A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation

Qingfeng Niu, Zhe Song, Kai Tang, Lixian Chen, Lisi Wang, Ting Ban, Zhongxin Guo, Chanhong Kim, Heng Zhang, Cheng-Guo Duan, Huiming Zhang, Jian-Kang Zhu, Jiamu Du () and Zhaobo Lang ()
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Qingfeng Niu: Chinese Academy of Sciences
Zhe Song: Chinese Academy of Sciences
Kai Tang: Purdue University
Lixian Chen: Chinese Academy of Sciences
Lisi Wang: Chinese Academy of Sciences
Ting Ban: Chinese Academy of Sciences
Zhongxin Guo: Fujian Agriculture and Forestry Universtiy
Chanhong Kim: Chinese Academy of Sciences
Heng Zhang: Chinese Academy of Sciences
Cheng-Guo Duan: Chinese Academy of Sciences
Huiming Zhang: Chinese Academy of Sciences
Jian-Kang Zhu: Chinese Academy of Sciences
Jiamu Du: Southern University of Science and Technology
Zhaobo Lang: Chinese Academy of Sciences

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: Abstract In plants, RNA-directed DNA methylation (RdDM) is a well-known de novo DNA methylation pathway that involves two plant-specific RNA polymerases, Pol IV and Pol V. In this study, we discovered and characterized an RdDM factor, RDM15. Through DNA methylome and genome-wide siRNA analyses, we show that RDM15 is required for RdDM-dependent DNA methylation and siRNA accumulation at a subset of RdDM target loci. We show that RDM15 contributes to Pol V-dependent downstream siRNA accumulation and interacts with NRPE3B, a subunit specific to Pol V. We also show that the C-terminal tudor domain of RDM15 specifically recognizes the histone 3 lysine 4 monomethylation (H3K4me1) mark. Structure analysis of RDM15 in complex with the H3K4me1 peptide showed that the RDM15 tudor domain specifically recognizes the monomethyllysine through an aromatic cage and a specific hydrogen bonding network; this chemical feature-based recognition mechanism differs from all previously reported monomethyllysine recognition mechanisms. RDM15 and H3K4me1 have similar genome-wide distribution patterns at RDM15-dependent RdDM target loci, establishing a link between H3K4me1 and RDM15-mediated RdDM in vivo. In summary, we have identified and characterized a histone H3K4me1-specific binding protein as an RdDM component, and structural analysis of RDM15 revealed a chemical feature-based lower methyllysine recognition mechanism.

Date: 2021
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DOI: 10.1038/s41467-021-23637-4

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