Interplay between active chromatin marks and RNA-directed DNA methylation in Arabidopsis thaliana

• Published in: PLoS genetics Vol. 9; no. 11; p. e1003946
• Main Authors: Greenberg, Maxim V C, Deleris, Angelique, Hale, Christopher J, Liu, Ao, Feng, Suhua, Jacobsen, Steven E
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.11.2013; Public Library of Science (PLoS)
• Subjects: Arabidopsis - genetics; Arabidopsis Proteins - genetics; Arabidopsis thaliana; Chromatin; Chromatin - genetics; DNA methylation; DNA Methylation - genetics; DNA sequencing; DNA Transposable Elements - genetics; Epigenesis, Genetic; Gene Expression Regulation, Plant; Gene Silencing; Genes; Genetic aspects; Histone Demethylases - genetics; Histones; Jumonji Domain-Containing Histone Demethylases - genetics; Life Sciences; Lysine - genetics; Medical research; Methylation; Mutation; Nucleotide sequencing; Oligonucleotide Array Sequence Analysis; Physiological aspects; RNA - genetics; RNA sequencing; France
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1003946

DNA methylation is an epigenetic mark that is associated with transcriptional repression of transposable elements and protein-coding genes. Conversely, transcriptionally active regulatory regions are strongly correlated with histone 3 lysine 4 di- and trimethylation (H3K4m2/m3). We previously showed that Arabidopsis thaliana plants with mutations in the H3K4m2/m3 demethylase JUMONJI 14 (JMJ14) exhibit a mild reduction in RNA-directed DNA methylation (RdDM) that is associated with an increase in H3K4m2/m3 levels. To determine whether this incomplete RdDM reduction was the result of redundancy with other demethylases, we examined the genetic interaction of JMJ14 with another class of H3K4 demethylases: lysine-specific demethylase 1-like 1 and lysine-specific demethylase 1-like 2 (LDL1 and LDL2). Genome-wide DNA methylation analyses reveal that both families cooperate to maintain RdDM patterns. ChIP-seq experiments show that regions that exhibit an observable DNA methylation decrease are co-incidental with increases in H3K4m2/m3. Interestingly, the impact on DNA methylation was stronger at DNA-methylated regions adjacent to H3K4m2/m3-marked protein-coding genes, suggesting that the activity of H3K4 demethylases may be particularly crucial to prevent spreading of active epigenetic marks. Finally, RNA sequencing analyses indicate that at RdDM targets, the increase of H3K4m2/m3 is not generally associated with transcriptional de-repression. This suggests that the histone mark itself--not transcription--impacts the extent of RdDM.