--- _id: '9487' abstract: - lang: eng text: Cytosine DNA methylation is considered to be a stable epigenetic mark, but active demethylation has been observed in both plants and animals. In Arabidopsis thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic background. However, the extent and function of demethylation by DEMETER-LIKE (DML) proteins in WT plants is not known. Using genome-tiling microarrays, we mapped DNA methylation in mutant and WT plants and identified 179 loci actively demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA hypermethylation. Reintroducing WT DML genes restores most loci to the normal pattern of methylation, although at some loci, hypermethylated epialleles persist. Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation by DML enzymes primarily occurs at the 5′ and 3′ ends, a pattern opposite to the overall distribution of WT DNA methylation. Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation. article_processing_charge: No article_type: original author: - first_name: Jon full_name: Penterman, Jon last_name: Penterman - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Jin Hoe full_name: Huh, Jin Hoe last_name: Huh - first_name: Tracy full_name: Ballinger, Tracy last_name: Ballinger - first_name: Steven full_name: Henikoff, Steven last_name: Henikoff - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer citation: ama: Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences. 2007;104(16):6752-6757. doi:10.1073/pnas.0701861104 apa: Penterman, J., Zilberman, D., Huh, J. H., Ballinger, T., Henikoff, S., & Fischer, R. L. (2007). DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.0701861104 chicago: Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2007. https://doi.org/10.1073/pnas.0701861104. ieee: J. Penterman, D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L. Fischer, “DNA demethylation in the Arabidopsis genome,” Proceedings of the National Academy of Sciences, vol. 104, no. 16. National Academy of Sciences, pp. 6752–6757, 2007. ista: Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. 2007. DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences. 104(16), 6752–6757. mla: Penterman, Jon, et al. “DNA Demethylation in the Arabidopsis Genome.” Proceedings of the National Academy of Sciences, vol. 104, no. 16, National Academy of Sciences, 2007, pp. 6752–57, doi:10.1073/pnas.0701861104. short: J. Penterman, D. Zilberman, J.H. Huh, T. Ballinger, S. Henikoff, R.L. Fischer, Proceedings of the National Academy of Sciences 104 (2007) 6752–6757. date_created: 2021-06-07T09:38:21Z date_published: 2007-04-17T00:00:00Z date_updated: 2021-12-14T08:55:12Z day: '17' department: - _id: DaZi doi: 10.1073/pnas.0701861104 extern: '1' external_id: pmid: - '17409185' intvolume: ' 104' issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.0701861104 month: '04' oa: 1 oa_version: Published Version page: 6752-6757 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: DNA demethylation in the Arabidopsis genome type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 104 year: '2007' ...