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In this study, we found that mutation of DECREASED IN DNA METHYLATION 1 (DDM1) in soybean leads to genome-wide chromatin homogenization, characterized by a loosening of heterochromatin and a tightening of euchromatin. This remodeling triggers 2 distinct molecular pathways: in heterochromatin, increased release of small RNAs activates the noncanonical RdDM pathway; while in euchromatin, transposable elements (TEs) are enriched with H3K9me2 modifications, which in turn activate the CMT2 pathway. Together, these pathways drive a pronounced burst of CHH methylation at the whole genome level. This epigenetic remodeling correlates with massive transcriptional dysregulation, upregulating stress responses and downregulating photosynthesis, linking local H3K9me2 changes on TEs, ultimately leading to severe phenotypes. Our findings reveal a unique, bidirectional pathway for CHH regulation in plants with complex chromatin states remodeling.<\/jats:p>","DOI":"10.1093\/plcell\/koag250","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T11:49:11Z","timestamp":1787140151000},"source":"Crossref","is-referenced-by-count":0,"title":["Chromatin homogenization triggers burst of CHH methylation in soybean"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5907-6219","authenticated-orcid":false,"given":"Lesheng","family":"Cao","sequence":"first","affiliation":[{"name":"Institute of Carbon Neutrality, Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University , Harbin 150040 ,","place":["China"]},{"name":"College of Life Science, Northeast Forestry University , Harbin 150040 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