ABSTRACT: In plants, RNA-directed DNA methylation (RdDM) pathway is a well-known de novo DNA methylation pathway that is involved in many important biological processes, such as pathogen defense, stress response and plant development. RdDM involves two plant-specific RNA polymerases, Pol IV and Pol V. In previous studies, several genetic screen systems, including a release of silencing 1 (ros1) suppressor screen, have been designed and used to discover new RdDM components. Through the ros1 suppressor screen, several new RdDM components, such as RDM1 and KTF1, have been reported. In this study, we isolated a new ros1 suppressor mutant, rdm15. Through DNA methylome and whole-genome siRNA analyses, we showed that RDM15 was required for RdDM-dependent DNA methylation and siRNA accumulation at a subset of RdDM target loci. Our further investigation revealed that RDM15 mainly contributes to Pol V-dependent downstream siRNA accumulation, and can interact with NRPE3B, a subunit specific to Pol V. DNA methylation and histone modifications are known to interact with each other to determine DNA methylation and chromatin states. Here, we showed that RDM15 can specifically recognize the histone 3 lysine 4 monomethylation (H3K4me1) mark by its C-terminal tudor domain. The structure of RDM15 tudor domain in complex with an H3K4me1 peptide highlights the specific recognition of H3K4me1 by an aromatic cage and specific hydorgen bonding interactions, which is different from all previously reported lower methyllysine recognition mechanisms. In addition, at the genome wide level, RDM15 and H3K4me1 showed similar distribution patterns at RDM15-dependent RdDM loci, suggesting that RDM15 recognition of H3K4me1 is associated with RDM15 function in RdDM. In summary, we identified and characterized a histone H3K4me1 specific binding protein as a new RdDM component, and the structural analysis of RDM15 revealed a new type of chemical feature-based lower methyllysine recognition mechanism.
