Recognition of H3K9me1 by maize RNA‐directed DNA methylation factor SHH2

RNA‐directed DNA methylation (RdDM) is a plant‐specific de novo DNA methylation pathway, which has extensive cross‐talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMOLOG 2 (SHH2) is an H3K9me1 reader. Our structural studies reveal that H3K9me1 recognition is achieved by recognition of the methyl group via a classic aromatic cage and hydrogen‐bonding and salt‐bridge interactions with the free protons of the mono‐methyllysine. The di‐ and tri‐methylation states disrupt the polar interactions, decreasing the binding affinity. Our study reveals a mono‐methyllysine recognition mechanism which potentially links RdDM to H3K9me1 in maize. The maize RNA Polymerase V‐binding protein SHH2 employs a hydrogen‐bonding and salt bridge interaction network to specifically recognize mono‐methyllysine on histone H3, which differs from other known methyllysine readers. SHH2 thus potentially links maize RNA‐directed DNA methylation to this histone modification.