not proof of transcriptional causality. Selected Results, Methods, scientific abstract, actual figures and strain-table rows were inspected. RT-qPCR mRNA kinetics are not direct measurements of initiation rate. Native abstract lookup returns NOT_IN_ABSTRACT; direct full-text matching supports the quotation, not a native VERIFIED verdict. - reference: DOI:10.1534/genetics.112.143016 snippet: Cells with prior NaCl exposure have a faster gene-expression response to H2O2. notes: Guan et al. 2012, PMID:22851651, PMC3454879; complete opening sentence of the Figure 4 caption, contiguous in publisher HTML with chemical subscripts retained as text. BY4741-background laboratory yeast received 0.7 M NaCl for 60 minutes, washing and 240 minutes of stress-free YPD recovery (two generations in Results), then 0.5 mM H2O2, compared with mock-treated cells. No significant pre-challenge expression difference at FDR 0.05 does not prove identical baselines. Figure 4 includes induced and repressed genes; only the enhanced-induction subset supports this activation phenotype. The 449-gene count is not a count of induced genes. Methods and Figure 4A sample through 40 minutes, whereas Results describes a 60-minute response. Figure 5 shows TSA2 mRNA kinetics by qPCR; nup42 deletion reduces the priming benefit, while nup100 naive and primed responses are both fast, not simple evidence of a universal mechanism. Four-to-five generation resistance persistence is a different endpoint. Relevant Results, Methods, scientific abstract and actual Figures 4 and 5 were inspected; raw data were not reanalyzed. Native abstract-verifier results are retained separately in the source sidecar; exact publisher full-text matching supports this caption quotation. discussions: - discussion_id: transcriptional-memory-endpoint-and-hierarchy prompt: Preserve enhanced reactivation after repression as the defining endpoint. kind: CURATION_TODO status: OPEN rationale: Compare induced transcript responses under matched later test conditions and genetic backgrounds, after intervening repression. Continued expression, transcript or reporter persistence, a chromatin mark, peripheral localization or a gene alone does not establish this phenotype. Transcript abundance does not by itself distinguish synthesis from degradation. No identical first and second stimulus, prior production of a particular transcript, fixed duration, universal mitotic inheritance or shared chromatin mechanism is required. Carbon-source memory (traitmech:000706) spans growth and induction endpoints and is not reparented wholesale. Memory of acquired stress resistance (traitmech:000712) concerns retained resistance, not faster transcription. Anticipation and bet hedging are also not exact equivalents. Unqualified transcriptional memory, epigenetic memory and priming are not asserted as exact synonyms. METPO:1000059 phenotype is the conservative parent pending hierarchy review; existing records are unchanged. posed_by: codex posed_date: '2026-10-13' - discussion_id: transcriptional-memory-evidence-limits prompt: Resolve strain provenance and assay-specific mechanisms before extending this draft. kind: KNOWLEDGE_GAP status: OPEN rationale: Sump and Guan report different laboratory assays, not independent replication of the same experiment. Laboratory and engineered yeast backgrounds are qualified evidence, not natural canonical taxa. Sump's retrieved v2 strain table has a CHO1 DBY1428 figure locator and an HTA1-mCherry versus Methods Pho88 description discrepancy; no strain-wide extrapolation follows. Selected publisher and XML text agrees after normalization, not complete byte-level version equivalence. Publisher figure images were inspected at limited resolution, without numerical reanalysis. Bounded publisher, qualified MED and Crossref checks on 2026-10-12 exposed no linked correction or retraction; this does not prove notice absence. No causal graph, exact synonym, external equivalence or species-wide phenotype is asserted. Source access challenges and caption discrepancies are retained in the source-verification sidecar. posed_by: codex posed_date: '2026-10-13' - discussion_id: transcriptional-memory-historical-identity prompt: Reconcile deprecated lexical neighbors without reactivating their identifiers. kind: CURATION_TODO status: OPEN rationale: Pinned and inspected current METPO releases mark METPO:1000108 epigenetic modification and METPO:1000310 transcription factor deprecated below ObsoleteClass, with OMO:0001000 and no replacement or consider annotation in those graphs. OMO means out of scope, but METPO issue 521 disputes the mechanical reason assignment. Original historical definitions and parent axioms remain unassessed; labels alone do not prove historical nonequivalence. This operational physiological phenotype is accepted independently from primary experiments, not by reactivating those terms or assuming a sequence-feature meaning. Ignored/hidden available files, retained historical trees, normalized trait semantics, pending changes and ontology graphs revealed no exact active record in the inspected scope. No historical exact-equivalence claim is made. The pinned ontology is unchanged; discovery is not exhausted. posed_by: codex posed_date: '2026-10-13' curation_history: - timestamp: '2026-10-13T00:34:29Z' curator: codex action: MINTED_TRAITMECH_ID changes: Added enhanced transcriptional reactivation memory with two DOI references and contiguous full-text snippets. Preserved synthetic induction, transcript-endpoint, duration, source-version and historical-identity limits. Reserved 000713, v589 and 1066600-1066699 after ignored/hidden, retained-tree, independent-copy and pending-PR checks. No canonical examples or mechanism graph; existing records unchanged. Timestamp is the observed UTC decision. llm_assisted: true - timestamp: '2026-10-13T01:22:19Z' curator: codex action: CORRECTED_EVIDENCE_PROVENANCE changes: Replaced the D'Urso background-attribution snippet with the authors' own confirmation sentence for Figure 7A, addressing review issue 1904. Retained selected-gene, two-hour recovery, unshown-USV1, four-generation and assay limits; no definition or identifiers changed. llm_assisted: true - timestamp: '2026-10-13T01:56:28Z' curator: codex action: CORRECTED_SNIPPET_SELF_CONTAINMENT changes: Replaced the anaphoric D'Urso confirmation with Guan 2012's self-contained Figure 4 result sentence, addressing review issue 1905 without extending the quotation budget. Preserved prior evidence checks as history. Qualified Guan's four-hour recovery, mixed induced/repressed gene set and assay timing discrepancy; definition, identifiers and PROPOSED status are unchanged. llm_assisted: true