{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T15:07:24Z","timestamp":1789398444566,"version":"build-2803163510"},"reference-count":78,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Plant Biol J"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    <jats:list list-type=\"bullet\">\n                      <jats:list-item>\n                        <jats:p>Rationale: Plants experience diverse biotic and abiotic stresses that can induce changes in DNA methylation. However, comparisons among existing studies are complicated by differences in analytical methods and experimental designs. We aimed to identify shared and stress\u2010specific DNA methylation responses across studies.<\/jats:p>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>Methods: We reanalysed 16 whole\u2010genome bisulphite sequencing datasets from 13 Arabidopsis thaliana studies using a unified bioinformatics pipeline. Differentially methylated regions (DMRs) were assessed in the CG, CHG and CHH contexts and examined in relation to genes, transposable elements (TEs), Gene Ontology terms, gene\u2010proximal TE superfamilies and epimutation\u2010prone loci.<\/jats:p>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>Results: Global methylation levels were generally stable, whereas the number and genomic distribution of DMRs varied according to stress type and methylation context. CG\u2010DMRs occurred primarily in gene bodies, while CHG\u2010 and CHH\u2010DMRs were enriched in TEs. Functional analysis identified shared stress\u2010related processes across conditions. Gene\u2010proximal LINE\/L1, RathE1_cons and DNA\/HAT elements were enriched for stress\u2010responsive methylation changes. A subset of stress\u2010associated CG\u2010DMRs overlapped loci known to accumulate stable epimutations over generations.<\/jats:p>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>Conclusions: Standardized cross\u2010study analysis revealed both shared and stress\u2010specific methylation patterns. The association of stress\u2010responsive DMRs with gene\u2010proximal TEs and epimutation\u2010prone loci suggests potential links among environmental responses, genome regulation and long\u2010term epigenetic variation.<\/jats:p>\n                      <\/jats:list-item>\n                    <\/jats:list>\n                  <\/jats:p>","DOI":"10.1111\/plb.70291","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T14:30:43Z","timestamp":1789396243000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["<scp>DNA<\/scp>\n                    methylome responses to biotic and abiotic stress in\n                    <i>Arabidopsis thaliana<\/i>\n                    : A multi\u2010study analysis"],"prefix":"10.1111","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-5318-9481","authenticated-orcid":false,"given":"R.","family":"Behl","sequence":"first","affiliation":[{"name":"Research Unit Environmental Simulation (EUS) Helmholtz Munich  Neuherberg Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3653-3805","authenticated-orcid":false,"given":"J. J.","family":"Gallo\u2010Franco","sequence":"additional","affiliation":[{"name":"International Center for Tropical Agriculture (CIAT), CGIAR  Cali Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5843-0535","authenticated-orcid":false,"given":"R. R.","family":"Hazarika","sequence":"additional","affiliation":[{"name":"Plant Epigenomics, TUM School of Life Sciences Technical University of Munich  Freising Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2325-2342","authenticated-orcid":false,"given":"Z.","family":"Zhang","sequence":"additional","affiliation":[{"name":"Plant Epigenomics, TUM School of Life Sciences Technical University of Munich  Freising Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2433-047X","authenticated-orcid":false,"given":"F.","family":"Wilming","sequence":"additional","affiliation":[{"name":"Plant Epigenomics, TUM School of Life Sciences Technical University of Munich  Freising Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9825-867X","authenticated-orcid":false,"given":"J. P.","family":"Schnitzler","sequence":"additional","affiliation":[{"name":"Research Unit Environmental Simulation (EUS) Helmholtz Munich  Neuherberg Germany"},{"name":"Ecosystem Physiology, Faculty of Environment and Natural Resources University Freiburg  Freiburg Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9343-4996","authenticated-orcid":false,"given":"C.","family":"Lindermayr","sequence":"additional","affiliation":[{"name":"Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC\u2010M), Helmholtz Munich  Neuherberg Germany"},{"name":"TUM School of Life Sciences Technical University Munich  Weihenstephan Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7962-2907","authenticated-orcid":false,"given":"F.","family":"Johannes","sequence":"additional","affiliation":[{"name":"Plant Epigenomics, TUM School of Life Sciences Technical University of Munich  Freising Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,14]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"crossref","first-page":"1931","DOI":"10.1007\/s00299-022-02901-x","article-title":"DNA methylation dynamics in response to abiotic and pathogen stress in plants","volume":"41","author":"Arora H.","year":"2022","journal-title":"Plant Cell Reports"},{"key":"e_1_2_10_3_1","doi-asserted-by":"crossref","first-page":"2144","DOI":"10.3390\/ijms19072144","article-title":"Dynamic DNA methylation in plant growth and development","volume":"19","author":"Bartels A.","year":"2018","journal-title":"International Journal of Molecular Sciences"},{"key":"e_1_2_10_4_1","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/nature10555","article-title":"Spontaneous epigenetic variation in the Arabidopsis thaliana methylome","volume":"480","author":"Becker C.","year":"2011","journal-title":"Nature"},{"key":"e_1_2_10_5_1","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1002\/dvg.22877","article-title":"The Arabidopsis information resource: Making and mining the \u201cgold standard\u201d annotated reference plant genome","volume":"53","author":"Berardini T.Z.","year":"2015","journal-title":"Genesis"},{"key":"e_1_2_10_6_1","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.pbi.2016.12.007","article-title":"Gene body DNA methylation in plants","volume":"36","author":"Bewick A.J.","year":"2017","journal-title":"Current Opinion in Plant Biology"},{"key":"e_1_2_10_7_1","doi-asserted-by":"crossref","DOI":"10.3389\/fpls.2018.01447","article-title":"DNA methylation and the evolution of developmental complexity in plants","volume":"9","author":"Br\u00e4utigam K.","year":"2018","journal-title":"Frontiers in Plant Science"},{"key":"e_1_2_10_8_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0192170","article-title":"Induction of epigenetic variation in Arabidopsis by over\u2010expression of DNA METHYLTRANSFERASE1 (MET1)","volume":"13","author":"Brocklehurst S.","year":"2018","journal-title":"PLoS One"},{"key":"e_1_2_10_9_1","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1111\/nph.12029","article-title":"Four 13\u2010lipoxygenases contribute to rapid jasmonate synthesis in wounded Arabidopsis thaliana leaves: A role for lipoxygenase 6 in responses to long\u2010distance wound signals","volume":"197","author":"Chauvin A.","year":"2013","journal-title":"The New Phytologist"},{"key":"e_1_2_10_10_1","doi-asserted-by":"crossref","first-page":"1638","DOI":"10.1093\/plphys\/kiab025","article-title":"Lipoxygenase functions in 1O2 production during root responses to osmotic stress","volume":"185","author":"Chen T.","year":"2021","journal-title":"Plant Physiology"},{"key":"e_1_2_10_11_1","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/nrg.2016.139","article-title":"Regulatory activities of transposable elements: From conflicts to benefits","volume":"18","author":"Chuong E.B.","year":"2017","journal-title":"Nature Reviews. 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