{"day":"12","OA_place":"publisher","volume":11,"author":[{"last_name":"Shahzad","first_name":"Zaigham","full_name":"Shahzad, Zaigham"},{"id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","full_name":"Hollwey, Elizabeth","first_name":"Elizabeth","last_name":"Hollwey"},{"last_name":"Moore","first_name":"Jonathan D.","full_name":"Moore, Jonathan D."},{"full_name":"Choi, Jaemyung","last_name":"Choi","first_name":"Jaemyung"},{"full_name":"Cassin-Ross, Gaëlle","last_name":"Cassin-Ross","first_name":"Gaëlle"},{"full_name":"Rouached, Hatem","last_name":"Rouached","first_name":"Hatem"},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"}],"date_updated":"2025-10-23T11:15:25Z","project":[{"grant_number":"725746","name":"Quantitative analysis of DNA methylation maintenance with chromatin","call_identifier":"H2020","_id":"62935a00-2b32-11ec-9570-eff30fa39068"}],"scopus_import":"1","article_type":"original","quality_controlled":"1","date_created":"2025-10-16T13:11:21Z","acknowledgement":"We thank P. Baduel and V. Colot for sharing SV data, A. Muyle for gbM conservation data and X. Feng, C. Dean, E. Coen and Zilberman lab members for constructive comments on the paper. This work was supported by a European Research Council grant (725746) to D.Z., LUMS Startup grant (STG-188) to Z.S. and US National Science Foundation grant (MCB-2334561) to H.R. This study would not have been possible without Arabidopsis 1001 genome, methylome and transcriptome resources. Open access funding provided by Institute of Science and Technology (IST Austria).","date_published":"2025-09-12T00:00:00Z","doi":"10.1038/s41477-025-02108-4","publisher":"Springer Nature","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations","OA_type":"hybrid","has_accepted_license":"1","corr_author":"1","type":"journal_article","file_date_updated":"2025-10-23T11:13:58Z","pmid":1,"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"citation":{"ieee":"Z. Shahzad <i>et al.</i>, “Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations,” <i>Nature Plants</i>, vol. 11. Springer Nature, pp. 2084–2099, 2025.","apa":"Shahzad, Z., Hollwey, E., Moore, J. D., Choi, J., Cassin-Ross, G., Rouached, H., … Zilberman, D. (2025). Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-025-02108-4\">https://doi.org/10.1038/s41477-025-02108-4</a>","ista":"Shahzad Z, Hollwey E, Moore JD, Choi J, Cassin-Ross G, Rouached H, Robinson MR, Zilberman D. 2025. Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations. Nature Plants. 11, 2084–2099.","mla":"Shahzad, Zaigham, et al. “Gene Body Methylation Regulates Gene Expression and Mediates Phenotypic Diversity in Natural Arabidopsis Populations.” <i>Nature Plants</i>, vol. 11, Springer Nature, 2025, pp. 2084–99, doi:<a href=\"https://doi.org/10.1038/s41477-025-02108-4\">10.1038/s41477-025-02108-4</a>.","chicago":"Shahzad, Zaigham, Elizabeth Hollwey, Jonathan D. Moore, Jaemyung Choi, Gaëlle Cassin-Ross, Hatem Rouached, Matthew Richard Robinson, and Daniel Zilberman. “Gene Body Methylation Regulates Gene Expression and Mediates Phenotypic Diversity in Natural Arabidopsis Populations.” <i>Nature Plants</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41477-025-02108-4\">https://doi.org/10.1038/s41477-025-02108-4</a>.","ama":"Shahzad Z, Hollwey E, Moore JD, et al. Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations. <i>Nature Plants</i>. 2025;11:2084-2099. doi:<a href=\"https://doi.org/10.1038/s41477-025-02108-4\">10.1038/s41477-025-02108-4</a>","short":"Z. Shahzad, E. Hollwey, J.D. Moore, J. Choi, G. Cassin-Ross, H. Rouached, M.R. Robinson, D. Zilberman, Nature Plants 11 (2025) 2084–2099."},"PlanS_conform":"1","intvolume":"        11","ddc":["580"],"month":"09","page":"2084-2099","department":[{"_id":"MaRo"},{"_id":"DaZi"}],"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"abstract":[{"lang":"eng","text":"Genetic variation is generally regarded as a prerequisite for evolution. In principle, epigenetic information inherited independently of DNA sequence can also enable evolution, but whether this occurs in natural populations is unknown. Here we show that single-nucleotide and epigenetic gene body DNA methylation (gbM) polymorphisms explain comparable amounts of expression variance in <jats:italic>Arabidopsis thaliana</jats:italic> populations. We genetically demonstrate that gbM regulates transcription, and we identify and genetically validate many associations between gbM polymorphism and the variation of complex traits: fitness under heat and drought, flowering time and accumulation of diverse minerals. Epigenome-wide association studies pinpoint trait-relevant genes with greater precision than genetic association analyses, probably due to reduced linkage disequilibrium between gbM variants. Finally, we identify numerous associations between gbM epialleles and diverse environmental conditions in native habitats, suggesting that gbM facilitates adaptation. Overall, our results indicate that epigenetic methylation variation fundamentally shapes phenotypic diversity in a natural population."}],"publication":"Nature Plants","oa_version":"Published Version","external_id":{"pmid":["40940427"]},"_id":"20479","file":[{"date_created":"2025-10-23T11:13:58Z","access_level":"open_access","date_updated":"2025-10-23T11:13:58Z","relation":"main_file","checksum":"6a3f6cffdc934b8a2015c3c247f5a92a","file_id":"20524","file_size":7746662,"success":1,"creator":"dernst","content_type":"application/pdf","file_name":"2025_NaturePlants_Shahzad.pdf"}],"year":"2025","publication_identifier":{"issn":["2055-0278"]}}