7DE9

crystal structure of Arabidopsis RDM15 tudor domain in complex with an H3K4me1 peptide

Summary for 7DE9

• Entry DOI: 10.2210/pdb7de9/pdb
• Descriptor: Transcriptional regulator, Histone H3.2 (3 entities in total)
• Functional Keywords: tudor domain, histone, epigenetics, dna methylation, gene regulation
• Biological source: Arabidopsis thaliana (Mouse-ear cress); More
• Total number of polymer chains: 2
• Total formula weight: 9169.19

Authors

Song, Z.,Du, J. (deposition date: 2020-11-03, release date: 2021-04-07, Last modification date: 2025-04-09)

Primary citation

Niu, Q.,Song, Z.,Tang, K.,Chen, L.,Wang, L.,Ban, T.,Guo, Z.,Kim, C.,Zhang, H.,Duan, C.G.,Zhang, H.,Zhu, J.K.,Du, J.,Lang, Z.
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.
Nat Commun, 12:3367-3367, 2021

PubMed 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.

PubMed: 34099688
DOI: 10.1038/s41467-021-23637-4

Experimental method

X-RAY DIFFRACTION (1.711 Å)