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In its long-term form, cellular memory often reflects interactions between\n                    <jats:italic>cis<\/jats:italic>\n                    -acting chromatin states and diffusible\n                    <jats:italic>trans<\/jats:italic>\n                    -acting regulators, experimentally difficult to separate\n                    <jats:italic>in vivo<\/jats:italic>\n                    . A key challenge is to develop a quantitative and reliable framework that captures the duration of cellular memory without prior mechanistic knowledge. The FLOWERING LOCUS C (FLC) gene illustrates this problem and opportunity: a Polycomb\/Trithorax\n                    <jats:italic>cis<\/jats:italic>\n                    -acting chromatin switch at FLC produces bistable ON\/OFF transcriptional states, while\n                    <jats:italic>trans<\/jats:italic>\n                    -acting factors such as VERNALIZATION INSENSITIVE 3 (VIN3) and FLOWERING LOCUS T (FT) modulate transitions between those states. While laboratory studies typically view memory as the persistence of a state after a signal disappears, annual field censuses reveal a time-integrative mode of memory where\n                    <jats:italic>FLC<\/jats:italic>\n                    integrates fluctuating environmental signals over past intervals. To quantify such long-term effects systematically, we formalized the thermal memory interval (TMI), the time window of past environmental cues that best predicts current gene expression\u2014as a consistent metric. We applied TMI to the VIN3\u2013FLC\u2013FT module in perennial\n                    <jats:italic>Brassicaceae<\/jats:italic>\n                    with divergent life histories: Arabidopsis halleri subsp. gemmifera and\n                    <jats:italic>Eutrema japonicum<\/jats:italic>\n                    , introduced here to test generality across species. TMIs distinguished spring versus autumn FLC states and revealed distributed memory across the VIN3-FLC-FT network, with intervals from 1\u2013150 days, extending previously reported timescales. Crucially, a regression model forecasted dynamics in an independent year, showing that integrated thermal history explains the timing of seasonal phase switching across the VIN3\u2013FLC\u2013FT network. While TMIs require dense time-series data and do not by themselves reveal molecular mechanism, they offer a robust, quantitative, and generalizable framework: TMIs can be extended to other genes and to alternative environmental or physiological variables, enabling direct, comparative quantification of cellular memory across genes, species, and contexts.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0336733","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T17:24:39Z","timestamp":1787160279000},"page":"e0336733","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Conserved gene- and network-level thermal memory intervals in two divergent perennial crucifers in nature"],"prefix":"10.1371","volume":"21","author":[{"given":"Yoshikazu","family":"Endo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haruki","family":"Nishio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oguchi","family":"Taichi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyoko","family":"Yamane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria Faith","family":"Eseese","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1238-8025","authenticated-orcid":true,"given":"Clarissa Frances","family":"Frederica","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroshi","family":"Kudoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8625-7872","authenticated-orcid":true,"given":"Diana Mihaela","family":"Buzas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,8,19]]},"reference":[{"issue":"5258","key":"pone.0336733.ref001","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1126\/science.272.5258.54","article-title":"Immunological memory and protective immunity: understanding their relation","volume":"272","author":"R Ahmed","year":"1996","journal-title":"Science"},{"issue":"5","key":"pone.0336733.ref002","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/nrm3789","article-title":"What are memories made of? 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