{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T10:23:23Z","timestamp":1789122203105,"version":"build-2803163510"},"reference-count":23,"publisher":"The Company of Biologists","issue":"9","license":[{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"crossref","award":["25K2243005"],"award-info":[{"award-number":["25K2243005"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100005946","name":"Hokkaido University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100005946","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>ONSEN is a heat-activated Ty1\/copia retrotransposon in Arabidopsis thaliana controlled by heat shock factors (HSFs) and epigenetic silencing. Heat shock element (HSE)-like sequences in ONSEN long terminal repeats (LTRs) contribute to heat responsiveness, but relationships among sequence architecture, basal DNA methylation and natural variation remain unclear. We combined transcription-factor motif prediction, transposable-element comparisons, methylome and RNA sequencing (RNA-seq) data, and Arabidopsis genome assemblies. In silico disruption of five HSE cores eliminated HSF-family motif compatibility in the selected design and all 5119 exact-guanine\u2013cytosine (GC) alternatives. Across 16 curated Columbia-0 terminal windows, ONSEN contained 33\u201349 non-redundant HSF motif-coordinate placements per 800\u00a0bp window and was strongly enriched relative to 1930 non-ONSEN transposable elements across score thresholds and continuous metrics. Direct comparison with 779 non-ONSEN LTR retrotransposons showed selectively elevated basal CHH methylation (where H = A, C or T) at ONSEN termini. Genome-wide RNA-seq analysis revealed broad heat-responsive gene and transposable-element changes, including strong ONSEN induction, whereas candidate-window analysis distinguished ONSEN from most HSF-rich non-ONSEN outliers. ONSEN-like variants across eight accessions generally retained HSF-compatible motifs while altering predicted DNA binding with one finger-family motif composition. Together, these findings define ONSEN terminal regions as HSF-rich regulatory sequences that retain heat-responsive potential within a methylated chromatin context and identify candidates for functional analysis.<\/jats:p>","DOI":"10.1242\/bio.062799","type":"journal-article","created":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T09:55:30Z","timestamp":1787306130000},"source":"Crossref","is-referenced-by-count":0,"title":["Heat-responsive\n                    <i>ONSEN<\/i>\n                    long terminal repeats integrate heat shock factor motifs, DNA methylation and natural sequence variation in\n                    <i>Arabidopsis<\/i>"],"prefix":"10.1242","volume":"15","author":[{"given":"Baibhav R.","family":"Barbaruah","sequence":"first","affiliation":[{"name":"Hokkaido University 1 Division of Life Science, Graduate School of Life Science , , Sapporo 060-0810 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rahmadani P.","family":"Airlangga","sequence":"additional","affiliation":[{"name":"Hokkaido University 1 Division of Life Science, Graduate School of Life Science , , Sapporo 060-0810 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8070-5005","authenticated-orcid":false,"given":"Hidetaka","family":"Ito","sequence":"additional","affiliation":[{"name":"Hokkaido University 2 Faculty of Science , , Sapporo 060-0810 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"237","published-online":{"date-parts":[[2026,9,11]]},"reference":[{"key":"2026091105213790900_BIO062799C1","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1186\/s13059-021-02348-5","article-title":"Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana","volume":"22","author":"Baduel","year":"2021","journal-title":"Genome Biol."},{"key":"2026091105213790900_BIO062799C2","doi-asserted-by":"publisher","first-page":"e1004115","DOI":"10.1371\/journal.pgen.1004115","article-title":"How a retrotransposon exploits the plant's heat stress response for its activation","volume":"10","author":"Cavrak","year":"2014","journal-title":"PLoS Genet."},{"key":"2026091105213790900_BIO062799C3","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1104\/pp.106.091322","article-title":"A heat-inducible transcription factor, HsfA2, is required for extension of acquired thermotolerance in","volume":"143","author":"Charng","year":"2007","journal-title":"Plant Physiol."},{"key":"2026091105213790900_BIO062799C4","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1266\/ggs.20-00019","article-title":"ONSEN shows different transposition activities in RdDM pathway mutants","volume":"95","author":"Hayashi","year":"2020","journal-title":"Genes Genet. 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