7de9 | pdb_00007de9
crystal structure of Arabidopsis RDM15 tudor domain in complex with an H3K4me1 peptide
Structural highlights
FunctionPDS5C_ARATH Cohesin cofactor dispensable during the meiotic division but playing an important role in DNA repair by homologous recombination (HR) probably by helping SMC5/SMC6 complex (PubMed:26648949). Regulator of sister chromatid cohesion in mitosis which may stabilize cohesin complex association with chromatin (PubMed:26648949). May couple sister chromatid cohesion during mitosis to DNA replication (By similarity). Cohesion ensures that chromosome partitioning is accurate in both meiotic and mitotic cells and plays an important role in DNA repair (PubMed:26648949).[UniProtKB:Q29RF7][1] Publication Abstract from PubMedIn 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. 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.,Niu Q, Song Z, Tang K, Chen L, Wang L, Ban T, Guo Z, Kim C, Zhang H, Duan CG, Zhang H, Zhu JK, Du J, Lang Z Nat Commun. 2021 Jun 7;12(1):3367. doi: 10.1038/s41467-021-23637-4. PMID:34099688[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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