Mechanistic basis for maintenance of CHG DNA methylation in plants

Jian Fang, Jianjun Jiang, Sarah M. Leichter, Jie Liu, Mahamaya Biswal, Nelli Khudaverdyan, Xuehua Zhong () and Jikui Song ()
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Jian Fang: University of California
Jianjun Jiang: University of Wisconsin-Madison
Sarah M. Leichter: University of Wisconsin-Madison
Jie Liu: University of Wisconsin-Madison
Mahamaya Biswal: University of California
Nelli Khudaverdyan: University of California
Xuehua Zhong: University of Wisconsin-Madison
Jikui Song: University of California

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: Abstract DNA methylation is an evolutionarily conserved epigenetic mechanism essential for transposon silencing and heterochromatin assembly. In plants, DNA methylation widely occurs in the CG, CHG, and CHH (H = A, C, or T) contexts, with the maintenance of CHG methylation mediated by CMT3 chromomethylase. However, how CMT3 interacts with the chromatin environment for faithful maintenance of CHG methylation is unclear. Here we report structure-function characterization of the H3K9me2-directed maintenance of CHG methylation by CMT3 and its Zea mays ortholog ZMET2. Base-specific interactions and DNA deformation coordinately underpin the substrate specificity of CMT3 and ZMET2, while a bivalent readout of H3K9me2 and H3K18 allosterically stimulates substrate binding. Disruption of the interaction with DNA or H3K9me2/H3K18 led to loss of CMT3/ZMET2 activity in vitro and impairment of genome-wide CHG methylation in vivo. Together, our study uncovers how the intricate interplay of CMT3, repressive histone marks, and DNA sequence mediates heterochromatic CHG methylation.

Date: 2022
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31627-3

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DOI: 10.1038/s41467-022-31627-3

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