enhanced transcriptional reactivation memory

traitmech:000713 · CLASS · PROPOSED

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.

Trait evidence (2)

DOI:10.7554/eLife.77646
Upon Anchor Away of Opi1, reactivation was faster than activation

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.
DOI:10.1534/genetics.112.143016
Cells with prior NaCl exposure have a faster gene-expression response to H2O2.

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.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.7554/eLife.77646

Parent traits (1)

phenotype METPO:1000059

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (3)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Preserve enhanced reactivation after repression as the defining endpoint.

CURATION TODO OPEN transcriptional-memory-endpoint-and-hierarchy · raised by codex · 2026-10-13

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Resolve strain provenance and assay-specific mechanisms before extending this draft.

KNOWLEDGE GAP OPEN transcriptional-memory-evidence-limits · raised by codex · 2026-10-13

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Reconcile deprecated lexical neighbors without reactivating their identifiers.

CURATION TODO OPEN transcriptional-memory-historical-identity · raised by codex · 2026-10-13

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Curation history

2026-10-13T00:34:29Z · MINTED_TRAITMECH_ID · codex
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.
2026-10-13T01:22:19Z · CORRECTED_EVIDENCE_PROVENANCE · codex
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.
2026-10-13T01:56:28Z · CORRECTED_SNIPPET_SELF_CONTAINMENT · codex
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.

Recorded curation sessions

2026-10-13T00:37:46Z · claude-code
- CREATE — Add enhanced transcriptional reactivation memory as a qualified proposed phenotype
  Created traitmech:000713 with primary DOI:10.7554/eLife.77646 and DOI:10.7554/eLife.16691, contiguous full-text Results snippets, qualified synthetic induction and transcript endpoints, historical identity TODO, and v589 proposal reserving 1066600-1066699. Bounded ignored/hidden and retained-tree novelty plus current pending/upstream reservation checks are retained in the source-verification sidecar. Canonical examples, exact synonyms, equivalence xrefs and causal graphs are omitted. Existing records, protected spore germination, pinned ontology and snippet baseline are unchanged. Native validation, artifact generation and immutable scientific review are separate required gates; no claim of discovery exhaustion.
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2026-10-13T00:38:24Z · codex
- AUDIT — Correct creator attribution without rewriting the immutable history entry
  The preceding immutable record history/records/enhanced_transcriptional_reactivation_memory/2026-10-13T003746Z-claude-code-cf0b17.yaml inherited the scaffolder default actor name claude-code because --actor-name was omitted. Its model gpt-5 and agent_tool codex fields were supplied correctly. The actual actor for that CREATE event was Codex, not Claude Code; no Claude execution is asserted. This successor corrects provenance only, leaving the original entry and TraitRecord unchanged. Future commands explicitly supply --actor-name codex.
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2026-10-13T01:24:20Z · codex
- EDIT — Quote the cited paper's own transcriptional-memory result
  Address review issue 1904 by replacing D'Urso's attributed background sentence with its complete own-confirmation sentence. Rechecked contiguous primary XML and publisher text and actual Figure 7A; retained selected-gene, two-hour recovery, USV1 not shown, four-generation and caption limits. Original quote spelling was source-faithful; provenance was the accepted defect. Updated guarded writer, source sidecar, proposal notes and tests. Existing histories and review bundles remain immutable.
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2026-10-13T01:59:23Z · codex
- EDIT — Replace anaphoric confirmation with a self-contained primary result
  For PR 1903 issue 1905, replaced the D Urso 2016 snippet with Guan 2012 DOI 10.1534/genetics.112.143016 Figure 4 caption opening. Exact publisher text and source identity were checked and actual Figures 4 and 5 inspected. Qualified four-hour recovery, mixed induced/repressed genes and Results versus Methods timing discrepancy. Prior source checks and curation history are retained; definition, identifiers and PROPOSED status unchanged. Native checks and regenerated artifact gates are recorded separately.
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