Heat-responsive ONSEN long terminal repeats integrate heat shock factor motifs, DNA methylation and natural sequence variation in Arabidopsis

Barbaruah, Baibhav R.; Airlangga, Rahmadani P.; Ito, Hidetaka

Heat-responsive ONSEN long terminal repeats integrate heat shock factor motifs, DNA methylation and natural sequence variation in Arabidopsis

Barbaruah, Baibhav R.; Airlangga, Rahmadani P.; Ito, Hidetaka

Biology Open, 2026, 15(9), 062799

Permalink : https://hdl.handle.net/2115/100327

このアイテムのアクセス数:124件（2026-11-06 19:30 集計）

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論文情報

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アクセス権	open access
URI	https://hdl.handle.net/2115/100327
タイトル	Heat-responsive ONSEN long terminal repeats integrate heat shock factor motifs, DNA methylation and natural sequence variation in Arabidopsis
著者	Barbaruah, Baibhav R. ; Airlangga, Rahmadani P. ; Ito, Hidetaka
著者名 Barbaruah, Baibhav R.
著者名 Airlangga, Rahmadani P.
ORCID 0000-0002-8070-5005 著者名 Ito, Hidetaka
言語	英語
キーワード	Arabidopsis thaliana
	ONSEN
	Heat shock factor
	Heat shock element
	DNA methylation
	Retrotransposon
発行日	2026-09-11
出版者	The Company of Biologists
収録物名	Biology Open
巻(号)	15(9)
ページ	062799
ページ数	39
抄録	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-seq data, and Arabidopsis genome assemblies. In silico disruption of five HSE cores eliminated HSF-family motif compatibility in the selected design and all 5,119 exact-GC alternatives. Across 16 curated Col-0 terminal windows, ONSEN contained 33–49 non-redundant HSF motif-coordinate placements per 800-bp window and was strongly enriched relative to 1,930 non-ONSEN transposable elements across score thresholds and continuous metrics. Direct comparison with 779 non-ONSEN LTR retrotransposons showed selectively elevated basal CHH methylation 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 (DOF)-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.
資源タイプ	学術雑誌論文
出版タイプ	Version of Record
権利情報	Creative Commons Attribution 4.0 International
権利情報	This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.
EISSN	2046-6390
関連情報 (isIdenticalTo)	出版社版DOI https://doi.org/10.1242/bio.062799