Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

• Published in: Nature structural & molecular biology Vol. 21; no. 1; pp. 64 - 72
• Main Authors: Stroud, Hume, Do, Truman, Du, Jiamu, Zhong, Xuehua, Feng, Suhua, Johnson, Lianna, Patel, Dinshaw J, Jacobsen, Steven E
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.01.2014; Nature Publishing Group
• Subjects: 631/208/176/1988; 631/449; Arabidopsis - genetics; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Arabidopsis Proteins - physiology; Arabidopsis thaliana; Biochemistry; Biological Microscopy; Chromatin; Deoxyribonucleic acid; DNA; DNA Methylation; DNA, Plant; Epigenesis, Genetic; Epigenetic inheritance; Epigenetics; Genetic aspects; Genetic research; Life Sciences; Membrane Biology; Methylation; Molecular biology; Physiological aspects; Protein Structure; Proteins; United States
• ISSN: 1545-9993; 1545-9985; 1545-9985
• DOI: 10.1038/nsmb.2735

Non-CG methylation is abundant in plants, but its functions are poorly understood. A new study has uncovered the contributions of each non-CG methyltransferase, including the poorly characterized methyltransferase CMT2, to DNA methylation patterning and gene silencing. The results suggest that non-CG methyltransferases participate in self-reinforcing loop mechanisms with histone H3 K9 methylation and small RNAs to control gene silencing throughout the Arabidopsis genome. DNA methylation occurs in CG and non-CG sequence contexts. Non-CG methylation is abundant in plants and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however, its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana . We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo . CMT2 preferentially binds histone H3 Lys9 (H3K9) dimethylation and methylates non-CG cytosines that are regulated by H3K9 methylation. We revealed the contributions and redundancies between each non-CG methyltransferase in DNA methylation patterning and in regulating transcription. We also demonstrate extensive dependencies of small-RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the landscapes of histone modification and small noncoding RNA.