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While many studies have reported the transcriptomic profile and pursue molecular mechanism in response to Fe limitation, little is known if epigenetic factors play a role in response to Fe\u2010deficiency. In this study, whole\u2010genome bisulfite sequencing analysis, high\u2010throughput RNA\u2010Seq of mRNA, small RNA and transposable element (TE) expression with root and shoot organs of rice seedlings under Fe\u2010sufficient and Fe\u2010deficient conditions were performed. The results showed that widespread hypermethylation, especially for the CHH context, occurred after Fe\u2010deficiency. Integrative analysis of methylation and transcriptome revealed that the transcript abundance of Fe\u2010deficiency\u2010induced genes was negatively correlated with nearby TEs and positively with the 24\u2010nucleotide siRNAs. The ability of methylation to affect the physiology and molecular response to Fe\u2010deficiency was tested using an exogenous DNA methyltransferase inhibitor (5\u2010azacytidine), and genetically using a mutant for domains rearranged methyltransferase 2 (DRM2), that lacks CHH methylation. Both approaches resulted in decreased growth and Fe content in rice plants. Thus, alterations in specific methylation patterns, directed by siRNAs, play an important role in acclimation of rice to Fe\u2010deficient conditions. Furthermore, comparison with other reports suggests this may be a universal mechanism to acclimate to limited nutrient availability.<\/jats:p>","DOI":"10.1111\/tpj.15318","type":"journal-article","created":{"date-parts":[[2021,5,12]],"date-time":"2021-05-12T05:12:48Z","timestamp":1620796368000},"page":"727-739","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":41,"title":["DNA methylation is involved in acclimation to iron\u2010deficiency in rice (\n                    <i>Oryza sativa<\/i>\n                    )"],"prefix":"10.1111","volume":"107","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3812-583X","authenticated-orcid":false,"given":"Shuo","family":"Sun","sequence":"first","affiliation":[{"name":"State Key Laboratory of Plant Physiology and Biochemistry College of Life Sciences Zhejiang University Hangzhou Zhejiang 310058 P.R. 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China"},{"name":"Australian Research Council Centre of Excellence in Plant Energy Biology Department of Animal, Plant and Soil Science School of Life Science La Trobe University Victoria 3086 Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huixia","family":"Shou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Physiology and Biochemistry College of Life Sciences Zhejiang University Hangzhou Zhejiang 310058 P.R. China"},{"name":"The Provincial International Science and Technology Cooperation Base on Engineering Biology International Campus of Zhejiang University Haining Zhejiang 314400 P.R. 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